G3335-90173 TOF Q-TOF Concepts

Agilent 6200 Series TOF
and 6500 Series Q-TOF

LC/MS System
Concepts Guide
The Big Picture
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In This Guide...
The Concepts Guide presents “The Big Picture” behind the
Agilent TOF and Q-TOF LC/MS system to help you analyze
samples on your Agilent time-of-flight or quadrupole
time-of-flight mass spectrometer system. This guide helps you
understand how the hardware and software work together.
1 Overview
Learn how the Agilent 6200 Series TOF and 6500 Series Q-TOF
LC/MS system helps you do your job and how the hardware and
software work.
2 Instrument Preparation
Learn the concepts you need to prepare the instrument for
sample acquisition.
3 Methods with Acquisition Parameters

Learn concepts to help you enter instrument control parameter
values and set up methods with acquisition parameters.
4 Data Acquisition
Learn concepts to help you enter information to run individual
samples or a worklist of samples, and to help you acquire data
and monitor runs.
Agilent 6200 Series TOF and 6500 Series Q-TOF LC/MS System Concepts Guide 3
4 Agilent 6200 Series TOF and 6500 Series Q-TOF LC/MS System Concepts Guide
Content
1 Overview
How does the TOF and Q-TOF system help you do your job? 10
Help for applications 11
Help for data acquisition 11
Help for data analysis 13
How do different ion sources work? 16
Electrospray ionization (ESI) and Dual ESI 17
Dual Agilent Jet Stream Electrospray Ionization (Dual AJS
ESI) 21
Atmospheric pressure chemical ionization (APCI) 22
Atmospheric pressure photoionization (APPI) 24
Multimode ionization (MMI) 25
HPLC-Chip 27
How does the Agilent TOF and Q-TOF mass spectrometer
work? 28
Innovative Enhancements in the Agilent 6560 Ion Mobility
Q-TOF 33
Innovative Enhancements in the Agilent 6550 iFunnel
Q-TOF 35
Innovative Enhancements in the Agilent 6545 Q-TOF 37
Innovative Enhancements in the 6540 and 6538 Q-TOF 38
Innovative Enhancements in the 6530 Q-TOF 39
Agilent Jet Stream Thermal Gradient Technology 40
Front-end ion optics 42
LC preparation 50
LC module setup 50
Column equilibration and conditioning 53
TOF and Q-TOF preparation – calibration and tuning 55
TOF mass calibration 56
Tuning choices 58
Tune reports 68
Storage and retrieval of tune results and Instrument Mode 69
Tune Set Point Modifications for Medium and Large
Proteins 71
Real-time displays 72
Instrument Status Window 72
Real-time parameter values (Actuals) 73
Real-time Chromatogram Plot and Spectral Plot windows 75
System logbook 77

Parameter entry 82
LC parameter entry 82
TOF and Q-TOF parameter entry 82
Automatic TOF and Q-TOF parameter changes during a run 83
Acquisition tab 84
General TOF and Q-TOF parameters 85
Ion source parameters 86
TOF and Q-TOF acquisition parameters 88
Setup of TOF and Q-TOF reference mass correction
(recalibration) 95
TOF and Q-TOF chromatogram setup 99
Q-TOF Advanced Parameters for Ion Mobility 100
Setting parameters to acquire a data file in All Ions MS/MS
mode 102
Method saving, editing and reporting 105
Saving a method with data acquisition parameters 105
Method editing 107
Method reporting 108
4 Data Acquisition
Interactive single sample setup 110
Sample information 110
Data File information 111
Some of the Additional Information parameters 111
Worklist setup 112
Worklist menus 113
Sample entry 114
Script entry 116
Entry of additional sample information (show, add
columns) 117
Worklist import 118
Report setup 122
Run setup 123
Estimate of worklist file size 124
Data acquisition for samples and worklists 128
What you can monitor during a run 128
What you can do during a run 129
Agilent 6200 Series TOF and 6500 Series Q-TOF LC/MS System
1
Overview
How does the TOF and Q-TOF system help you do your job? 10
Help for applications 11
Help for data acquisition 11
Help for data analysis 13
How do different ion sources work? 16
Electrospray ionization (ESI) and Dual ESI 17
Dual Agilent Jet Stream Electrospray Ionization (Dual AJS ESI) 21
Atmospheric pressure chemical ionization (APCI) 22
Atmospheric pressure photoionization (APPI) 24
Multimode ionization (MMI) 25
HPLC-Chip 27
How does the Agilent TOF and Q-TOF mass spectrometer work? 28
Innovative Enhancements in the 6540 and 6538 Q-TOF 38
Innovative Enhancements in the 6530 Q-TOF 39
Agilent Jet Stream Thermal Gradient Technology 40
Front-end ion optics 42
This chapter provides an overview of the Agilent 6200 Series

TOF LC/MS and Agilent 6500 Series Q-TOF LC/MS systems and
the system components and how they work together to help you
get your job done.
9
1 Overview
How does the TOF and Q-TOF system help you do your job?
How does the TOF and Q-TOF system help you do your job?
You can set up an Agilent 6200 Series Time-of-Flight LC/MS
(TOF) system and the Agilent 6500 Series Quadrupole
Time-of-Flight LC/MS (Q-TOF) system in several configurations:
ESI – Electrospray Ionization • For normal flow LC/MS with a binary pump, quaternary
APCI – Atmospheric Pressure pump, well-plate sampler (or autosampler or HTC/HTS
Chemical Ionization autosampler) and ESI or Dual ESI with Agilent Jet Stream
APPI - Atmospheric Pressure Thermal Gradient Technology - Agilent 6530 Quadrupole
Photo Ionization Time-of-Flight, Agilent 6540 Quadrupole Time-of-Flight,
HPLC-Chip/MS – High Agilent 6545 Quadrupole Time-of-Flight, Agilent 6550
Performance Liquid iFunnel Quadrupole Time-of-Flight, Agilent 6560 Ion Mobility
Chromatography on a Chip Quadrupole Time-of-Flight, and Agilent 6230 Time-of-Flight.
MALDI – Matrix-Assisted Laser • For normal flow LC/MS with a binary pump, quaternary
Desorption Ionization pump, well-plate sampler (or autosampler or HTC/HTS
MMI - Multimode Ionization autosampler) and ESI, Dual ESI, APCI, APPI, or MMI ion
sources.
• For microflow LC/MS with a capillary pump, micro well-plate
sampler and ESI, Dual ESI, APCI or MMI ion sources.
• For nanoflow LC/MS with a nanopump, micro well-plate
sampler and nano-ESI source or HPLC-Chip/MS interface
(used in place of standard or dual nanospray source) to
increase reliability and boost performance with narrow peak
dispersion and lower dead volumes.
• Agilent 6200 Series TOF or 6500 Series Q-TOF LC/MS system
with an AP-MALDI or PDF-MALDI source.
Each Agilent system has advantages for high throughput sample

screening with highly sensitive detection and accurate mass
assignment. Each uses the same Agilent 6200 Series TOF or 6500
Series Q-TOF LC/MS software to enable these advantages.
The Agilent Accurate-Mass 6530 Q-TOF, the Agilent UHD

Accurate-Mass 6540 Q-TOF LC/MS, the Agilent 6545 Q-TOF
LC/MS, the Agilent 6550 iFunnel Q-TOF LC/MS, and Agilent
6560 Ion Mobility Q-TOF LC/MS systems are the only Q-TOF
instruments that can use the Agilent Jet Stream Technology.
The Agilent 6230 TOF LC/MS system is the only TOF that can
use the Agilent Jet Stream Technology. This technology utilizes
Overview 1
Help for applications
a super-heated sheath gas to collimate the nebulizer spray

which dramatically increases the number of ions that enter the
mass spectrometer.
Help for applications

You can use one or more of the Agilent 6200 Series TOF or 6500
Series Q-TOF LC/MS systems in the following application areas
(for example):
• Combinatorial chemistry target compound analysis
• Natural products screening
• Compound profiling (such as bioavailability and pK)
• Protein/peptide identification and characterization
• Metabolomics
• Biomarker discovery
• Impurity profiling
Paired with Agilent Infinity and Infinity II Series LCs, the 6500
Series Q-TOF LC/MS delivers fast, sensitive, reproducible
analyses of small and large molecules.
• Reproducible mass accuracy
• Low picogram and femtomole limits of detection
• Fast MS/MS operation (for the Q-TOF)
Help for data acquisition

Please refer to this guide, the Agilent MassHunter Workstation
Software - Data Acquisition Familiarization Guide, the
Agilent MassHunter Workstation Software - Data Acquisition
Quick Start Guide or the online Help for the Data Acquisition
program.
To help you use the Agilent 6200 Series TOF and the 6500 Series
Q-TOF LC/MS systems for these applications, the software lets
you perform the following tasks in a single window:
1 Overview
Help for data acquisition
Prepare the instrument

To learn how to get started with • Start and stop the instruments from the software.
the Agilent 6200 Series TOF and • Download settings to the Agilent 1100, 1200, 1260 Infinity or
6500 Series Q-TOF, see the Quick 1290 Infinity liquid chromatograph and the TOF and Q-TOF
Start Guide. mass spectrometer in real time to control the instrument.
To learn more about how to use • See if the 6200 Series TOF and 6500 Series Q-TOF parameters
the Agilent 6200 Series TOF and are within the limits to produce the specified mass accuracy
6500 Series Q-TOF with real and resolution with a Checktune, Quicktune or Standard
samples and data, see the tune report.
Familiarization Guide. • Optimize TOF and Q-TOF parameters automatically or
manually through the Agilent tuning program.
To learn how to perform individual • Monitor the actual conditions of the instrument.
tasks with the TOF and Q-TOF
LC/MS, see the online Help. Press • View the Real-time Plot for chromatograms, spectra, and
F1 to access the online Help. instrument parameters (both DAD, TOF and Q-TOF) and
print a Real-time Plot report.
To learn more about an Agilent • View the centroided line spectrum of a peak or the mass
1100 or 1200 LC module or 1260 or range profile spectrum of a peak in real time.
1290 Infinity LC module, see the
Agilent 1100 LC, 1200 LC, 1260 Set up data acquisition methods
Infinity LC or 1290 Infinity LC User
Guide for the module. • Enter and save parameter values for all LC modules and the
Agilent 6200 Series TOF and 6500 Series Q-TOF to a data
To learn more about the 6200 acquisition method.
Series TOF or the 6500 Series • Enable reference mass correction and select reference
Q-TOF, see the Maintenance Guide standard masses to correct the mass assignments during
for that instrument. a sample run.
• Select and label the total ion chromatograms or extracted ion
To learn how to install the system,
chromatograms that you want to appear in the real-time plot.
see the Installation Guide.
• Set up time segments for each run where parameters change
with the time segment or with the experiments within the
time segment.
• Print an acquisition method report.
Overview 1
Help for data analysis
Acquire data
• Enter sample information and pre- or post-analysis programs
(scripts) and run single samples interactively
A worklist is a list of a sequence of • Enter and automatically run both individual samples and
samples that you enter and run sequences of samples in a worklist
automatically with the Data
Acquisition program.
• Set up pre- and post-analysis scripts to run between samples
in a worklist.
• Set up and run a worklist.

Agilent MassHunter Workstation Software - Qualitative Analysis
Qualitative Analysis is the primary program you use to work
with your TOF and Q-TOF data. You can use the Find
Compounds capability to confirm the presence of known
compounds with targeted MS/MS data, identify unknowns with
auto MS/MS data and do molecular feature extraction with MS
data. You can also search the data file for the presence of
specified formulas.
Agilent also designed the Qualitative Analysis program to

present large amounts of data for review in one central location.
With the program you can perform these operations for any
type of mass spectrometer data that you open:
• Extract and display chromatograms.
• View and extract peak spectra.
• Subtract background.
• Integrate chromatograms.
You can also set up methods to automatically do the tasks in the

list, as well as others, when you open the data files. The
software also provides preconfigured templates for basic
reporting and enables the capability to create custom reports in
Microsoft Excel.
1 Overview
Please refer to the Agilent MassHunter Workstation Software -

Qualitative Analysis Familiarization Guide or the online Help
for the Qualitative Analysis software and the online Help or
Reporting Training DVD for the Report Designer Add-in. The
Report Designer Add-in allows you to customize the templates
that are used when you print a report.
You can also purchase the Agilent MassHunter BioConfirm

Program which allows you to view the digest list for the protein
sequences currently displayed. You can also compare a
reference data file to other data files using the Comparative
Analysis program which is available with BioConfirm. Please
refer to the Agilent MassHunter BioConfirm Quick Start Guide
or the Agilent MassHunter BioConfirm Familiarization Guide or
the online Help for the Qualitative Analysis program for more
information.
Agilent MassHunter IM-MS Browser program

The MassHunter IM-MS Browser is an application that supports
interactive browsing and visualization of data from single
LC-IM-MS data files, extraction of various 2D and 3D subsets of
that data, exporting of extracted data in a variety of formats,
and collision cross section calculations.
The IM-MS Reprocessing program is a utility that allows you to

make certain modifications to an existing IM-MS data file.
Both of these utilities are included with the MassHunter Data

Acquisition program for versions that support the IM-QTOF.
These programs have a separate installation disk than the Data
Acquisition program.
Agilent MassHunter Workstation Software - Quantitative

Analysis
Agilent also provides you with the opportunity to quantitate
your data. Agilent has designed the quantitative analysis
software to help quantitate very low amounts of material with
the following unique features:
• Provides a curve-fit assistant to test all fits and statistics on
curve quality
Overview 1
• Integrates with an automated, parameter-free integrator that

uses a novel algorithm
• Presents a Batch-at-a-Glance results window to help you
review and operate on an entire batch of data at once
• Automatically detects and identifies outliers
Please refer to the Agilent MassHunter Workstation

Quantitative Analysis Software Familiarization Guide or the
online Help for the Quantitative Analysis software. You can
access the Familiarization Guide directly from the online Help.
For the Report Designer Add-in, please refer to the online Help
or the Reporting Training DVD. The Report Designer Add-in
allows you to customize the templates that are used when you
print a report. The Report Designer is used with the
MassHunter Qualitative Analysis program and with the
MassHunter Quantitative Analysis program.
1 Overview
How do different ion sources work?
How do different ion sources work?

The Agilent 6200 Series TOF and 6500 Series Q-TOF LC/MS
systems operate with the following interchangeable atmospheric
pressure ionization (API) sources:
• “Electrospray ionization (ESI) and Dual ESI” on page 17
• “Dual Agilent Jet Stream Electrospray Ionization (Dual AJS
ESI)” on page 21
• “Atmospheric pressure chemical ionization (APCI)” on
page 22
• “Atmospheric pressure photoionization (APPI)” on page 24
• “Multimode ionization (MMI)” on page 25
• “HPLC-Chip” on page 27
The sources that are used are the B-type sources.

N O TE
Overview 1
Electrospray ionization (ESI) and Dual ESI

You control the spray chamber Electrospray ionization relies in part on chemistry to generate
parameters (nebulizer pressure, analyte ions in solution before the analyte reaches the mass
drying gas flow and temperature, spectrometer. As shown in Figure 1, the LC eluent is sprayed
and capillary voltage) when you (nebulized) into a spray chamber at atmospheric pressure in the
set up a method in the Method and presence of a strong electrostatic field and heated drying gas.
Run Control view, described in The electrostatic field occurs between the nebulizer, which is at
Chapter 4. ground in the Agilent design, and the capillary, which is at high
voltage.
The spray occurs at right angles to the capillary. This design

reduces background noise from droplets, increases sensitivity,
and keeps the capillary cleaner for a longer period of time.
HPLC inlet For Dual ESI, a second

nebulizer is utilized for the
introduction of reference
mass ions. From an
nebulizer
ionization perspective, the
mechanism is the same.
capillary
solvent
spray
heated drying gas
Figure 1 Electrospray ion source
1 Overview
Electrospray ionization (ESI) consists of four steps:

1 Formation of ions
2 Nebulization
3 Desolvation
4 Ion evaporation
Formation of ions
Ion formation in API-electrospray occurs through more than
one mechanism. If the chemistry of analyte, solvents, and
buffers is correct, ions are generated in solution before
nebulization. This results in high analyte ion concentration and
good API-electrospray sensitivity.
Preformed ions are not always required for ESI. Some

compounds that do not ionize in solution can still be analyzed.
The process of nebulization, desolvation, and ion evaporation
creates a strong electrical charge on the surface of the spray
droplets. This can induce ionization in analyte molecules at the
surface of the droplets.
Nebulization
Nebulization (aerosol generation) takes the sample solution
through these steps:
a Sample solution enters the spray chamber through a
grounded needle called a nebulizer.
b For high-flow electrospray, nebulizing gas enters the spray
chamber concentrically through a tube that surrounds the
needle.
c The combination of strong shear forces generated by the
nebulizing gas and the strong voltage (2–6 kV) in the spray
Overview 1
chamber draws out the sample solution and breaks it into

droplets.
d As the droplets disperse, ions of one polarity
preferentially migrate to the droplet surface due to
electrostatic forces.
e As a result, the sample is simultaneously charged and
dispersed into a fine spray of charged droplets, hence the
name electrospray.
Because the sample solution is not heated when the aerosol is

created, ESI does not thermally decompose most analytes.
Desolvation and ion evaporation

Before the ions can be mass analyzed, solvent must be removed
to yield a bare ion.
A counter-current of neutral, heated drying gas, typically

nitrogen, evaporates the solvent, decreasing the droplet
diameter and forcing the predominantly like surface-charges
closer together (see Figure 2).
Figure 2 Desorption of ions from solution
Coulomb repulsion – repulsion When the force of the Coulomb repulsion equals that of the
between charged species of the surface tension of the droplet, the droplet explodes, producing
same sign smaller charged droplets that are subject to further
evaporation. This process repeats itself, and droplets with a
high density of surface-charges are formed. When charge
density reaches approximately 108 V/cm3, ion evaporation
occurs (direct ejection of bare ions from the droplet surface).
1 Overview
These ions are attracted to and pass through a capillary

sampling orifice into the ion optics and mass analyzer.
The importance of solution chemistry

The choice of solvents and buffers is a key to successful
ionization with electrospray. Solvents like methanol that have
lower heat capacity, surface tension, and dielectric constant,
promote nebulization and desolvation. For best results in
electrospray mode:
• Adjust solvent pH according to the polarity of ions desired
and the pH of the sample.
• To enhance ion desorption, use solvents that have low heats
of vaporization and low surface tensions.
• Select solvents that do not neutralize ions through gas-phase
reactions such as proton transfer or ion pair reactions.
• To reduce the buildup of salts in the ion source, select more
volatile buffers.
Multiple charging
Electrospray is especially useful for analyzing large
biomolecules such as proteins, peptides, and oligonucleotides,
but can also analyze smaller molecules like drugs and
environmental contaminants. Large molecules often acquire
more than one charge. Because of this multiple charging, you
can use electrospray to analyze molecules as large as 150,000 u
even though the mass range (or more accurately mass-to-charge
range) for a typical quadrupole LC/MS instrument is around
3000 m/z. For example:
100,000 u / 10 z = 1,000 m/z
The optional Agilent MassHunter When a large molecule acquires many charges, a mathematical
BioConfirm Software performs the process called deconvolution is used to determine the actual
calculations to accomplish molecular weight of the analyte.
deconvolution.
Overview 1
Dual Agilent Jet Stream Electrospray Ionization (Dual AJS ESI)
Dual Agilent Jet Stream Electrospray Ionization (Dual AJS

ESI)
With the Dual AJS ESI source, the nebulizing gas for the
reference spray can be switched for high flow or low flow
applications. The second sprayer improves the reference mass
stability over a wide range of LC conditions. Low flow
applications are typically less than 200 μL/minute. If the flow is
approximately 200 μL/minute, either low or high flow may be
appropriate.
You connect the tubing here for low

flow applications.
Figure 3 Dual AJS ESI source plumbed for high flow application
Both the Dual AJS ESI and the Dual ESI source support two
nebulizers for different applications: the standard nebulizer
(G1958-60098) and the capillary (or microflow) LC/MS
nebulizer (G1946-60260). The main differences are:
• The machined tip of the capillary LC/MS nebulizer has a
smaller exit orifice and internal taper.
• The internal diameter (ID) of the internal needle for the
capillary LC/MS nebulizer is 50 μm versus 120 μm for the
“standard” nebulizer needle.
The recommended flow range (1 to 50 μL/minute) really is

capillary flow, whereas flows from 50 to 250 μL/minute are
typically described as microflow.
1 Overview
Atmospheric pressure chemical ionization (APCI)

APCI is a gas-phase chemical ionization process. The APCI
technique passes LC eluent through a nebulizing needle, which
creates a fine spray. The spray is passed through a heated
ceramic tube, where the droplets are fully vaporized (Figure 4).
The resulting gas/vapor mixture is then passed over a corona

discharge needle, where the solvent vapor is ionized to create
reagent gas ions. These ions in turn ionize the sample molecules
via a chemical ionization process. The sample ions are then
introduced into the capillary.
HPLC inlet nebulizer (sprayer)
vaporizer
(heater)
drying gas
corona capillary
discharge
needle
Figure 4 Atmospheric pressure chemical ionization (APCI) source
APCI requires that the analyte be in the gas phase for ionization
to occur. To vaporize the solvent and analyte, the APCI source is
typically operated at vaporizer temperatures of 400 to 500°C.
APCI is applicable across a wide range of molecular polarities.

It rarely results in multiple charging, so it is typically used for
Overview 1
molecules less than 1,500 u. Because of this molecular weight

limitation and use of high-temperature vaporization, APCI is
less well-suited than electrospray for analysis of large
biomolecules that may be thermally unstable. APCI is well
suited for ionization of the less polar compounds that are
typically analyzed by normal-phase chromatography.
1 Overview
Atmospheric pressure photoionization (APPI)
Atmospheric pressure photoionization (APPI)

With the APPI technique, LC eluent passes through a nebulizing
needle to create a fine spray. This spray is passed through a
heated ceramic tube, where the droplets are fully vaporized.
The resulting gas/vapor mixture passes through the photon
beam of a krypton lamp to ionize the sample molecules
(Figure 5). The sample ions are then introduced into the
capillary.
APPI and APCI are similar, with APPI substituting a lamp for
the corona needle for ionization. APPI often also uses an
additional solvent or mobile phase modifier, called a “dopant”,
to assist with the photoionization process.
APPI is applicable to many of the same compounds that are

typically analyzed by APCI. APPI has proven particularly
valuable for analysis of nonpolar compounds.
HPLC inlet nebulizer (sprayer)
vaporizer
(heater)
drying gas
capillary
UV lamp
Figure 5 Atmospheric pressure photoionization (APPI) source
Overview 1
Multimode ionization (MMI)

The multimode source is an ion source that can operate in three
different modes: APCI, ESI or simultaneous APCI/ESI. The
multimode source incorporates two electrically separated,
optimized zones: one for ESI and one for APCI. During
simultaneous APCI/ESI, ions from both ionization modes enter
the capillary and are analyzed simultaneously by the mass
spectrometer.
Figure 6 Multimode source
ESI and APCI are essentially incompatible processes because

each needs its own conditions for aerosol drying and electrical
fields. However, it is possible to form ions simultaneously from
ESI and APCI if the two ionization regions are separated in
space.
Multimode ionization (MMI) is useful for screening of

unknowns, or whenever samples contain a mixture of
compounds where some respond by ESI and some respond by
APCI. In these cases, the multimode source obviates the need to
run the samples twice to accomplish a complete analysis.
1 Overview
Unlike the APCI and APPI sources where the temperature of the
vaporizer is monitored, in the multimode source the actual
vapor temperature is monitored. As a result, the vaporizer is
typically set to between 200 and 250°C.
Overview 1
HPLC-Chip
HPLC-Chip
Traditional nanospray mass spectrometry has proven its
potential as a cost-effective, sensitive and reproducible
technique for the identification of peptides at femtomole to
atomol levels. However, connecting nano capillaries, columns
and valves frequently is a tedious procedure and requires user
skills and routine. When handled incorrectly, nano flow
connections are prone to leakage which are difficult to detect
and result in poor system performance and extended downtime
of the complete system. Quartz nanospray needles are prone to
blockages and require frequent replacement.
With the invention of HPLC-Chip technology, Agilent is

significantly reducing the need for user interaction and making
nanospray a rugged state-of-the-art technology.
The cornerstone of chip technology is the HPLC-Chip, a
3-dimensional structure made of sandwiched polyimide films.
Grooves of specific dimensions are laser-ablated into a layer of
polyimide film. The lamination of a top and bottom layer then
forms channels of trapezoidal or triangular shape inside the
chip which can either be used as capillaries or, if filled with
packing material, as nanocolumns. One end of the chip tapers
off into a polyimide nanospray emitter.
Figure 7 HPLC-Chip making process
1 Overview
How does the Agilent TOF and Q-TOF mass spectrometer work?
6200 Series TOF The Agilent TOF is an orthogonal acceleration time-of-flight
mass spectrometer (oa-TOF). The acceleration pulse applied to
send the ions down the flight tube is orthogonal to the direction
that ions are entering the mass analyzer. This geometry
minimizes the effect of the entrance velocity on the flight time,
leading to higher resolution.
6500 Series The Agilent 6500 Series Q-TOF LC/MS is a liquid
Q-TOF chromatograph Q-TOF mass spectrometer that performs MS/MS
using a quadrupole, a hexapole (collision cell) and
a time-of-flight unit to produce spectra. The quadrupole selects
precursor ions that are fragmented in the collision cell into
product ions, which are then impelled to the detector, at an
angle perpendicular to the original path.
The Agilent 6500 Series Q-TOF LC/MS supports several
atmospheric pressure ionization (API) sources. A common
atmospheric sampling interface introduces ions from these
various sources into the mass spectrometer vacuum system.
Figure 8 shows the complete Agilent 6520

Q-TOF LC/MS schematic, including AJS
ESI ion source, ion transfer optics, beam
shaping optics, ion pulser, flight tube, and
detector.
Figure 8 Schematic of Agilent 6520 Q-TOF LC/MS
Overview 1
Figure 9 shows the

complete Agilent 6530
Q-TOF schematic, with
major improvements
identified.
These improvements are

described below
(“Innovative
Enhancements in the
6530 Q-TOF” on page 39).
Figure 9 Schematic of Agilent 6530 Q-TOF LC/MS with major improvements circled
1 Overview
Figure 10 shows the

complete Agilent
6538/6540 Q-TOF
schematic, with major
improvements identified.

described below
(“Innovative The Agilent 6540 Q-TOF
Enhancements in the supports the Agilent Jet
6540 and 6538 Q-TOF” on Stream Technology. The
page 38). Agilent 6538 does not.
Figure 10 Schematic of Agilent 6540 UHD Accurate-Mass Q-TOF LC/MS with major improvements circled
Overview 1
This figure shows the Agilent

6545 Q-TOF schematic, with
major improvements
identified.
described below (“Innovative
Enhancements in the Agilent
6545 Q-TOF” on page 37).
The Agilent 6545 Q-TOF supports

the Agilent Jet Stream ESI and the
Dual Agilent Jet Stream ESI. Other
sources supported are ESI, Dual
ESI, HPLC-Chip, APCI, APPI,
Multimode, nanoESI, Dual
nanoESI, MALDI and GC-APCI.
Figure 11 Schematic of Agilent 6545 Q-TOF LC/MS with major improvements circled
1 Overview
This figure shows the

iFunnel Q-TOF schematic,
with major improvements
identified. The Agilent 6550 iFunnel Q-TOF supports the
Agilent Jet Stream ESI and the Dual Agilent
Jet Stream ESI.
described below
(“Innovative
Enhancements in the
Agilent 6550 iFunnel
Q-TOF”).
Figure 12 Schematic of Agilent 6550 iFunnel Q-TOF LC/MS with major improvements circled
Overview 1
Innovative Enhancements in the Agilent 6560 Ion Mobility Q-TOF
This figure shows the

iFunnel Q-TOF schematic,
with major improvements
identified. The Agilent 6560 Ion Mobility Q-TOF supports the Agilent Jet
Stream ESI and the Dual Agilent Jet Stream ESI. Other sources
supported are ESI, Dual ESI, HPLC-Chip, APCI, APPI,
described below
(“Innovative Multimode, nanoESI, Dual nanoESI, MALDI and GC-APCI.
Enhancements in the
Agilent 6560 Ion Mobility
Q-TOF”).
Figure 13 Schematic of Agilent 6560 Ion Mobility Q-TOF LC/MS with major improvements circled
Innovative Enhancements in the Agilent 6560 Ion Mobility

Q-TOF
Front funnel
Ions generated in the source region are carried into the front
funnel through a single bore capillary. The front funnel
improves the sensitivity by efficiently transferring gas phase
ions into the trapping funnel while pumping away excess gas
and neutral molecules. The front funnel operates at high
pressure.
1 Overview
Innovative Enhancements in the Agilent 6560 Ion Mobility Q-TOF
Trapping funnel
The trapping funnel accumulates and releases ions into the
drift tube. The continuous ion beam from the electrospray
process has to be converted into a pulsed ion beam prior to ion
mobility separation. The trapping funnel operates by first
storing and then releasing discrete packets of ions into the drift
tube.
Also, a tapered section at the exit region of the trapping funnel

is designed to focus the ion packets into the drift cell to avoid
ion losses and improve resolution and sensitivity. The result is a
high abundance, well confined packet of ions entering the drift
tube resulting in high drift resolution and high sensitivity.
Drift tube
The drift cell is approximately 80 cm long and generally
operated at 20 V/cm or less drift field. Ions are separated as
they pass through the drift tube based on their collision cross
section and charge. Ions with larger collision cross sections
undergo a higher number of collisions with drift gas molecules
compared to ions with smaller collision cross section.
Therefore, larger ions travel through the drift tube slower than
the smaller ions. Also, ions with higher charge states experience
a higher electric force, and hence travel at a higher velocity,
compared to ions with lower charge states. The drift tube is
operated under low field limit conditions allowing the
instrument to generate accurate structural information for
compounds. Under the low electric field conditions the mobility
is not dependent on the electric field but rather on the structure
of the molecule and its interaction with the buffer gas. In
addition to separating ions based on their structures,
experiments can be performed to quantify this collision cross
section value.
Rear funnel
Ions exiting the drift tube enter the rear funnel which
efficiently refocuses and transfers ions to the mass analyzer
through a hexapole ion guide.
Overview 1
Innovative Enhancements in the Agilent 6550 iFunnel Q-TOF

See Figure 12 on page 32 for a schematic of the 6550 Q-TOF.
Dual Agilent Jet Stream Electrospray

The Dual Agilent Jet Stream Electrospray source allows you to
modify it for high flow and low flow applications. See “Dual
Agilent Jet Stream Electrospray Ionization (Dual AJS ESI)” on
page 21 for more information.
iFunnel Technology
The iFunnel Technology encompasses two enhancements to the
Agilent 6550 iFunnel Q-TOF: the Agilent Jet Stream technology,
a hexabore capillary and the Dual Ion Funnel technology.
Figure 14 The iFunnel Technology
Ions are generated using an electrospray ion source where the

analyte is simultaneously ionized and desolvated from the
liquid matrix. The iFunnel includes the application of Agilent
Jet Stream Technology (first introduced with the 6530) which
improves sensitivity via thermal gradient focusing and
enhanced desolvation.
1 Overview
The next innovative enhancement is the use of a short hexabore

capillary. It has 6 capillary inlets and samples up to 10X more
ion rich gas from the source. It captures the majority of the gas
from the source region. See Figure 15. The hexabore capillary
transmits a high gas/ion volume into the ion optic system.
Figure 15 Hexabore capillary
The Dual Ion Funnel (DIF) technology is the next enhancement.

The DIF technology removes the gas and neutral noise but
captures the ions. It also extends the turbo pump’s lifetime. The
Dual Ion Funnel technology can transmit ions efficiently at as
high a pressure as possible. The first ion funnel has a pressure
between 7 and 14 Torr. The second ion funnel is a low pressure
ion funnel (1 to 3 Torr). The ion funnel works by having the RF
voltage focus the ions to the center and having the DC voltage
accelerate the ions to the exit. See Figure 16.
Agilent Hexabore Dual Stage

Jet Stream Capillary Ion Funnel
Technology
Figure 16 The Dual Ion Funnel technology
Overview 1
Innovative Enhancements in the Agilent 6545 Q-TOF
Innovative Enhancements in the Agilent 6545 Q-TOF

Enhanced Wide Bore Lens 2

Identical to the lens 2 design used in the 6560, a larger orifice is
used in the 6545. Ions are still conditioned via DC and RF
voltages prior to quad transmission or isolation, but ions will
not get in close proximity to the lens surface. The possible risk
of ion deposition on the surface is greatly reduced, leading to an
increased robustness of the system under high ion current
conditions.
Slicer design
The slicer design on the 6545 is identical to the 6550. It has 2
different sizes of the opening: a larger one for high sensitivity
applications, and a smaller one for high resolution applications.
The positions can be changed in the Tune Context and are
saved as part of the tune file. In total, 10 positions are usable: 4
positions for the high sensitivity, and 6 positions for high
resolution.
Improved pulser design

Thermal and longterm stability of the pulser is optimized by
better process control of the delay time, leading to less
variations in mass accuracy.
Improved Power Supplies

In comparison to the 6540, changes were made to the
feed-through as well as the type of power supply for better
thermal and other environmental stability. As a consequence,
better resolution is achieved with this change.
Dual Agilent Jet Stream Electrospray

The Dual Agilent Jet Stream Electrospray source allows you to
modify it for high flow and low flow applications. See “Dual
Agilent Jet Stream Electrospray Ionization (Dual AJS ESI)” on
1 Overview
Innovative Enhancements in the 6540 and 6538 Q-TOF
page 21 for more information.
Innovative Enhancements in the 6540 and 6538 Q-TOF

Ion Beam Compression Technology

The first improvement is the Ion Beam Compression Technology
(IBC) which cools and focuses the ion beam. This technology
simultaneously maximizes ion transmission and reduces beam
divergence. Active Ion Beam Compression is achieved with
Agilent Axial Ion Acceleration Technology applied to a tapered
ion guide design.
Ion beam compression provides up to a 10-fold compression

and cooling which helps in creating a much denser and thinner
ion beam that passes through a narrower slit leading into the
slicer and pulser region. The narrowed, cooled and condensed
beam is a key factor in enabling the gain in mass resolution to
40,000 while maintaining excellent sensitivity.
Figure 17 Ion Beam Compression Technology
Extended Flight Tube with Enhanced Mirror Technology (EMT)

The second improvement is that the flight tube for the
6538/6540 Q-TOF is now five feet long.
Overview 1
Innovative Enhancements in the 6530 Q-TOF
The 1 ppm/C Expansion Coefficient for the Inner Flight Tube

virtually eliminates calibration drift due to flight tube
elongation. The second order temporal focusing ion mirror uses
a high transmission Harp Grid for maximum sensitivity.
New Fast Bipolar Detector

The third innovative enhancement is the new Fast Bipolar
detector. The scintillator is ultra fast and highly efficient. Also,
the new ultra fast response PMT design continues the tradition
of high dynamic range and detector lifetime.
Figure 18 Fast Bipolar Detector
Innovative Enhancements in the 6530 Q-TOF

Ions are generated using an electrospray ion source where the

analyte is simultaneously ionized and desolvated from the
liquid matrix. The first of three (3) innovative Agilent
enhancements is found in the application of Agilent Jet Stream
Technology (denoted as 1 in Figure 9) which improves
sensitivity via thermal gradient focusing and enhanced
desolvation. This technology is described in detail below
(“Agilent Jet Stream Thermal Gradient Technology” on
1 Overview
Agilent Jet Stream Thermal Gradient Technology
page 40).
The desolvated ions then enter the mass spectrometer via an

innovative resistive and highly inert capillary transfer tube
(denoted as 2 in Figure 9) that improves ion transmission and
allows virtually instantaneous polarity switching.
Further increase in ion transmission is obtained by

improvement of the pumping speed in vacuum stage 2, resulting
in better ion capture by the first octopole (denoted as 3 in
Figure 9). The ions next pass through the optics and into the
quadrupole analyzer. The quadrupole analyzer consists of four
parallel hyperbolic rods through which selected ions based on
their mass to charge ratio are filtered.
The ions passing through the quadrupole analyzer are then

directed through the collision cell where they are fragmented.
The collision cell is actually a hexapole filled with nitrogen, the
same gas that is used as the drying gas. The collision cell design
has axial acceleration for high speed MS/MS analysis. Fragment
ions formed in the collision cell are then sent to the TOF to
enable a user to isolate and examine product ions with respect
to precursor ions.

This technology is supported on the Agilent 6530 Quadrupole
Time-of-Flight mass spectrometer, the Agilent 6540 UHD
Accurate-Mass Quadrupole Time-of-Flight mass spectrometer,
the Agilent 6550 iFunnel Quadrupole Time-of-Flight mass
spectrometer and the Agilent 6230 Accurate-Mass
Time-of-Flight mass spectrometer.
Agilent Jet Stream Technology enhances analyte desolvation by

collimating the nebulizer spray and creating a dramatically
“brighter signal.” The addition of a collinear, concentric,
super-heated nitrogen sheath gas (Figure 19) to the inlet
assembly significantly improves ion drying from the
electrospray plume and leads to increased mass spectrometer
signal to noise. The Agilent 6530 Q-TOF gets
Overview 1
attomole-to-low-femtomole sensitivity for superior trace level

analyses.
Figure 19 Agilent Jet Stream Electrospray Ion Source
Agilent Jet Stream thermal gradient focusing consists of a

superheated nitrogen sheath gas that is introduced collinear
with and concentric to the pneumatically assisted electrospray.
Thermal energy from the superheated nitrogen sheath gas is
focused to the nebulizer spray producing the most efficient
desolvation and ion generation possible. The enhanced
desolvation results in more ions entering the sampling capillary
as shown in Figure 19 and concomitant improved signal to
noise. Parameters for the Agilent Jet Stream Technology are the
superheated nitrogen sheath gas temperature and flow rate,
and the nozzle voltage.
The capillary is a resistive capillary that improves ion

transmission and allows virtually instantaneous polarity
switching.
1 Overview
Front-end ion optics

For information on the various ion sources, see “How do
different ion sources work?” on page 16
After the API source forms ions, the Agilent 6200 Series TOF or
6500 Series Q-TOF LC/MS system performs the following
operations, organized according to the stages of the ion path
and the vacuum stages of the TOF or Q-TOF. See Figure 8 on
page 28 for details.
Ion enrichment (Vacuum stage 1)

Ions produced in an API source are electrostatically drawn
through a drying gas and then pneumatically conducted
through a heated sampling capillary into the first stage of the
vacuum system. The majority of drying gas and solvent vapor
are deflected by the skimmer and exhausted by a rough pump.
The ions that pass through the skimmer pass into the second
stage of the vacuum system.
Ion transport 1 (Vacuum stage 2 and vacuum stage 3)

An octopole ion guide is a set of In this stage the ions are immediately focused by an octopole
small parallel metal rods with a ion guide. Radio frequency voltage applied to the parallel
common open axis through which octopole rods repel ions above a particular mass range toward
the ions can pass. the center of the rod set. The ions pass through the octopole ion
guide because of the momentum obtained from being drawn
from atmospheric pressure through the sampling capillary.
In a Q-TOF and in the Agilent G6224 and G6230 TOF, the

octopole spans both the 2nd and the 3rd vacuum stages. Ions
exit the octopole and pass through two focusing lenses and an
RF lens.
In an Agilent 6220 TOF, the ions exit the first ion guide and pass
into the third stage of the vacuum system. In the third stage of
the vacuum, the ions are passed onto a second octopole
assembly (octopole 2) which then sends the ion on to the beam
shaping assembly.
Overview 1
Ion transport 2 (Vacuum stage 4 for 6220 TOF only)

In this fourth vacuum pumping stage, the pressure is now low
enough that there are few collisions of the ions with gas
molecules.
The following sections are only part of the Q-TOF LC/MS instrument. The
N O TE next section in the TOF instrument is the Beam shaping (Vacuum stage 4
for both 6220 TOF and Q-TOF) on page 45.
Ion selection (Vacuum stage 4 for Q-TOF only)

Lens 2 RF The phase of lens 2 RF is matched to that of the subsequent
quadrupole resulting in a significantly increased sensitivity.
Dynamic lens 2 DC and RF values are additionally used to
further increase m/z dependent transmission upon isolation.
Quad mass The quadrupoles consist of hyperbolic rods that optimize ion
filters transmission and spectral resolution. There tends to be more
ion loss with circular rods.
Pre-filter The end section of the quadrupole also consists of short
hyperbolic rods, but their RF voltages are only high enough to
guide ions into the collision cell.
Ion fragmentation 2 (Vacuum stage 4 for Q-TOF only)

Ions selected by the quadrupole are then passed to the collision
cell where they are fragmented.
The axial acceleration collision cell is a high pressure hexapole
assembly with its axial acceleration adjusted to maximize
sensitivity while eliminating crosstalk.
Crosstalk occurs when product ions from a previously selected

precursor appear in a product ion spectrum of a subsequently
selected precursor because of slow clearance from the collision
cell. This creates a composite product ion spectrum which can
be difficult to interpret.
1 Overview
The components that contribute to this higher sensitivity and

faster response are
• Small diameter hexapole collision cell
• High frequency hexapole collision cell
• Linear axial acceleration
• High pressure collision cell
• High speed digital electronics
The collision cell contains nitrogen, the same gas that is used in
the ion source. The small diameter of the hexapole assembly
assists in capturing fragmented ions.
Why a hexapole? The geometry of a hexapole provides

advantages in two domains: ion focusing and ion transmission.
• The first advantage is in ion focusing where a quadrupole is
better than a hexapole, which is better than an octopole, that
is, quadrupole > hexapole > octopole.
• The second advantage involves ion transmission across
a wide mass range, or m/z bandwidth. In this case, the
octopole is better than the hexapole, which is better than the
quadrupole.
The hexapole is chosen because, overall, it is the best for both

ion focusing and ion transmission.
Collision cell design The collision cell hexapole consists of six

resistively coated rods used to generate a potential difference
across the length of the collision cell.
A potential difference is always present. This ensures that the

precursor ions coming from the quadrupole or fragment ions
generated in the collision cell are transmitted and not allowed
to drift around at random.
Sweeping out the ions in this manner avoids the issue of

crosstalk where residual product ions from a previous
experiment can interfere with the product ion spectrum of
a subsequent experiment. A collision energy voltage is applied
over the accelerating linear voltage to generate fragments or
product ions.
Overview 1
Beam shaping (Vacuum stage 4 for both 6220 TOF and Q-TOF)
In the Agilent 6538 and 6540 UDH Accurate-Mass Q-TOF, ions
enter the ion beam compression technology. Ion beam
compression provides up to a 10-fold compression and cooling
which helps in creating a much denser and thinner ion beam
that passes through a narrower slit leading into the slicer and
pulser region.
In the TOF, ions enter a second octopole ion guide of similar

design to the first octopole but with a lower direct current
potential. This second octopole ion guide accelerates the ions
and prepares them for beam shaping. For TOF, the fourth
vacuum stage contains Octopole 2 and the beginning of the
slicer assembly.
To facilitate beam shaping, lenses focus the ions so that as they

pass through the 4th vacuum stage they will enter the
time-of-flight analyzer as a parallel beam. The more parallel the
ion beam, the higher the resolution in the resulting mass
spectrum. After the ions have been shaped into a parallel beam,
they pass through a slit opening into the fifth and last vacuum
stage where the time-of-flight analysis takes place.
Flight tube/Mass Analyzer (Vacuum stage 4 for 6224/6230 TOF)

(Vacuum stage 5 for 6220 TOF and 6500 Series Q-TOF)
Ion pulser The nearly parallel beam of ions passes into the time-of-flight
ion pulser. The ion pulser is a stack of plates, each one (except
the back plate) with a center hole. The ions pass into this stack
from the side just between the back plate and the first plate
with its center hole. To start the flight of the ions to the
detector, a high voltage (HV) pulse is applied to the back plate.
The applied pulse accelerates the ions through the stack of
pulser plates, acting as a rapid-fire ion gun.
Flight tube The ions leave the ion pulser and travel through the flight tube,
which is about one meter in length (see Figure 8). At the
opposite end of the flight tube is an ion “mirror”, which reflects
the ions that arrive near the end of the flight tube towards the
ion pulser. Because the ions entered the ion pulser with a
certain amount of forward momentum orthogonal to the flight
1 Overview
direction in the flight tube, they never return to the ion pulser,
but move to where the ion detector is mounted.
The ion mirror increases the resolving power of the instrument

by effectively doubling the flight distance (from one meter to
two meters) in the same space, and by performing a refocusing
operation so that ions having different initial velocities still
arrive simultaneously at the detector.
Because the calculation for the mass of each ion depends on its
flight time in the flight tube, the background gas pressure must
be very low. Any collision of an ion with residual gas slows the
ion on its path to the detector and affects the accuracy of the
mass calculation.
Ion detection Figure 20 shows a schematic of the Agilent 6500 Series Q-TOF
LC/MS detector.
Figure 20 Agilent 6200 Series TOF or 6500 Series Q-TOF detector, with
potentials shown for positive operation
Overview 1
At the surface of the ion detector is a microchannel plate

(MCP), a very thin plate containing a set of microscopic tubes
that pass from the front surface to the rear of the plate. When
an ion hits the front surface of the MCP, an electron escapes and
begins the process of electrical signal amplification. As freed
electrons collide with the walls of the microscopic tubes, an
ever-increasing cascade of electrons travels to the rear of the
plate. Roughly 10 times more electrons exit the MCP than
incoming ions contact the surface.
These electrons are then focused onto a scintillator, which,

when struck by electrons, produces a flash of light. The light
from the scintillator is focused through two small lenses onto
a photomultiplier tube (PMT), which produces the electrical
signal read by the data system. The reason for producing an
optical signal from the MCP electrons is because the output of
the MCP is at roughly -6000 volts. The light produced by the
scintillator passes to the PMT, which has a signal output at
ground potential.
1 Overview
2
Instrument Preparation
LC preparation 50
LC module setup 50
Column equilibration and conditioning 53
TOF and Q-TOF preparation – calibration and tuning 55
TOF mass calibration 56
Tuning choices 58
Tune reports 68
Storage and retrieval of tune results and Instrument Mode 69
Tune Set Point Modifications for Medium and Large Proteins 71
Real-time displays 72
Instrument Status Window 72
Real-time parameter values (Actuals) 73
Real-time Chromatogram Plot and Spectral Plot windows 75
System logbook 77
Learn about the concepts that can help you prepare the
instrument for use.
This chapter assumes that the hardware and software are

installed, the instrument is configured and the performance
verified. If this has not been completed, see the Agilent 6200
Series Time-of-Flight LC/MS System Installation Guide or the
Agilent 6500 Series Quadrupole Time-of-Flight LC/MS System
Installation Guide.
49
LC preparation
LC preparation
To install, configure and start the To prepare the LC for sample runs, you usually do three tasks:
LC modules, see the Installation • Set up the LC modules for operation
Guide.
• Equilibrate or condition the column
• Monitor the plot baseline to assure pump and column
stability (See “Real-time displays” on page 72.)
See the Quick Start Guide and You can also view the system logbook for explanations of errors.
online Help for instructions on how (See “System logbook” on page 77.)
to prepare the LC for a sample run.
LC module setup
You set up the LC modules in the Instrument Status window
through the shortcut menus. The Instrument Status window is
also called the Dashboard. You can get help on any of the
devices by clicking the button in the device pane.
Figure 21 Instrument Status window (or Dashboard) with shortcut menu for Column Comp.
Table 1 shows you the tasks that you may perform to set up the
LC modules and the menu items where you can do the tasks.
You can do most of these tasks using the shortcut menu.
Instrument Preparation 2
LC module setup
Table 1 Tasks to set up the LC modules
If you have this And you want to: How:

module:
Autosampler Change volumes for the installed syringe Done in the Device Configuration user
interface
Well-Plate Sampler Change volumes for the installed syringe Done in the Device Configuration user
(WPS) or µWPS or interface
h-ALS or h-ALS-SL or
h-ALS-SL+
Select tray type and its position Right-click the device panel and click Assign
Wellplates, Edit Wellplate Types
Reset injector, Move Home, Needle Up or Down, Right-click the device panel and click Reset
set the valve mainpass or the bypass Sampler, Home Arm, Needle Up/Down,
Switch Valve to Bypass/Mainpass, Switch
Thermostat On, Wash Needle
HTC/HTS Update the plate assignments on the computer Right-click the device panel and click Update
Plate Assignment
Reset the injector Right-click the device panel and click Reset
injector
Binary, isocratic, and Turn the pump on, off or place in Standby Right-click the device panel and click Switch
quaternary pumps Pump On/Off
Set the date and time for automatic pump turnon Right-click the device panel and click Control
Set up to monitor solvent levels Right-click the device panel and click Bottle
Fillings
CapPump Do same tasks as binary pump Same menu items as binary pump
Purge the pump Right-click the device panel and click Purge
On/Off
Set mixer and filter volumes Right-click the device panel and click
Configuration
Enable a fast change in solvent composition Right-click the device panel and click Start
Fast Composition Change
Do a flow sensor calibration Right-click the device panel and click

Calibration
LC module setup
Table 1 Tasks to set up the LC modules (continued)

module:
Nanopump Do the same tasks as CapPump Same menu items as CapPump except for
Accuracy Calibration (flow sensor)
Thermostat. Column Turn the right or left controller on or off Right-click the device panel and click
Compartment (TCC) Configuration
Set the maximum controller temperatures Right-click the device panel and click Set
Temperature
Enter information for the instrument columns Tools > Analytical Column Setup
Diode Array Det. (DAD) Turn UV or Visible lamp on Right-click the device panel and click UV
Lamp On; Vis Lamp On
Set the date or time for automatic DAD turnon Right-click the device panel and click Control
Calibrate the DAD wavelength Right-click the device panel and click
Calibration
Bring the baseline of the plot to zero Right-click the device panel and click
Balance
Show an intensity plot for the detector Right-click the device panel and click
Intensity plot
Flexible Cube Switch pump on or off Right-click the device panel and click Switch
pump on or Switch pump off.
Display the Control dialog box. Right-click the device panel and click
Control.
Display the Method Setup dialog box Right-click the device panel and click
Method.
Execute a pump command Right-click the device panel and click

Execute pump command.
Supercritical Fluid Display the Injector Wash dialog box Right-click the device panel and click
Chromatography (SFC) Injector Wash.
Display the Method Setup dialog box Right-click the device panel and click
Method.
Display the SFC Control dialog box Right-click the device panel and click
Control.
Column equilibration and conditioning
Table 1 Tasks to set up the LC modules (continued)

module:
Fluorescence Detector Ignite the UV lamp Right-click the device panel and click Switch
(FLD) on. To turn off the lamp, click Switch off.
Display the detector’s method setup dialog box Right-click the device panel and click
Method.
Display the detector’s control dialog box Right-click the device panel and click
Control.
Balance the detector Right-click the device panel and click

Balance.

You can set up to equilibrate or condition a column in different
ways with the Data Acquisition program.
Equilibration Column equilibration eliminates any previously separated
compounds or impurities from the column after runs with
solvent of a single composition. To equilibrate a column before a
sample run, you pass the solvent that you intend to use for the
run through the column for a period of time.
Conditioning Column conditioning returns column characteristics to their
initial state after a gradient run. To condition a column before a
sample run, you pass the solvent of initial composition through
the column for a period of time.
Equilibration
You can equilibrate a column in one of three ways:
• Interactively
You change the loaded method set points to the solvent
composition for the run, no volume for the injection, higher
than normal flow rates and no data storage. You can then
immediately apply these set points to the instrument and
interactively stop the run when the column is ready.
• With a method in an interactive run

You can save the method with the set points mentioned in the
above paragraph, and then do a run. The run uses the
method stop time. You can also use a post run time within a
sample method to equilibrate the column.
For more information on worklists, • With a parameter in a worklist
see Chapter 4, “Data Acquisition”. You can set up a blank run in a worklist to use as your
equilibration run. Or you can set up an equilibration time for
any sample run, where the system waits the specified time
before injecting the sample. For both cases, the data is
stored.
Conditioning
You can condition a column in one of three ways:
• With one of the first two procedures described in the
Equilibration paragraphs.
You enter pump conditions to bring the column to its initial
condition. You can also condition the column by setting a
post-run time in the method.
• With a script in a worklist
The LC conditioning script, SCP_LCCondition, is part of the
Data Acquisition software. When you enter the script into the
worklist, you specify the method that you will use for the run.
If a TOF or Q-TOF is connected to the LC, you can also enter
a parameter that diverts the LC eluent to waste. With this
script, there is no injection and no data storage.
TOF and Q-TOF preparation – calibration and tuning
TOF and Q-TOF preparation – calibration and tuning

See the Installation Guide for After you start the instrument, you calibrate and tune the TOF
instructions on how to install and and Q-TOF. This section presents the background information to
start the TOF or Q-TOF and perform help you understand calibration and tuning as they are
an initial auto tune. implemented in the Agilent TOF and Q-TOF LC/MS system.
To learn how to tune and calibrate The following distinctions show how tuning, optimization and
the TOF or Q-TOF, see the Quick calibration are related in the Agilent MassHunter Workstation
Start Guide and online Help. Software.
Tuning Tuning is the process of adjusting both the quadrupole (for the
Q-TOF) and TOF parameters to achieve the following goals:
• Maximize signal intensity and maintain acceptable
resolution, or
• Maximize resolution and maintain acceptable signal intensity
See “Tuning choices” on page 58 The Agilent MassHunter Workstation software and its
to learn more about Agilent tuning documentation and online Help use the words “tuning” and
tools. “optimization” interchangeably.
Agilent Auto Tunes for the Q-TOF include Quick Tune, Initial
Tune, Mass Calibration / Check, Standard Tune, Transmission
Tune, FPS System Tune, System Tune, and Set Detector Gain.
Some of these tunes only work for tuning the TOF part of the
instrument. All of the TOF auto tune tools perform both
automatic calibration and tuning.
Agilent Auto Tune for a TOF mass spectrometer includes Initial

Auto Tune, Mass Calibration / Check, Quick Tune, Standard
Tune, and Set Detector Gain.
Calibration Calibration is the process of assigning accurate masses based
on the known masses of standard compounds, introduced either
prior to or while running the sample.
Customizing The user interface in the Tune & Calibration tab changes based
on many options:
• Type of mass spectrometer - Some options are only
available if you have a specific instrument. For example, the
SWARM tune is only available for the 6545 Q-TOF mass
spectrometer.
TOF mass calibration
• Instrument State tab - The options changed based on the

parameters in the Instrument State tab. For example, the
small mass auto tune options are only available if you select
Low (1700 m/z) for the Mass Range for a 6545 Q-TOF. Also,
the FPS Tune is only available if you select Enabled in the
Fast Polarity Switching list.
• Preferences tab - Some tabs are only visible if you mark the
appropriate option in this tab.

Any time that you want to ensure mass accuracy of the
instrument, you do a calibration. You do mass calibrations by
passing a calibrant with known masses from the calibrant bottle
through the mass spectrometer. You can do an automatic mass
calibration, or you can do a manual mass calibration.
Automatic Mass Calibration

Before you calibrate the instrument, you have to set the
instrument state to the proper instrument mode, mass range
and fast polarity switching mode. You set these values on the
Instrument State tab.
When you change the mass range or enable/disable fast polarity

switching on the Instrument State tab, the pulser frequency is
changed which results in the DEI pulser warming up or cooling
down. If the calibration is performed too soon, the DEI may still
be heating up or cooling down which can result in drift. See the
online Help for more information on the Instrument State tab.
Automatic calibrations take place when you click Mass

Calibration / Check, Quick Tune, Standard Tune, System
Tune, and Initial Tune in the Tune & Calibration tab.
Figure 22 Tune & Calibration tab of the Tune window for a 6545 Q-TOF
Manual Mass Calibration

You set up a manual calibration from the Manual Mass
Calibration tab in the Tune window (Figure 23). If this tab is not
visible, you need to mark the Show Manual TOF Mass
Calibration check box in the Preferences tab. You can modify
the mass list that is used when you do a Manual Mass
Calibration.
Figure 23 Manual Mass Calibration tab of the Tune window
See Chapter 3, “Methods with During sample analysis the system corrects the calibration with
Acquisition Parameters,” starting the introduction of a standard containing reference masses, if
on page 81, to learn more about you enable the correction through the method.
mass correction using reference
standards. The calibration equations used are proprietary.
Tuning choices
Tuning choices
You can see the tuning choices available to you on the Tune &
Calibration tab (Figure 24). Notice that you must specify the
part of the instrument to tune for the Q-TOF instrument. Also,
starting with the B.02.01 release, not all of the tuning choices
are available with all sources.
With the ESI, Dual ESI, Dual AJS ESI, Multimode, APPI and
APCI ion sources, you can run Check Tune, Quick Tune, and
TOF Mass Calibration. You can only run Standard Tune, Set
Detector Gain and Initial Tune (TOF) if one of the supported
sources in Table 2 is installed. The Dual ESI source can run all
tuning choices with all instruments.
Table 2 Supported Sources for All Auto Tunes
Instrument Model Number Supported Sources for All Auto Tunes
6224 TOF ESI, Dual ESI
6230 TOF Dual ESI, AJS ESI, Dual AJS ESI
6520 Q-TOF ESI, Dual ESI
6530A/B Q-TOF ESI, Dual ESI, AJS ESI, Dual AJS ESI
6538 Q-TOF ESI, Dual ESI
6540A/B Q-TOF ESI, Dual ESI, AJS ESI, Dual AJS ESI
6545 Q-TOF Dual ESI, Dual AJS ESI
Also, the Instrument Mode affects which autotunes are

available to use. If the Instrument Mode is Extended Dynamic
Range (2 GHz) mode, then you can perform any of the
autotunes. If the Instrument Mode is not Extended Dynamic
Range mode, then you cannot perform the Initial Tune. You set
the Instrument Mode on the Instrument State tab.
Tuning choices
The Mass Range also affects which tunes are supported. You
can run all tunes if the Mass Range is Standard (3200 m/z). If
the Mass Range is Low (1700 m/z), you cannot run an Initial
Tune or a Set Detector Gain. If the software is version B.05.01
SP1 or later, it is possible and recommended for small molecule
applications to perform an additional Quad Tune in the 1700
m/z range. Doing this leads to a performance increase for
molecules < 300 m/z. If you have an Agilent 6545 Q-TOF and you
select Low (1700 m/z) for the Mass Range, then you have three
options for tuning for this Mass Range plus an option to tune
for Fragile Ions for the lowest Mass Range.
All the automatic tuning choices calibrate the TOF using eight
to ten masses, except for the 1700 mass range, which calibrates
using six masses.
If Fast Polarity Switching is enabled on a Q-TOF instrument,

only two options are available. You can run the Mass
Calibration / Check auto tune or the FPS System Tune.
Figure 24 Tune & Calibration tab for a 6545 Q-TOF instrument with Fast
Polarity Switching enabled
Tuning choices
Figure 25 Autotune tab for an Agilent 6550 iFunnel Q-TOF instrument
Initial Auto Tune

See the Installation Guide for When you select this option after installation or major service,
instructions on how to do an Initial the system automatically adjusts all the tunable parameters to
Autotune optimize signal, resolution and mass axis calibration.
Table 2 on page 58 shows all of the sources that you can use to
run an Initial Auto Tune. On all instrument models, you can
perform an Initial Tune with a Dual ESI source.
You set the Instrument Mode to Extended Dynamic Range in

the Instrument State tab before running an Initial Auto Tune.
You only use Initial Auto Tune under special circumstances

because the process takes a long time to complete.
• After you install the hardware and software
• After your TOF analyzer has been vented for maintenance or
service
• If you no longer have the previous tune files or parameters
• If Standard Autotune does not work
Tuning choices
Instrument Time for Initial Auto Tune Time for Initial Auto Tune
(TOF) (Quadrupole)
Agilent 6538A, 6540A, up to 60 minutes for each up to 60 minutes

6550A and 6560A polarity
Q-TOF
Other Q-TOF up to 30 minutes for each up to 60 minutes

instruments polarity
TOF instruments up to 30 minutes for each N/A

polarity
During the Initial Auto Tune process for the TOF, the system
goes through the following steps without your intervention.
a Resets any current tune parameters to original defaults
b Performs a coarse TOF mass axis calibration
c Adjusts all the tunable parameters automatically
d Performs a final TOF mass axis calibration
e Prints a tune report at the end of the Autotune process
For Q-TOF instruments, after running an Initial Auto Tune

(TOF), you need to adjust the Collision Cell Gas pressure. You
can find this procedure in the online Help.
During the Initial Auto Tune process for the quadrupole, the
system goes through steps a, c, d and e.
Mass Calibration / Check

You can perform a Mass Calibration / Check with any
instrument mode selected and with any of the following sources
installed:
• ESI
• AJS ESI (Agilent Jet Stream ESI)
• Dual ESI
• Dual AJS ESI (Dual Agilent Jet Stream ESI)
• MMI
• APPI
Tuning choices
• APCI
Agilent designed the instrument so that it does not need

frequent autotunes. Periodically, you may want to perform Mass
Calibration / Check on both the TOF and the Quadrupole to
ensure that the parameters are still optimized. You do not need
to perform a Calibration / Check on the Quadrupole as often as
a Calibration / Check on the TOF.
Standard Tune
These tools perform many of the same optimization operations
as the Initial Tune tools but use the current settings as starting
values and does a limited set of ion optic ramps.
run a Standard Tune. On all instrument models, you can
perform a Standard Tune with a Dual ESI source.
The Standard Tune for the Quadrupole and for the TOF part of
the instrument do subsets of the Initial Auto Tune actions, and
they use the current tune parameters as starting points rather
than using the factory defaults.
Standard Tune on the TOF takes about 10 to 15 minutes, and

Standard Tune on the Quadrupole takes about 10 to 15 minutes
to complete.
Quick Tune (TOF)

Quick Tune on the TOF part of the instrument automatically
adjusts the most commonly required subset of tunable
parameters.
You can perform a Quick Tune with any instrument mode

selected and with any of the following sources installed:
• ESI
• AJS ESI (Agilent Jet Stream ESI)
• Dual ESI
• Dual AJS ESI (Dual Agilent Jet Stream ESI)
• MMI
Tuning choices
• APPI
• APCI
Quick Tune takes 3 to 5 minutes because the software is

optimizing only the most significant parameters followed by a
calibration. You cannot select this option if you have selected
either Quadrupole or Both as the part of the instrument to
tune.
During Quick Tune the system goes through the following steps:
a Automatically opens the calibrant valve
b Adjusts the vertical Q (Vert Q) and bottom slit parameters
in the Beam Shaping Optics (optimizes transmission)
c Adjusts the middle mirror of the compound TOF ion
mirror (optimizes resolution)
d Does a mass axis calibration after the final adjustment
e Prints a tune report
Set Detector Gain

Set Detector Gain adjusts the PMT voltage to obtain consistent
gain (amplification) of the ion current into electrical current. In
the Extended Dynamic Range (2 GHz) mode, it also adjusts the
preamp offset values and the time delay between gain channels.
This tool is a subset of Initial Auto Tune. You can only select
this option if you click TOF as the part of the instrument to
tune.
run a Set Detector Gain. On all instrument models, you can
perform a Set Detector Gain with a Dual ESI source.
You set the Instrument Mode to Extended Dynamic Range (2

GHz) in the Instrument State tab before running the Set
Detector Gain algorithm.
Tuning choices
SWARM Tune - System Tune or Transmission Tune

The Agilent 6545 Q-TOF mass spectrometer uses a different
tune algorithm. The new auto tune uses both Particle Swarm
Optimization (PSO) and a simplex algorithm within the physical
constraints of the mass spectrometer.
• For a well-known parameter, the auto tune uses the
simplex algorithm to maximize speed.
• For unknown behavior, PSO is used.
• PSO and simplex are interchanged between coarse and
fine adjustment.
• All the parameters are bound within the knowledge of ion
physics, to limit the search space.
• The theory of mass spectrometry is built into the
algorithm so that no ion storage or ion blocking occurs
during optimization.
During TOF resolution tuning, a certain abundance amount is

sacrificed to reach the target resolution. For the parameters
where resolution and sensitivity go together, it is easy to make
the decision. For parameters where resolution and sensitivity
are inversely proportional, a compromise is needed. The general
rule is that for a one percent increase in resolution you sacrifice
four percent in sensitivity.
For example, if resolution goes from 27000 to 30000 (10%

increase), the algorithm will sacrifice the intensity up to 31%
• Setting 1: gives 27000 Resolution and 1.00 M Peak Height
Between setting 1 and setting 2, the algorithm picks setting 2.
Between setting 1 and setting 3, the algorithm picks setting 1.
If you select Low (1700 m/z) for the Mass Range, then you have
three additional low mass tune options. You can select a smaller
range to use when tuning. If you select one of the two lower
mass ranges for the auto tune, you can also mark whether or not
there are Fragile Ions.
Tuning choices
For optic transmission, the swarm optimization does not

change a single parameter but a set of parameters. The graph
below displays the results from all parameters in the optics rail
from Oct 1 DC down. As the optimization is going down along
the optics path, the optimization ensures that there is no ion
trapping during tuning. If a parameter further in the optics path
has higher potential than the previous, ions would stop and
form a potential well to trap ions. You can check the second
graph in Figure 26 to see that the potential continually
decreases.
Figure 26 Graphs displayed during a SWARM Auto Tune
To find the best combination of all parameters, the SWARM tune

does the following:
• The red line represents the best scores achieved by the
swarm. See Figure 27 on page 66.
• After one particle achieves the best score, the other particles
try to learn from the leading score particle (also called social
influence).
• The population average score improves over time as more
and more particles reconfirm that they can reproduce a
similar result from the best score and even score higher when
combined with their own experience (also called personal
influence).
Tuning choices
Figure 27 SWARM multi dimensional tuning to find the best combination of all parameters
Manual Tune
See the online Help for detailed instructions to help you
manually tune the TOF or Q-TOF instrument. Only perform a
manual tune if the Autotune options produce a result that fails.
Order of using Autotune choices

for Classic Use the tuning options in the following order:
Autotune 1 Mass Calibration / Check tune for the TOF
If necessary, continue.
2 Quick Tune for the TOF (does not exist for the quadrupole)
3 Standard Tune for the TOF and Quadrupole - You must select
Standard (3200 m/z) for the Mass Range and High
Resolution for the Slicer Mode.
4 Initial Tune for the TOF and Quadrupole
If an Initial Tune cannot complete, contact Agilent Support.
Tuning choices
for SWARM Use the tuning options in the following order:

Auto Tune 1 Mass Calibration / Check tune for the Q-TOF
2 Transmission Tune (if you selected Low (1700 m/z) for the
Mass Range). You can try successively higher mass ranges.
3 System Tune - You must select Standard (3200 m/z) for the
Mass Range and High Resolution for the Slicer Mode.
If the System Tune cannot complete, contact Agilent Support.
Tune reports
Tune reports
At the end of every Check Tune, Quick Tune, Standard Tune,
Transmission Tune, or System Tune, the system generates a
printable Tune report in Excel. The TOF and Quad tune reports
let you know if optimization limits are met. For a TOF tune, the
report also lets you know if the mass calibration is satisfactory
or not. To print previous tune reports, you click the Tune
Report button in the Tune & Calibration tab.
Storage and retrieval of tune results and Instrument Mode

You can store the tuning parameters in a single file (*.tun) using
the Save or Save As buttons in the Instrument State tab. You
can also load tune files in the Instrument State tab (Figure 28).
The Mass Range, the Fast Polarity Switching option, the Slicer
Mode, and the Instrument Mode are also stored in the tune file.
Fast Polarity Switching is not supported for the 6560 Ion
Mobility Q-TOF.
Figure 28 Instrument State tab
Instrument Modes
You select from four different instrument modes.
High Resolution (4 GHz, High Res Mode) In this mode, the

system acquires data at a 4 GHz ADC rate while special
processing is performed in real time on the mass peaks detected
in each transient, weighting the apex data of the mass peaks
much more heavily than the shoulders. This leads to narrower
peaks in the summed transients (the mass spectra) and hence
improves resolution. The Mass Range can only be set to Low
(1700 m/z) or Standard (3200 m/z) if the Instrument Mode is set
to this value.
4 GHz (High Resolution Mode disabled) In this mode, no

processing is used at the transient level; however, the system
acquires data at a 4 GHz ADC rate. The Mass Range can only be
set to Low (1700 m/z) or Standard (3200 m/z) if the Instrument
Mode is set to this value.
Extended Dynamic Range (2 GHz) In this mode, the system

acquires data at a 4 GHz ADC rate in dual channel mode. One
channel is recorded at a high detector gain while the other
channel operates at a low detector gain. The firmware stitches
the two channels together to produce a scan with a sampling
rate of 2 GHz, which results in a greatly increased dynamic
range. The Mass Range can only be set to Low (1700 m/z) or
Standard (3200 m/z) if the Instrument Mode is set to this value.
Extended Mass Range (2 GHz) In this mode, the system

acquires data at a 2 GHz ADC rate. The Mass Range can be set
to Low (1700 m/z), Standard (3200 m/z), or High (10,000).
This is the only mode that you can use with the highest mass
range.
Tune Set Point Modifications for Medium and Large Proteins
Tune Set Point Modifications for Medium and Large Proteins

For medium and large proteins, the charge envelope may extend
beyond 3200 m/z. It is recommended that you acquire your
intact protein data in the Extended Mass Range (1 GHz) mode
on the Agilent 6200 Series TOF and Agilent 6520/6530 Q-TOF as
this allows the extended mass range needed for larger proteins.
If you are acquiring a protein and the charge states are “cut-off”
in one of the other modes, you can switch to this mode with the
extended mass range.
If you are acquiring medium and large protein data, it is also

recommended that the Quad AMU be raised to 300 amu instead
of using the value established by the Auto Tune algorithm. This
provides the Quad with enough power to transmit the high mass
ions through the quad. Failure to increase the Quad AMU will
result in a mass spectrum where the charge envelope appears to
be “cutoff” for the higher charge state ion clusters.
To adjust the Quad AMU, do the following steps:

1 Switch to the Tune Context.
2 Click the Manual Tune tab.
3 Click the Quad Tab.
4 For the Quad AMU, type 300 for the new value.
5 Save the tune value to save the new Quad AMU value. Then
exit the Tune Context.
Real-time displays
Real-time displays
Instrument Status Window

The Instrument Status window is also called the Dashboard.
You can see if a module is On, Off or in Standby by observing the
color of the bar in the title for each device pane. The title bar
also includes words describing the current state of each device.
The Instrument Status Bar appears at the bottom of the
Instrument Status window. You can see the overall state of the
Instrument in this Instrument Status Bar.
Figure 29 Instrument Status window
Table 3 Colors of Instrument States
Instrument State Color
On—Preparing/Not ready Yellow
On—Ready Green
On—Waiting, Pre-run or Purple

post-run
On—Running, Injecting Blue
Standby Light Gray—To see if the pump, TOF or Q-TOF

is in Standby mode or off, you can also look for
the check mark in the shortcut menu.
Off Dark Gray
Error condition Red
Real-time parameter values (Actuals)

What you can display
You select parameters and states to monitor for each
instrument module in the Actuals window.
Figure 30 Actuals Selection dialog box
The parameters and states for each module listed below are
available for display.
See the online Help for
descriptions of each of these Table 4 Actuals available for display
parameters and states.
Module Parameter or State
All modules Run Time, Run State, Ready State, Ready Type, Not
Ready Text Long, Not Ready Text Short, Rawdata State,
Error State
ALS Vial, Sample, Volume, Needle, Command, Injectmode,

Tray Type A, Tray Type B, Overlap, Injectstatus, Temp,
Therm Power
Table 4 Actuals available for display
Module Parameter or State
WPS, µWPS, h-ALS, The same as ALS except no Vial and addition of Drawn
h-ALS-SL and Volume, Sample Position and Needle Position
h-ALS-SL+
Binary Pump Solvent Ratio A, Solvent Ratio B, Flow, Pressure, Ripple,

Fill A,B, A1, B1, A2, B2, Power, Channel Name A, B,
Solvent Selection A, B
Capillary Pump Same as binary pump with no Fill A1, A2, B1, B2 and
with the addition of Solvent Ratio C, Solvent Ratio D, Fill
C, Fill D, Primary Flow, EMPV, Purge Status, Purge
Channel, Purge Time and Pump Op Mode
Nanopump Same as capillary pump with addition of FSAC State

and FSAC Step. FSAC stands for Flow Sensor Accuracy
Calibration. When you click the Accuracy Calibration
shortcut menu, these values show you the status of the
step in the test procedure.
Thermostatted Left Temp, Left Temp Set, Right Temp, Right Temp set,
Column Column Valve, Therm Power
Compartment
35900E Current Vial
DAD G1315C, Sample Wl A-H, Sample Bw A-H, Reference On A-H,

G1315D, G4212A, Reference Wl A-H, Reference Bw A-H, UV Lamp, Vis
G4212B, G1365C and Lamp
G1365D
DAD G1315A, Sample Wl A-E, Sample Bw A-E, Reference On A-E,
G1315B, G1365A, and Reference Wl A-E, Reference Bw A-E, UV Lamp, Vis
G1365B Lamp
TOF or Q-TOF Rough Vacuum, High Vacuum, Gas Temp, Vaporizer

Temp, Drying Gas Flow, Nebulizer Pressure, Capillary
Current, Chamber Current, Corona Voltage, Charging
Voltage, Control State, Cal/Ref Mass, LC Stream,
(for the 6560 Q-TOF) IM Hex Entrance, IM Hex RF, Drift
Tube Entrance Voltage and many more parameters
Real-time Chromatogram Plot and Spectral Plot windows

What you can display
You can display plots in the Chromatogram Plot window and in
the Spectrum Plot window.
Table 5 Chromatogram plots available for display
Module Plot type
Pumps Pressure vs. time
Thermostatted Column Temperature Left, Temperature Right vs. time

Compartment
35900E ADC signal vs. time
DAD Signals A-H vs. time
TOF or Q-TOF Any chromatogram set up in the Chromatogram tab

of the Method Editor window:
• Any segment or scan of a total ion chromatogram
(TIC) or extracted ion chromatogram (EIC)
• Method set points and actual conditions
What you can do with the displays
Table 6 What you can do with plots and spectra
Display type What you can do
Signal plots Change range of intensity or time, freeze and zoom the
plot
Pump parameters Change range of intensity or time, freeze and zoom the
plot
TOF or Q-TOF spectra Autoscale the axes, freeze and zoom the plot; toggle
between a line spectrum and a profile spectrum; toggle
between a mass x-axis and a time x-axis, change to a
display of DAD spectra (from line spectra only)
Profile vs. Centroid spectral displays

Centroid spectra for the TOF and Q-TOF display the abundance
vs. mass for the calculated centroid of the peak. Profile spectra
display the abundance vs. mass over the mass range of the peak.
Figure 31 Centroid and profile plots in the Spectrum Plot window
The default display is to plot abundance vs. mass, but you can
change the x-axis to time. To do this, right-click the Spectrum
Plot window and click Show Time from the shortcut menu. Click
Show Mass to return to the Abundance vs. Mass plot.
System logbook
System logbook
What you can view in the system logbook
The system logbook does not list The Logbook Viewer displays the dates and times when system
any changes to a method or events take place:
worklist. • Run starts, stops and aborts
• Method loaded
• Tuning and calibration operations
• Unexpected software errors
• Device driver errors, warnings and alerts including leak
detection, vial not found, lamp burned out
• Device powered off or reconfigured
• Start up and shutdown
• Worklist events
• Method log files
When you open the Logbook Viewer, the software loads and
displays the most recent entries in the log file.
Figure 32 Logbook Viewer
The logbook also displays additional information about each

event. Since the display of individual columns can be turned on
and off, not all of these columns may be visible at any given
time.
System logbook
Table 7 Columns available for display in the Logbook Viewer
Column Name Description
Time Date and time of the event
Event Type Normal event or error
Event Source The module that produced the event (Worklist, Instr Mgr,
App UI, Launcher, DA Mgr)
Category More information about the event (e.g. Startup,

Shutdown, Worklist Start, Worklist End, Run Started, Run
Stopped, Run Aborted, Method Loaded)
Description More information about the event
User Name of the user who started the acquisition engines

when the event occurred
What you can do with the system logbook

Move the cursor over an icon to The system deletes logbook entries that are older than the value
see the tooltips, which help you set in the System logbook purge dialog box. You can select a
perform the correct task. value from 1 day to 2 weeks. You click Tools > Purge Settings to
display this dialog box.
See the online Help for
instructions on how to work with A copy of the logbook is automatically archived in the
the logbook. \MassHunter\Log\Acq\Archive\Logbook folder. If you want to
view an archived logbook, click File > Open in the Logbook
Viewer program and select the .log that you want to view. You
can also save the logbook at any time by clicking File > Save
Logbook As.
Most of the tasks that you can do with the logbook help you
view the entries you need to see more easily.
Table 8 Tasks you can perform with the logbook
If you want to do this: Click this menu item or icon:
View an individual entry Edit > Find
View selected entries only Edit > Filter
Change column types and size View menu
System logbook
Table 8 Tasks you can perform with the logbook
If you want to do this: Click this menu item or icon:
View recent events View > Refresh
Archive entries File > Save or Shortcut menu >

Export
Open, close, or save the logbook File menu
View method log files (method.log file File > Open

in the Acq. or DA method folder)
Print the logbook Shortcut menu > Export or

File > Print
Change how long entries are saved in Tools > Purge Settings
the logbook
Notification through the Taskbar

You can configure the system logbook to automatically display
messages from the taskbar. You can specify the type of messages
to display and how many messages to display at a time. By
default, this feature is disabled. To enable automatic logbook
notification, right-click on the Logbook icon in the Taskbar and
click Configure. After you have selected how many messages to
display and the type of messages, you then right-click the
logbook icon in the system tray and click Enable Notification.
Messages are still saved in the logbook whether or not you have
enabled automatic notification.
System logbook
3
Methods with Acquisition Parameters
Parameter entry 82
General TOF and Q-TOF parameters 85
TOF and Q-TOF acquisition parameters 88
Ion source parameters 86
Setup of TOF and Q-TOF reference mass correction (recalibration) 95
TOF and Q-TOF chromatogram setup 99
mode 102
Method saving, editing and reporting 105
Saving a method with data acquisition parameters 105
Method editing 107
Method reporting 108
See the online Help for You use this chapter to learn about the concepts that can help
instructions on setting up methods you set up methods containing data acquisition parameters.
and parameter descriptions.
81
Parameter entry
Parameter entry
LC parameter entry
Most of the LC parameter entries are the same as those that you
can change with the Agilent 1200 LC control module and with
other Agilent software products, such as Agilent ChemStation.
Figure 33 LC parameter entry in the Method Editor window
TOF and Q-TOF parameter entry

Even though parameter entry is straightforward for the TOF
and Q-TOF, the background information in this section can help
you make the correct entries to produce the best results.
• Automatic parameter changes during a run
• General TOF and Q-TOF parameters
• Ion source parameters
• TOF and Q-TOF data acquisition parameters
• Setup for reference mass correction (recalibration)
• TOF and Q-TOF chromatogram setup
Methods with Acquisition Parameters 3
Automatic TOF and Q-TOF parameter changes during a run
Figure 34 Q-TOF parameter entry in the Method Editor window
Automatic TOF and Q-TOF parameter changes during a run

You can set some TOF and Q-TOF method set points to be
different at different points in time during the run. The
different time points in the method are called time segments.
Within each time segment, you can have different sets of
parameters, called experiments.
Many parameters can be changed for different time segments.

Some parameters can be changed for different experiments in
the same time segment. For example, the gas temperature,
drying gas flow rate, and the nebulizer pressure must be the
same for all experiments in the same time segment, but
fragmentor and capillary voltages can be different for different
experiments.
Acquisition Mode is only available if

your Q-TOF is a 6560.
Figure 35 Location for setup of Time Segments and Experiments
Acquisition tab
Per time segment set points are labeled with (Seg). Per
experiment set points are labeled with (Expt). All other set
points are per run. These set points can be found in these tabs.
• General Tab
• Source Tab
• Acquisition Tab
• Advanced Parameters Tab (for 6560 only) - These parameters
also can be different for different time segments.
Acquisition Mode
For the Agilent 6560 Ion Mobility Q-TOF, you can toggle between
IM-QTOF and QTOF-Only mode. In QTOF-Only mode, the
trapping funnel does not trap ions, but it simply lets all ions
pass through into the drift tube continuously.
Acquisition tab
You can set up time segments and experiments for changing
these parameters.
MS mode The MS mode spectral parameters can be set for

each time segment, and the Collision Energy parameters can be
set for each experiment.
• Q-TOF Spectral Parameters Tab - for each time segment
• Q-TOF Collision Energy Tab - for each experiment
Auto MS/MS mode (Q-TOF only) The parameters on the

following tabs can be set for each time segment.
• Q-TOF Spectral Parameters Tab
• Q-TOF Collision Energy Tab
• Q-TOF Precursor Selection I Tab
• Q-TOF Precursor Selection II Tab
• Q-TOF Preferred/Exclude Tab
General TOF and Q-TOF parameters
Targeted MS/MS mode (Q-TOF only) The parameters on the

following tabs can be set for each time segment.
• Q-TOF Spectral Parameters Tab
• Q-TOF Collision Energy Tab
• Q-TOF Targeted List Tab
See “TOF and Q-TOF acquisition parameters” on page 88 for

a description of the TOF, Auto MS/MS and Targeted MS/MS
modes and their parameters.
Agilent 6560 Ion For the Agilent 6560 Ion Mobility Q-TOF, if the Acquisition
Mobility Q-TOF Mode is IM-QTOF, then only the MS (Seg) option is available.
General TOF and Q-TOF parameters

You enter general TOF and Q-TOF parameters on the General
tab of either the TOF tab or the Q-TOF tab in the Method Editor
window.
Figure 36 General tab of the Q-TOF Method Editor window
Profile vs. centroid spectra

You can save mass spectral data as whole peaks over the mass
range of the peak, or you can save only the data for the mass
whose intensity appears in the “middle” of the peak. To limit the
number of peaks whose centroid data are saved or appear in the
Spectrum Plot window (line spectra), you can set an absolute or
relative threshold for both MS and MS/MS data.
Ion source parameters

See the online Help to view You can use several different sources with the Agilent TOF and
recommended parameter values Q-TOF LC/MS system:
for each ion source. • ESI
• Dual ESI
• AJS ESI
• Dual AJS ESI
• APCI
• APPI
• AP-MALDI
• PDF-MALDI
• Orthogonal Nanospray
• HPLC-Chip/MS interface
• Dual Orthogonal Nanospray
• Multimode (MMI)
• GC-APCI
Each of the sources uses different parameters for controlling

the ion source. The default parameters are set for a Dual ESI
(electrospray ionization) source. When you select a new ion
source in the Method Editor window, you see new parameter
options and boxes on the Source tab in the TOF tab or the
Q-TOF tab.
Figure 37 Source parameters in the Method Editor window
Tips for using the AP-MALDI or PDF-MALDI source

For instructions on how to set up • Tune the TOF or Q-TOF with an ESI source installed
and run samples with the • Make sure the Run Type in the Sample Run window is set to
AP-MALDI and PDF-MALDI inlet External Start.
and ion source, see the online
Help. • Set the proper settings in the AP-MALDI or PDF-MALDI
control software, and make sure that the desorption time is
For instructions on how to install not less than the MS TOF stop time.
the AP-MALDI or PDF-MALDI ion Autotune for the AP-MALDI and PDF-MALDI source is not
source, see the Installation Guide. supported. You can use Manual Tune to tune the instrument
when either of these sources is installed.
Before the AP-MALDI or the
PDF-MALDI is installed, in the
instrument configuration tool, the
LC must be removed from the
system configuration.
For more information on how to

set up the AP-MALDI to introduce
samples, refer to the Agilent
G1972A AP-MALDI LC/MSD Trap
SL System User Guide.
TOF and Q-TOF acquisition parameters

The Acquisition tab in Figure 39 contains acquisition
parameters that you can change with time segments.
Figure 38 Acquisition tab for the 6550 in the Method Editor window
Figure 39 Acquisition tab for the 6560 in the Method Editor window
The acquisition parameters you choose depend on what you are

trying to accomplish:
• If you want to pass all ions in a specified mass range through
the instrument with no fragmentation in the collision cell,
click MS (Seg) mode. This mode is automatically chosen for a
TOF instrument.
• If you don't know what you are looking for and must set up
boundary parameters for the precursor ion list, click Auto
MS/MS (Seg) mode.
• If you know the compounds and hence the precursor ions you
are looking for, click Targeted MS/MS (Seg) mode.
MS mode
In this mode the Q-TOF instrument behaves solely as a TOF
instrument with no quad isolation applied. You specify the mass
range and the acquisition rate and time to collect spectra.
Figure 40 MS (Seg) Mode parameters in the Acquisition tab
Transients vs. mass range The mass spectrum resulting from

a single pulse of voltage applied to the ion pulser is called
a transient. The recorded Mass Spectrum is, in reality, a result
of the application of multiple pulses to the ion pulser and
a summation of lower signal mass spectra, or transients.
(Figure 41)
For analyses that require one Mass Spectrum or scan per

second, the Agilent TOF and Q-TOF LC/MS software sums
10,000 transients before transferring the data from the
instrument back to the host computer to be written to disk. If
the target application involves high speed chromatography and
requires faster scanning, you can reduce the number of
transients per scan to increase the scans per second.
The length of transients is the time the system is allowed to

collect data for the transient in nanoseconds. On the Agilent
TOF and Q-TOF LC/MS, three mass range modes are available:
• Low (1,700 m/z)
• Standard (3,200 m/z)
• High (10,000 m/z) or High (20,000 m/z) - The value of the

High Mass Range depends on the type of instrument.
The transient length is set appropriately for each of these

modes.
Q-TOF
Front End
detector
ion pulser
Figure 41 Length of transients is measured from the ion pulser to the

detector
Targeted MS/MS mode (Q-TOF only)

In this mode you specify the precursor ion that you want the
quadrupole to select and pass through to the collision cell for
fragmentation. The TOF portion of the instrument then passes
all the product ions through to the detector, and you select the
ion you want to look at in the spectrum produced by the TOF.
Mobility Q-TOF Mode is IM-QTOF, you cannot click Targeted MS/MS (Seg). If
the Acquisition Mode is QTOF-Only, then you can click
Targeted MS/MS (Seg). If you click QTOF-Only, then you can
use all of the non-IM features.
Figure 42 The Spectral Parameters tab for Targeted MS/MS mode
Spectral Parameters These parameters are the same as those

for the TOF mode, but they are applied to both the quad (MS)
and the TOF components (MS/MS).
Collision Energy You can enter multiple fixed collision energies

(each collision energy is used), the slope and offset of a line, or
a table of collision energies.
Figure 43 The Collision Energy tab for Targeted MS/MS mode
For general method development you set the slope and offset for
a curve whose collision energy the system selects to match the
precursor ion, m/z, on the curve.
Targeted List For compounds for which you already know the
precursor ions, you can place the collision energy in the
targeted list for the precursor ion and vary its value to optimize
the abundance of the product ion.
Figure 44 Targeted List tab for Targeted MS/MS mode
The collision energies specified here override the values

specified in the Collision Energy tab.
Figure 45 Targeted List tab for Targeted MS/MS mode
Auto MS/MS (Q-TOF only)

In Auto MS/MS mode, two additional tabs appear: Precursor
Selection I and Precursor Selection II.
The Spectral Parameters tab contains the same parameters as

in Targeted MS/MS mode. The other four tabs are used to enter
the boundary parameters for selecting precursor ions.
Figure 46 Auto MS/MS mode with Precursor Selection 1 tab selected
The software sorts a list of possible precursor ions whose order

depends on the boundary parameters entered:
a Passes all ions through (TOF only) and sorts the list from
highest abundance to lowest (or by charge then
abundance)
b Excludes those masses in the specified mass range
c Sorts the list based on the priority of charges
d Moves preferred ions to the top of list in the order
specified
e Chooses the top ions on the list based on the entry for
maximum number of precursor ions per cycle (Max
Precursor per cycle)
f Excludes masses after a specified number of spectra have
been acquired and releases the exclusion after a specified
time (Active Exclusion)
Mobility Q-TOF Mode is IM-QTOF, you cannot click Auto MS/MS (Seg). If the
Acquisition Mode is QTOF-Only, then you can click Auto
MS/MS (Seg). If you click QTOF-Only, then you can use all of
the non-IM features.
Varying scan speed based on precursor abundance

You can adjust the number of transients as a function of the
precursor intensity. Varying the scan speed is very useful when
you have a complex sample, such as a protein digest. To use this
feature, you mark the Scan speed varied based on precursor

abundance check box on the Precursor Selection II tab.
When this feature is turned on, the MS/MS acquisition rate is

automatically adjusted based on precursor intensity, thus
spending less time on the more abundant peptides and more
time on the less abundant peptides. This should improve MS/MS
quality and hence database matching.
The variable MS/MS acquisition mode can result in one or more

additional precursors being examined per scan cycle as less
time is spent on more abundant precursors.
See the online Help for information on Abundance Dependent

Accumulation and Purity.
Figure 47 Auto MS/MS mode with Precursor Selection II selected
Setup of TOF and Q-TOF reference mass correction (recalibration)
Setup of TOF and Q-TOF reference mass correction

(recalibration)
You must do mass corrections Many applications need as small a deviation of accurate mass as
during a run in order to attain the possible. To obtain this accuracy, you recalibrate the mass axis
mass accuracy that Agilent for every spectrum with measurements of known reference
specifies for the TOF and Q-TOF. masses (i.e “lock masses”). You measure the masses of reference
compounds in a reference standard, which can be the Agilent
reference standard or one of your own choosing.
If you have an Agilent 6560 Ion Mobility Q-TOF, you can only
enable reference mass correction if the Acquisition Mode is
QTOF-Only. If the Acquisition Mode is IM-QTOF, then you
instead can use the IM-MS Data File Reprocessing Utility. See
the online Help for the IM-MS Browser program for more
information on this utility.
You can introduce the reference standard into the TOF system
in one of three ways:
• A calibrant delivery system (CDS) that automatically
introduces the standard to a reference sprayer (second
sprayer)— Dual ESI (0.2 to 1.5 mL/min flow rates only), Dual
AJS ESI and Dual nano ESI
• An external dispense pump—other ion sources
• Addition to the sample—other ion sources
Enabling reference mass correction

You set up and enable reference mass correction in the Ref Mass
tab within the TOF tab or the Q-TOF tab of the Method Editor
window.
Figure 48 Reference Masses tab
If you mark the Enable check box, the system uses reference
masses of the mass reference standard for automatic
recalibration of each acquired spectrum.
You must select the reference masses for each polarity in the
method. Reference masses are not only ion source dependent,
but also polarity dependent. To adjust both the a and t0 terms
requires at least two reference masses, spread across the
application mass range, such that the first reference mass is
<330 m/z and the second is 500 m/z or more above the first.
Using more reference masses improves recalibration results. Up
to 20 masses can be selected.
Using more reference masses can also increase the possibility of

a containment peak competing with a reference ion, causing
loss of mass accuracy for the entire mass range. In practice,
using two reference ions gives the best performance while
minimizing the chance of containment interference.
The reference masses specified for the method will be stored

with the method. These reference masses are also stored in the
file with acquired data as TOF or Q-TOF method parameters.
If you mark the Use Bottle A check box, the TOF or Q-TOF
controls the valve to introduce the internal reference standard
to the reference sprayer via the CDS.
The Ref Nebulizer parameter is only available if the source is

either Dual ESI, Dual AJS ESI or Dual nanoESI.
Number of required reference masses

To learn more about the underlying With two unknowns, a minimum of two known values are
calibration equation and required to determine both A and to. Practical considerations
coefficients, see “TOF mass also come into play. In order to get a good fit for both A and to
calibration” on page 56. then at least one reference mass needs to be at a low mass value
and there needs to be at least one reference mass at a higher
mass. Standard analytical practice also suggests that the low
m/z and high m/z reference masses bracket the masses of
interest.
Specifically, the reference mass correction algorithm requires

that one mass be at or below 330 m/z with a second mass that is
at least 500 m/z above the low mass ion in order to correct to
and A terms. If these conditions are not satisfied but at least
one reference mass is found, then only the A term will be
re-calibrated.
Selecting/editing list of reference masses

When creating a new method, the Agilent MassHunter
Workstation Software provides separate lists of reference
masses for each polarity. You can use the already provided mass
list, or you can create or edit a new mass list by right-clicking
the arrow to the left of each row in the Ref Mass tab.
Parameters for a reference mass correction

To know more about Segments and Scans To Average To increase the accuracy of the reference
Experiments, see “Automatic TOF mass correction, you can use a running average of the reference
and Q-TOF parameter changes mass values across several spectra. These mass values are used
during a run” on page 83. in determining the corrected calibration coefficients. The
default number of spectra used is five. Only odd values are
allowed.
The software averages only spectra from the same scan group,
and therefore a spectral average spans a spectral cycle.
A spectral cycle contains one spectrum for each of the
Experiments defined in a given Segment.
For example, if a Time Segment contains one Experiment with

Fragmentor voltage at 225 V and another Experiment with
Fragmentor voltage at 200 V, then a spectral cycle contains two
successive spectra, one at 225 V and another at 200 V.
Spectra from scans of different fragmentor voltage (or other

scan specific parameters) should not be summed and averaged
because they yield different masses.
Example The “Scans To Average” is 5. If the spectrum of interest is in the
nth cycle, then spectral data of the same Fragmentor voltage
from cycles n-2, n-1, n, n+1, n+2 are used in the average with
equal weights. If this Time Segment has defined one Fragmentor
voltage of 225 Experiment #1, and one Fragmentor voltage of
220 Experiment #2, and the current spectrum is the
Fragmentor voltage of 225 Experiment #1 of the nth cycle, the
spectra n-4, n-2, n, n+2, n+4 will be used for the average.
Reference Mass Window When the software attempts to find

the reference mass, it searches for the highest spectral peak in
the defined reference mass window, which is the window width
in parts per million (ppm). Recalibration using reference
masses of the internal reference standard does not replace
normal or external mass calibration. You must set the window
for recalibration small enough so the software does not pick
a spectral peak from the sample as the reference mass peak. 100
ppm is the recommended default value.
Reference Mass Minimum Height The “Reference Mass

Minimum Height” is the abundance in counts. The software uses
this height to exclude noise peaks and peaks of reference
masses that may fall within the detection window but that are
too small to be used for calibration. This is especially important
if you use reference masses that may be present in the tryptic
digest, such as the y1 ion (147 m/z for N-terminal Lys or 175 m/z
for N-terminal Arg), but may not be present in all spectra in the
run. Signals below 1,000 counts are generally too low to be used.
TOF and Q-TOF chromatogram setup
Signals above 200,000 counts for the reference mass ion can
negatively affect the reference mass correction.
TOF and Q-TOF chromatogram setup

In the Chromatogram tab, you also select the chromatograms or
the set points/actuals that you want to see in the
Chromatogram Plot window during the run.
Figure 49 Chromatogram tab in the TOF or Q-TOF tab
You can select the signal to plot (TIC, EIC, BPC, Set point,
Actual), the experiment type, the offset of the baseline for the
plot and the valid range of values in counts. You can also set the
mass range for the EIC.
Q-TOF Advanced Parameters for Ion Mobility

For the optimization and understanding the optical elements to
be changed, the next few images show how the tabs in the
Manual Tune tab match the different parts of the instrument. It
is not recommended to change these values in the Tune context,
but instead you make these changes in individual methods. The
different tabs in the Manual Tune > IM tab correspond to
different categories in the Advanced Parameters tab.
Figure 50 Ion Mobility parameters in the Manual Tune tab
Table 9 Manual Tune tabs and equivalent Category
Manual Tune Tab Category in Advanced Parameters
IM > Front Funnel IM FrontFunnel
IM > Trap IM Trap
IM > Drift Tube IM Drift Tube
IM > Rear Funnel IM RearFunnel
The IM Heater category and the IM category do not have tabs in

the Manual Tune tab.
IM Front Funnel The Trap Funnel RF is the most critical parameter for all
applications, as a too low value leads to defocused ions,
resulting in a loss in sensitivity. A value that is too high can lead
to excessive ion-heating, resulting in fragmentation of labile
molecules, or structural changes of molecules. A minor effect is
observed from the High Pressure Funnel RF; a lower value is
typically used for small and labile compounds.
IM Trap Trap grids low are the values when pulsing the ions out of the
trap. These values are the values when operating the
instrument in Q-TOF mode. Usually the exit grids do not need
any further adjustment from the autotune delivered with the
instrument. The high voltages (gray) are the sums of the grid
delta (top values) and the low values; these are the actual
applied voltages during trapping. Trap Exit Grid 2 Delta needs
to be reduced for small molecules and increased for large
molecules. In some cases, it might be advantageous to decrease
the total DC field in the trap by further reducing the delta
between Trap Exit and Trap Entrance (to as low as 0.5V)
combined with lowering the Trap Entrance Grid Low.
IM Drift Tube The best IM-MS resolution is achieved at maximum field
strength. This is calculated as the effective field ((Drift Tube
Entrance Voltage minus Drift Tube Exit Voltage) divided by
drift tube length). For accurate determination of collision cross
sections, this voltage needs to be changed stepwise. See the
Familiarization Guide for more information.
IM Rear Funnel For IM Rear Funnel parameters, the RF need to be reduced for
labile molecules. Depending on the total decrease, a drop in
IM-MS resolution might occur and will be part of the individual
compound optimization. In general, a delta of 2V between the
Rear Funnel Exit and IMS Hex Entrance should be maintained
for almost all applications. The total value of these voltages is
determined by the Octopole Entrance Lens; it should be another
delta of 1 to 2V between these.
All IM-MS parameters described in the Tune window are
accessible in the Advanced Parameters tab of the Q-TOF tab.
The table contains the Use Method column. If you mark this
column, then the value you specify is used instead of the value
in the tune file. Different samples require different parameters
to be changed from the tune file.
Setting parameters to acquire a data file in All Ions MS/MS mode

mode
In order to acquire a data file in All Ions MS/MS mode, it is
necessary to set up a method that has a Time Segment with at
least two and a maximum of four different Experiments
containing different Collision Energy values on a Q-TOF or
different Fragmentor voltages on a TOF.
The Agilent 6560 Ion Mobility Q-TOF can only have one fixed
collision energy in IM-QTOF mode.
The low energy Experiment provides MS information, and the

high energy Experiments provide MS/MS fragment information.
See the Qualitative Analysis Familiarization Guide for LC/MS
for more information on analyzing a data file that was acquired
in All Ions mode.
If you have a Q-TOF instrument, you set the Collision Energy to

0 in the first Experiment. In the subsequent Experiments
(channels), you set the Collision Energy to a higher value (for
example, 20 V). If you are creating a method for a Q-TOF with
different collision energies, you set the Fragmentor voltage at
the same value in each experiment. It should be set to a low
enough setting that no fragments are generated in the source
but at a high enough setting that you get enough precursor ions
transmitted to the skimmer. This value depends on the
compounds you are analyzing and their stability. You set the
Collision Energy and the Fragmentor voltage on the Source
tab.
Figure 51 First Experiment has a Collision Energy of 0 V
Figure 52 Second Experiment has a Collision Energy of 20 V
Since All Ions MS/MS is not an isolation MS/MS experiment,

you set the Mode to MS (Seg) on the Acquisition tab. For the
acquisition rate, you should attempt to get 8 to 10 data points
across the chromatographic peak for each collision energy
channel. For a typical peak width of 10 seconds at the base, the
recommended Rate for a 2-channel experiment (for example, 0
and 20 V) is 2 Hz; for a 3-channel experiment (for example, 0, 20
and 40 V) the recommended Rate is 3 Hz, and for a 4-channel
experiment (e.g. 0, 10, 20, 40 V), the Rate is 4 Hz.
It is highly recommended to use Collision Energy values of 10,

20 and 40 volts for the three high energy experiments because
those energies match the Collision Energy values that have
been used to acquire the accurate mass MS/MS spectra in all of
the MassHunter Personal Compound Databases and Libraries
(PCDLs) that can be used by the All Ions MS/MS algorithm in
the Qualitative Analysis program to select fragment ions.
On a TOF instrument, good starting values for the voltages for

pesticides are shown in Table 10.
Table 10 Fragmentor voltages for All Ions MS/MS Experiments
Number of Experiments Expt 1 Expt 2 Expt 3 Expt 4
2-channel 110 V 275 V
3-channel 110 V 180 V 300 V
4-channel 110 V 175 V 250 V 325 V
Setting up an experiment with two or three high energy

experiments allows the analysis of a large number of target
compounds that span a wide variety of compound stability.
While this allows selecting fragment ions with higher signal
from an optimized collision energy, it also decreases the time
that is spent on the precursor ion in the low energy channel,
thereby decreasing its signal. In a 2-channel, 3-channel and
4-channel experiment, the amount of time spent on the
collection of the precursor ion intensity is 50%, 33%, and 25%.
However, if a qualification of quantitative results on the
precursor ion in the low energy channel via fragment ion(s) in
the high energy channel is required, then the higher of the lower
limit of quantitation (LLOQ) for the precursor ion and the lower
limit of detection (LLOD) for the fragment ions will be the
actual LLOQ, and it may make sense to conduct a multi
high-channel experiment.
When you are setting up the experiments, you have the first
experiment have the low energy value, and then you increase
the Collision Energy or Fragmentor voltage for each
successive experiment. So, the highest Collision Energy or
Fragmentor voltage is in the last experiment.
Method saving, editing and reporting
Method saving, editing and reporting
Saving a method with data acquisition parameters

Adding Pre or Post Run Scripts before saving
To learn how to set up scripts, see Before you save a method, you can enter the pathway for the
your Agilent application engineer. customized scripts that start before or after a run. You do this
on the Properties tab.
Figure 53 Properties tab of the Method Editor window
Scripts can be written using any programming language. Scripts

provided by Agilent should not be modified since these files
may be overwritten when upgrading the Agilent software.
For more information on scripts, Below is a list of scripts that Agilent includes with the software
see the online Help. and that you can use with both methods and worklists.
Saving a method with data acquisition parameters
Table 11 System scripts and the actions they enable
Script name Actions the script enable
SCP_AcquireCalibrantData Sets “Cal/Ref Mass” to “Cal B” and

“LCStream” to “LC->Waste”. Allows you to
acquire data for the calibrant solution itself.
To be used only as the Pre-run script for
a method. The script itself does not do a run
and only augments an existing method. Do
not use as a standalone script in a worklist
run.
SCP_MSDivertValveToMS Sets the solvent divert valve to the “MS”

position.
SCP_MSDivertValveToWaste Sets the solvent divert valve to the “Waste”

position.
SCP_InstrumentStandby Puts the instrument in standby mode. This is

the same as clicking the “Standby” button
on the Instrument Status window.
SCP_LoadIdleMethod Loads a method to put the system in an idle

(MethodName) state. The first parameter is the method
name.
SCP_MSRefOff Turns off the MS reference ion solution (Ref

A)
SCP_PumpsAllandMSRefOff Turns off LC pumps and turns off the MS

reference ion solution.
SCP_PumpsAllOff Turns off all pumps.
SCP_LCCondition Starts a run for conditioning the LC part of

(MethodName, LCStream) the instrument. No data acquisition happens.
SCP_CalibrateTOFMassAxis Starts a TOF/Q-TOF mass axis calibration in

the active polarity using the default mass list
SCP_TraceOnOff Switches the trace to ON or OFF. The first

parameter must be either “on” or “off”.
SCP_ClearTrace Clears the trace file.
Method editing
Table 11 System scripts and the actions they enable (continued)
Script name Actions the script enable
SCP_ProcessQuantReport Runs a single sample Quant report.

Quantitative Analysis must be installed. Use
only as a Post Method script.
SCP_CTCReset Resets the CTC autosampler. If a drawer is

open, it will be closed.
Location of method folders

You can save methods to any folder on the system. The default
folder is D:\MassHunter\Methods\.
You can view the name and path of the currently loaded method
in the Properties tab of the Method Editor window (Figure 53).
Method editing
You can edit methods containing data acquisition parameters
using the Method Editor window of the Data Acquisition
software.
Use this location for method development. The set points are
sent to the instrument when the method is loaded and when
you click the Apply button after changing a parameter.
Methods can also contain Qualitative Analysis and Quantitative

Analysis parameters. You can modify the Qualitative Analysis
and Quantitative Analysis parts of the method in the DA tab in
the Method Editor window. See the Agilent MassHunter
Workstation Software Qualitative Analysis Familiarization
Guide or the online Help for the Qualitative Analysis program
for more information on the Qualitative Analysis software. See
the Agilent MassHunter Workstation Software Quantitative
Analysis Familiarization Guide or the online Help for the
Quantitative Analysis program for more information on the
Quantitative Analysis software.
Method reporting
Method reporting
You can see the parameters in a method in one of three ways:
• You click Method Report from the File > Print menu.
• You review the parameters in the Method Editor.
• You can see method parameters associated with a data file in
the Agilent MassHunter Workstation Qualitative Analysis
software.
Acquisition Method reports include this information:

• Method name, path and description
• List of configured LC modules and TOF or Q-TOF
• Parameter values for each LC module and for the TOF or the
Q-TOF
4
Data Acquisition
Interactive single sample setup 110
Worklist setup 112
Data acquisition for samples and worklists 128
Learn the concepts to help you understand the setup of single

samples for interactive data acquisition and the setup of single
samples and sequences of samples for automatic data
acquisition.
109
4 Data Acquisition
Interactive single sample setup
Interactive single sample setup

If you want to run just one sample at a time, you enter the
information for that sample in the Sample Run window.
Sample information
The sample information that the system records with the data
file is the sample name, vial position and other information in
the Sample Run window, such as Sample Type and Injection
Volume.
Sample information is not part of the method. It is stored with

the data file when the method currently loaded is run.
Injection Volume
You can specify an injection volume for the sample in this box.
You select the value As Method if you want to use the injection
volume specified in the method.
Figure 54 Sample Run window
Data Acquisition 4
Data File information
Data File information

The default folder for TOF/Q-TOF data is D:\MassHunter\Data.
Auto Increment If you want to use the same file name and have
the system automatically change the number at the end of the
file name, you turn auto-increment on. Then, you type a file
name that ends in the number 001, and the system makes sure
that a new file is created every time you re-run that sample.
Other folders
You can save your data to any folder on the system. You must
use the browse button to select a different folder. To open any
data file saved to a different folder than D:\MassHunter\Data,
you must browse to the different folder.
Some of the Additional Information parameters

Sample Type
You specify one of the following types for a single sample run:
Sample, Calibration, QC, Blank, DoubleBlank, Matrix,
MatrixDup, MatrixBlank, ConCal, TuneCheck, and
ResponseCheck.
Method Type
Acquisition Only, DA Only, or Both Acquisition and DA.
Run Types
This value is not shown by default. You can add it by clicking the
+ button and adding it using the Add Parameters dialog box.
Standard Start for LC runs
Manual Run for infusion runs with a syringe pump
External Start for AP-MALDI
LC Only Run for when you do not acquire MS data
4 Data Acquisition
Worklist setup
Worklist setup
Agilent developed worklists for the primary purpose of running
many samples automatically and then reporting on the
compounds found in the samples.
The worklist lets you enter sequences of samples—both single

and multiple samples—to be run automatically in the order of
their listing.
The worklist operates as a spreadsheet much like Excel. You can

copy, paste, and fill in columns as you would in Excel.
Figure 55 Example worklist
Selected Each line in the worklist table has a check box that allows you
sample to mark that line for processing or not. This can be useful if you
execution need to restart a worklist after some lines have already been
run.
Data Acquisition 4
Worklist menus
Worklist menus
You find all the tasks to create a worklist in the worklist menus.
• Add a single sample one at a time or add multiple single
samples all at once
• Add scripts before or after the worklist or between samples
in a worklist
• Add or show more sample information columns
• Add, insert or delete rows and columns
• Set up to print a worklist report or track a worklist run
Each menu has different commands available. Some commands

are only available in certain situations. For example, in the
column shortcut menu, you can only use the Insert Column (s)
command if you select a column that has been added using the
Add Column(s) menu.
Right-click upper left- Right-click column Select row and

hand corner of worklist Click Worklist to view Right-click cell to header to view right-click row to
to view worklist menu. top worklist menu. view cell menu. column menu. view row menu.
Figure 56 Worklist menus
4 Data Acquisition
Sample entry
Sample entry
One-at-a-time entry
You may want to do this to equilibrate the system before
running a worklist.
Multiple sample entry

If you want to add several single samples to the worklist at one
time, you use the menu selection to add multiple samples. You
can add different samples or one sample injected several times.
Sample When you add multiple samples, you can specify the data folder,
Information method names and injection volume.
Figure 57 Add Multiple Samples dialog box
Data Acquisition 4
Sample entry
Sample You can select the sample positions without having to type in
Position their values from the Sample Position tab on the Add Multiple
Samples dialog box.
Figure 58 Sample Position tab of the Add Multiple Samples dialog box
Sample methods
You can create a .m method containing either acquisition
parameters, data analysis parameters or both. See the Quick
Start Guide or the online Help for instructions for creating the
method.
If you specify a method with both acquisition and data analysis

parameters in the worklist, you select which parts to run in the
Worklist Run Parameters dialog box for a worklist and in the
Sample Run window for a single sample run.
4 Data Acquisition
Script entry
Script entry
Scripts are special programs, that You can enter scripts to be run at the following times:
execute automatically. Agilent • Before or after samples as part of the method
includes scripts with the Agilent
MassHunter Workstation The sample method can include pre- and post-analysis
Software, and you can write your scripts. (See Chapter 3, Acquisition Methods)
own scripts. • Before or after samples in the worklist or batch (insert or
add scripts, respectively)
• Before or after a worklist and after data acquisition
(Figure 63 on page 123)
Scripts provided by Agilent should not be modified since these

files may be overwritten when upgrading the Agilent software.
For detailed instructions on how to enter scripts, see the online

Help. For instructions on how to create scripts, see your Agilent
application engineer.
Agilent includes scripts with the software to help you

automatically, instead of manually, execute processes such as
column conditioning and valve shutoff. See Table 11 on
page 106 for a list of possible scripts.
Data Acquisition 4
Entry of additional sample information (show, add columns)
Entry of additional sample information (show, add columns)

The default worklist contains only nine columns for sample
information.
Figure 59 Default worklist columns
You can access these capabilities You can add more columns in one of two ways:
through the worklist menu. • Show or hide columns that contain sample information
already available in the worklist
• Add columns for new sample information
Show/Hide/Order sample information

Note that hiding a column does With this dialog box you can hide any of the original default
not delete the column. To delete columns and show others. You can also change the order of the
the column, you must first show columns. The marked columns are shown in the worklist in the
the column in the worklist or order they appear in this dialog box.
batch.
Figure 60 Show/Hide/Order Columns dialog box
4 Data Acquisition
Worklist import
Add sample information columns

When you add columns, you can enter sample information and
values for compounds, masses and acquisition parameters. You
can also enter your own sample information, including
empirical formulas. You can add a column for the Molecular
Formula which can be used in the Qualitative Analysis program.
The Column Type MFC is only available if the Qualitative
Analysis program is installed on the same computer. The
Column Type Protein is only available if the MassHunter
BioConfirm program is installed.
When you add a column, it
appears in the Show/Hide/Order
Column dialog box.
Figure 61 Add Columns dialog box
Worklist import
You can populate a worklist with sample information from other
files in multiple ways:
• Use the Study Manager program which automatically creates
a worklist when you submit a study.
• Copy individual columns one at a time from an Excel
spreadsheet (or a csv file imported into Excel) and paste (or
fill) them into the TOF or Q-TOF worklist under the correct
header
You do this when you need to transfer information
infrequently or the information is different for each transfer.
• Import a csv file directly
You cannot import a partial list of You do this when you need to use the same parameters in a
the samples within the csv file. worklist frequently.
Data Acquisition 4
Worklist import
CSV file mapping

You use the Map File Generator program to modify a map file.
You start this program by clicking the Map File Generator icon
in the Agilent MassHunter Workstation > Acq Tools folder.
See the online Help for more information on this program.
You can import the csv file to add Your sample csv file contains a table of samples and attribute
or insert samples whether the information for each sample. The information in this file may
worklist is running or not. You can not correspond to the information needed in a TOF or Q-TOF
also import the file in an offline worklist in several ways.
session. • Some of the information may not be relevant.
• Some information may be missing.
• Column names of the sample attributes may not be the same
as those used by the Agilent MassHunter Workstation Data
Acquisition software.
You cannot import scripts into a You must first edit the sample csv file to put it into a form that
worklist. You must add them maps to TOF or Q-TOF sample data. You can specify these
directly. changes when you map to the TOF or Q-TOF data:
• Change the column header names
• Add new columns in the worklist
• Change data values
You can include a mapping section in front of the sample

information in the sample csv file or in a separate configuration
csv file. You use a configuration csv file when all the sample
information values are the same from import to import. You
also include the mapping section in the sample csv file when
new groups of samples with different dynamic mapping of
columns, such as amount of compounds analyzed, are added for
import.
Mapping for static worklist columns

Some worklist boxes are static and invariant, such as Sample
Name and Sample Position. These come under the heading,
Static Mapping, in the mapping section of the csv file.
4 Data Acquisition
Worklist import
Mapping for dynamic worklist columns

Some columns in a worklist are dynamic and change from
analysis to analysis. The mapping capability in the csv file lets
you specify additional columns to be added to the worklist. The
name of the added worklist column should use the same name
as the csv column specified. You then specify the column type in
the worklist, such as Compound, Mass, MS Parameter, User
Defined or Custom Parameter. These new columns to be added
to the worklist come under the heading, Dynamic Mapping, in
the mapping section of the csv file.
Data Value mapping Data values for some columns, such as

sample type, are limited to a drop-down list in the worklist and
do not match the same names as are in the csv file. Data value
mapping is preceded by the key words [Data Value Mapping]
Example mapping section

You want to import samples into a TOF or Q-TOF worklist, but
the column headers in the CSV import file (Excel spreadsheet)
are different from the worklist column headers. For example,
“Sample” is used instead of “Sample Name”, as shown below:
Table 12 Original sample table
Sample Acq MyData DA SampPos Sample Type Internal

Method Std A
AAA method1 qwwq method1 1 Standard 1
BBB method2 bbb method1 2 Sample 1
CCC method3 ccc method1 3 QualControl 1
One column header, “InternalStdA”, must be added as a new

column to the worklist. You can also add columns that do not
exist in the csv file, such as “Caffeine” in the section below.
Some data values are also different (e.g., Sample Type values).
Data Acquisition 4
Worklist import
Table 13 is the mapping section for the spreadsheet in Table 12.

This is the spreadsheet version of the mapping that lets the
worklist import program recognize columns of imported data.
Table 13 Mapping section for csv file

[Static Mapping]
Acq Method Acquisition Method
MyData DataFile Name
DA DataAnalysis Method
SampPos Sample Position
Sample Sample Name
[Dynamic Mapping]
(//Added column)
InternalStdA Compound 1
Caffeine Compound
[Data Value
Mapping]
Sample Unknown
QualControl QC
4 Data Acquisition
Report setup
Report setup
After you run the worklist, you can send a worklist report to
one or more of these locations: Screen, Printer, Excel File or
PDF File. You specify the report destination and the file path in
the Worklist Report Options dialog box.
You can also specify to print all of the columns that are part of
the table or to print only the visible columns, and you can select
a different Worklist Report template. You can modify the
worklist report template if you know how to modify an RDL
report.
Figure 62 Worklist Report Options dialog box
Data Acquisition 4
Run setup
Run setup
Before you run a worklist you select parameters for the entire
worklist.
• Start run types and the part of the method to run
• Paths for the acquisition method, data analysis method and
data file
• Whether or not to combine export output when also running
a Qualitative Analysis method
• Scripts to run before or after the worklist
• Free disk threshold
The free disk threshold is the amount of disk space in
gigabytes that must be available before the worklist starts.
Figure 63 Worklist Run Parameters dialog box
4 Data Acquisition
Estimate of worklist file size
Overlapped Data Analysis with Acquisition

You can choose to start the next data acquisition run when the
data analysis is complete, or for higher throughput of samples,
while data analysis of the previous sample is still running.
This option is selected in the Worklist Run Parameters dialog

box, in the Execution for Acquisition-DA list box. To overlap
data analysis with acquisition, select Asynchronous. To cause
data acquisition to wait until data analysis is complete, select
Synchronous.
Overlapped Injection
You can load a sample into the sample loop during a run that is
still completing. This option allows you to save time that is
required to load the sample before the run.
To select this option, mark the Overlapped Injection check box

in the Worklist Run Parameters. You also have to select this
option in the individual methods being used in the worklist.

Depending on your estimate of the file size of the worklist, you
may have to change the default value of the Free Disk
Threshold.
You can run a typical worklist sample to estimate the worklist

file size. Then, you observe the file size in Windows Explorer,
and multiply the observed file size by the number of samples in
the worklist.
The data file for profile data is compressed by a factor of 3 - 20,

depending on the complexity of the mass spectra acquired. This
new feature greatly reduces the data storage needed for profile
data.
The Instrument Mode selected for the Accurate-Mass TOF and

Accurate-Mass Q-TOF also affects the size of the data file. The
Agilent TOF and Q-TOF instruments now will acquire 2 times as
Data Acquisition 4
much data when operated in the 2 GHz mode (extended

dynamic range or extended mass range) or 4 times as much data
when operated in the 4 GHz mode (high resolution).
For an IM-QTOF data file, the typical file size is about 3 times
larger than what the equivalent non-IM LC-MS data file would
have been. A typical data file is very sparse (it has a lot of
zero-abundance points which are not written to disk), but how
sparse depends on the sample and lots of different conditions.
As an example of the size of a very complex data file, a 1 minute
method was run to acquire a raw data file of an injection of an
E-coli digest with collision energy applied; the data file was
around 180 MBytes in size (or around 3 MBytes/sec.) Many data
files are not this large or complex.
Method parameters that control file size

LC data is usually a small fraction of TOF or Q-TOF data. The
size of the acquired data file depends on these TOF or Q-TOF
method parameters:
• Data file storage type—Profile, Centroid, Both or None
Profile stores raw data as abundance values for evenly spaced
ion flight time. Centroid stores only the assigned peaks but not
the raw data. Both stores both Profile data and Centroid
data. None stores no data but does store spectrum metadata
and method parameters.
If you want to analyze your data in Qualitative Analysis using
either the Large Molecular Feature Extractor (LMFE)
algorithm or the Deconvolute (MS): Maximum Entropy
algorithm, you acquire in either Profile or Both modes.
Profile data is required for both of these algorithms.
• Total run time
• Setting of time segments
• Number of experiments that are defined
4 Data Acquisition
Approximate file size for stored Profile data

The file size per spectrum depends on three variables.
• Mass range
• Spectrum metadata
• Compression factor - the data file is compressed by a factor
of 2 to 20, depending on the complexity of the mass spectra
acquired
Mass range You can reduce data file size by reducing the mass
range of interest. Profile data are stored as abundance for each
flight time. If you restrict the mass range, the number of data
points in the spectrum depends on the mass calibration curve.
The table below shows the number of possible data points for a
given mass range using a typical mass calibration curve. The
Agilent 6540 UHD Accurate-Mass Q-TOF has approximately 25%
more data points.
Note that low masses require
more data points than high masses Table 14 Number of data points per spectrum for given mass ranges
because of the non-linear nature of
Mass range Number of data Number of data Number of data
the time to mass conversion. (Daltons) points (1 GHz) points (2 GHz) points (4 GHz)
50 to 750 50,000 100,000 200,000
50 to 1000 60,000 120,000 240,000
50 to 3000 100,000 200,000 400,000
250 to 1000 30,000 60,000 120,000
500 to 3000 60,000 120,000 240,000
250 to 3000 70,000 140,000 280,000
Each data point stored requires 12 bytes of storage. A mass

range of 250 to 3000 requires 840,000 bytes per spectrum at 1
GHz acquisition rate. If the scans/sec. equal 1, then the data
storage required for one minute worth of spectra before
compression is 50,400,000 bytes or about 48 MB. Then, this data
is compressed which means the actual data storage needed is
between 2.4 MB and 16 MB (with a compression ratio between 3
and 20).
Data Acquisition 4
If the run time on a run with one time segment is 5 minutes,

then one run requires between 12 MB and 80 MB of disk space.
A worklist with 10 samples using the same mass range requires
between 120 and 800 MB of disk space. If the scan rate is set to
20 scans per second, the data file could require a large amount
of disk space.
Spectrum metadata In addition to data points, information on

the spectrum, such as the instrument actuals and set points,
used during acquisition is stored with each spectrum. This
information takes 2884 bytes per spectrum or about 8.2 MB for
the worklist described above.
Storage of method parameters for each run also affects file size
but to a lesser degree than the file size of the spectrum. They
take up about 10,000 bytes before sample injection starts. For a
10-sample worklist, they take up less than 0.1 MB.
Approximate file size for Centroid data

Data is not stored as the abundance at evenly spaced ion flight
times. Rather, peak centroids are computed first. Each data
point is stored as a pair of values of mass and abundance. The
data storage required is 12 bytes per detected peak in the
spectrum. The number of peaks detected is dependent on the
number of compound peaks in the spectrum as well as the noise
in the background and the threshold set.
If the mass range is set as 250 to 3000 and the threshold is

appropriate, about 3000 to 5000 peaks are detected in one
spectrum. If the scans/sec. is 1, the run time 5 minutes, and ten
samples are in the worklist, then the disk space needed for
these samples is between 102 and 172.5 MB.
If you have a 2 GHz instrument, the disk space needed for these
samples is between 204 and 345 MB. If you have a 4 GHz
instrument, the disk space needed for these sample is between
408 and 690 MB.
Spectrum metadata and method parameters are also stored

with centroid data and comprise a greater percent of the file
size than with Profile data.
4 Data Acquisition
Data acquisition for samples and worklists
Data acquisition for samples and worklists
What you can monitor during a run

Tracking sample runs
The worklist shortcut menus contain an option called “Track
Worklist Run” that you can turn off or on. The default position
is on. With Track Worklist Run on, you can see what sample is
running at any time during the worklist run.
When you start a worklist run, the first sample row turns dark
blue, indicating that the sample in this row is running and data
is being acquired. When the data acquisition finishes, the first
sample row turns light blue to indicate that Data Analysis is
running.
If you have set Execution for Acquisition-DA to Asynchronous,

you will see both a dark blue and a light blue line to indicate
which lines are acquiring data and analyzing data.
Monitoring the Chromatogram Plot and Spectrum Plot windows

For more information on real-time You can also monitor the TIC or EIC chromatograms, LC
plots, see “Real-time displays” on parameters and mass spectra for each sample during the
page 72. worklist run. You can print a plot of the real-time data by
clicking the File > Print > Real-time Plot Report command.
Data Acquisition 4
What you can do during a run

Locked Mode
You can turn Locked Mode on or off using the toolbar icons in
the main toolbar. If Locked Mode is turned on, you cannot edit a
worklist or method while the data is being acquired. Also, the
data file is protected, so you cannot overwrite the data file if
you run this method or worklist again. If Locked Mode is turned
off, then you can edit the worklist during a run.
Editing current worklist during run

You can edit any sample row or batch row during a run as long
as the sample is located below the first row after the running
sample row. If the last selected row is executing, then all rows
are locked.
When you switch to a row to edit the sample, the “Track

Worklist Run” option automatically turns off. To see the sample
row running after your edit, you select this tracking option
again. The screen then automatically switches to that part of the
worklist with the sample that is running.
4 Data Acquisition
www.agilent.com
In This Book
The Concepts Guide
presents “The Big Picture”
behind the Agilent 6200
Series TOF and 6500 Series
Q-TOF LC/MS system to
help you to understand
how to use the TOF and
Q-TOF LC/MS system
components.
This guide includes
concepts for:
• Inner workings of the
TOF and Q-TOF MS
• Instrument Preparation
• Methods with
Acquisition Parameters
• Data Acquisition
 Agilent Technologies, Inc. 2014
Printed in USA
Revision A, December 2014
*G3335-90173*
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Agilent 6200 Series TOF

and 6500 Series Q-TOF

3 Methods with Acquisition Parameters

3 Methods with Acquisition Parameters

This chapter provides an overview of the Agilent 6200 Series

Each Agilent system has advantages for high throughput sample

The Agilent Accurate-Mass 6530 Q-TOF, the Agilent UHD

a super-heated sheath gas to collimate the nebulizer spray

Help for applications

Help for data acquisition

Prepare the instrument

Help for data analysis

Agilent also designed the Qualitative Analysis program to

You can also set up methods to automatically do the tasks in the

Please refer to the Agilent MassHunter Workstation Software -

You can also purchase the Agilent MassHunter BioConfirm

Agilent MassHunter IM-MS Browser program

The IM-MS Reprocessing program is a utility that allows you to

Both of these utilities are included with the MassHunter Data

Agilent MassHunter Workstation Software - Quantitative

• Integrates with an automated, parameter-free integrator that

Please refer to the Agilent MassHunter Workstation

How do different ion sources work?

The sources that are used are the B-type sources.

Electrospray ionization (ESI) and Dual ESI

The spray occurs at right angles to the capillary. This design

HPLC inlet For Dual ESI, a second

heated drying gas

Figure 1 Electrospray ion source

Electrospray ionization (ESI) consists of four steps:

Preformed ions are not always required for ESI. Some

chamber draws out the sample solution and breaks it into

Because the sample solution is not heated when the aerosol is

Desolvation and ion evaporation

A counter-current of neutral, heated drying gas, typically

Figure 2 Desorption of ions from solution

These ions are attracted to and pass through a capillary

The importance of solution chemistry

Dual Agilent Jet Stream Electrospray Ionization (Dual AJS

You connect the tubing here for low

The recommended flow range (1 to 50 μL/minute) really is

Atmospheric pressure chemical ionization (APCI)

The resulting gas/vapor mixture is then passed over a corona

HPLC inlet nebulizer (sprayer)

Figure 4 Atmospheric pressure chemical ionization (APCI) source

APCI is applicable across a wide range of molecular polarities.

molecules less than 1,500 u. Because of this molecular weight

Atmospheric pressure photoionization (APPI)

APPI is applicable to many of the same compounds that are

HPLC inlet nebulizer (sprayer)

Figure 5 Atmospheric pressure photoionization (APPI) source

Multimode ionization (MMI)

Figure 6 Multimode source

ESI and APCI are essentially incompatible processes because

Multimode ionization (MMI) is useful for screening of

With the invention of HPLC-Chip technology, Agilent is

Figure 7 HPLC-Chip making process

Figure 8 shows the complete Agilent 6520

Figure 8 Schematic of Agilent 6520 Q-TOF LC/MS