LCMS Q-TOF QuickReference

225-28865D
May 2020
LabSolutions™ LCMS
Instruction Manual
Quick Reference (for LCMS Q-TOF)
Read this manual thoroughly before you use the product.
Keep this manual for future reference.
This page is intentionally left blank.
Introduction
Read this Instruction Manual thoroughly before using
the product.
Thank you for purchasing Shimadzu analytical instrument workstation "LabSolutions
LCMS" (hereafter referred to as "the software" or "LabSolutions").
This manual describes the procedures for operating this product. Read this manual
thoroughly before using the product and operate the product in accordance with the
instructions in this manual.
Also, keep this manual for future reference.
This manual assumes that the reader is knowledgeable of basic operations of
Windows.For the operation of Windows, refer to the instruction manual that comes with
that product.
LCMS-9030 is referred to as "LCMS Q-TOF" in this manual.
Important
• If the user or usage location changes, ensure that this manual is always kept
together with the product.
• If this manual is lost or damaged, immediately contact your Shimadzu
representative to request a replacement.
• To ensure safe operation, contact your Shimadzu representative if product
installation, adjustment, or re-installation(after the product is moved).
Notice
• Information in this manual is subject to change without notice and does not represent
a commitment on the part of the vendor.
• Any errors or omissions which may have occurred in this manual despite the utmost
care taken in its production will be corrected as soon as possible, although not
necessarily immediately after detection.
• All rights are reserved, including those to reproduce this manual or parts thereof in
any form without permission from Shimadzu Corporation.
• Microsoft, Windows 7 and Windows 10 are registered trademarks of Microsoft
Corporation in the United States and/or other countries.
• Third-party trademarks and trade names may be used in this publication to refer to
either the entities or their products/services, whether or not they are used with
trademark symbol "TM" or "®".
• Adobe, Adobe logo and Adobe Acrobat Reader are trademarks or registered trademarks
of Adobe Systems Incorporated in the United States and/or other countries.
• LabSolutions is registered trademarks of Shimadzu Corporation in the United States and
Europe (Office for Harmonization in the Internal Market).
ã 2018-2020 Shimadzu Corporation. All rights reserved.
LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF) i

Introduction
Indications Used in Instruction Manuals
Indication Meaning
Emphasizes additional information that is provided to ensure
the proper use of this product.
The following symbols are used in this manual.
Indication Meaning
Indicates information provided to improve product performance.
Indicates the location of related reference information.
ii LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF)

Warranty
Warranty
Shimadzu provides the following warranty for this product.
1. Period
Please contact your Shimadzu representative for information about the period of this warranty.
2. Description
If a product/part failure occurs for reasons attributable to Shimadzu during the warranty period,
Shimadzu will repair or replace the product/part free of charge. However, in the case of products
which are usually available on the market only for a short time, such as personal computers and
their peripherals/parts, Shimadzu may not be able to provide identical replacement products.
3. Limitation of Liability
(1) In no event will Shimadzu be liable for any lost revenue, profit or data, or for special, indirect,
consequential, incidental or punitive damages, however caused regardless of the theory of
liability, arising out of or related to the use of or inability to use the product, even if Shimadzu
has been advised of the possibility of such damage.
(2) In no event will Shimadzu's liability to you, whether in contract, tort (including negligence), or
otherwise, exceed the amount you paid for the product.
4. Exceptions
Failures caused by the following are excluded from the warranty, even if they occur during the
warranty period.
(1) Improper product handling
(2) Repairs or modifications performed by parties other than Shimadzu or Shimadzu designated
companies
(3) Product use in combination with hardware or software other than that designated by Shimadzu
(4) Computer viruses leading to device failures and damage to data and software, including the
product's basic software
(5) Power failures, including power outages and sudden voltage drops, leading to device failures
and damage to data and software, including the product's basic software
(6) Turning OFF the product without following the proper shutdown procedure leading to device
failures and damage to data and software, including the product's basic software
(7) Reasons unrelated to the product itself
(8) Product use in harsh environments, such as those subject to high temperatures or humidity levels,
corrosive gases, or strong vibrations
(9) Fires, earthquakes, or any other act of nature, contamination by radioactive or hazardous
substances, or any other force majeure event, including wars, riots, and crimes
(10) Product movement or transportation after installation
(11) Consumables and equivalent items

Recording media such as CD-ROMs are considered consumable items.
LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF) iii

Introduction
* If there is a document such as a warranty provided with the product, or there is a

separate contract agreed upon that includes warranty conditions, the provisions of those
documents shall apply.
iv LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF)

Contents
Introduction Indications Used in Instruction Manuals ............... ii
Warranty .......................................................... iii
1 Starting Up
Preparing for 4
2 Analysis
2.1 Auto Tuning (Full Mode) .....................................
2.2 Auto Tuning (TOF Calibration Only) ..................... 8

2.2.1 Preparing Standard Sample ..................................... 8
Performing Single Analysis in 12

3 MS/MS (DDA) Analysis Mode
3.1 Creating a New Method File ..............................
3.2 Setting Parameters to Perform Single Analysis ..... 12

3.2.1 Setting LC Instrument Parameters ............................ 12
3.2.2 Setting MS Analysis Condition Parameters - MS/MS
(DDA) Mode ................................................... 13
3.2.3 Specifying Temperature, Gas Flowrate, and Other Items
for Interface and Ion Introduction Sections ................. 17
3.3 Saving a Method File ........................................ 18

3.4 Performing Single Analysis ................................. 18
3.5 Setting Parameters for Each Analysis Mode ......... 21
3.5.1 MS Mode ...................................................... 21
3.5.2 MS/MS Mode .................................................. 21
3.5.3 MRM Mode ................................................... 22

3.5.4 MS/MS (DDA) Mode .......................................... 23
3.5.5 MS/MS (DIA) Mode ........................................... 28
3.5.6 SIM Mode ..................................................... 31
Checking Results of 4.1 Opening Results of Single Analysis in the [MS

4 Single Analysis Data Analysis] Window ...................................... 32
4.2 Displaying Chromatograms ................................. 33
4.3 Displaying Mass Spectra ..................................... 35
LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF) v

Contents
4.4 Performing Background Subtraction .................... 39

4.5 Printing Analysis Results ................................... 41
4.6 Export Data in mzXML or mzML Format ............. 42
5 Batch Analysis 5.1 Creating a Batch Table ...................................... 43

5.2 Performing Batch Analysis .................................. 45
5.3 Export Data in mzXML or mzML Format ............. 46
Performing Single Analysis 49

6 in MRM Analysis Mode
6.1 Opening a Method File .....................................

6.2.2 Configuring Analysis Conditions for a Target - MRM
Analysis Mode ................................................. 50
6.2.3 Configuring Analysis Conditions for Mass Correction -
MS Analysis Mode ............................................ 52
6.2.5 Saving a Method File ......................................... 58

Performing Single Analysis 61

7 in SIM Analysis Mode
7.1 Opening a Method File .....................................

7.2.2 Configuring Analysis Conditions for a Target - SIM
Analysis Mode ................................................. 62
7.2.3 Configuring Analysis Conditions for Mass Correction -
MS Analysis Mode ............................................ 63

vi LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF)

Contents
8 Mass Correction 8.1 Internal Standard .............................................. 65

8.1.1 Preparing Sample for Mass Correction ....................... 65
8.1.2 Setting MS Instrument Parameters ........................... 67
8.1.3 Setting Mass Correction Parameters .......................... 68

8.2 External Standard (Using a Spectrum in the
Same File as the Standard) ................................ 72
8.2.1 Preparing Sample for Mass Correction ....................... 72
8.2.2 Setting MS Instrument Parameters ........................... 72

8.3 External Standard (Using a Spectrum in a
Different File as the Standard) ........................... 78
8.3.1 Performing Single Analysis on Sample for Mass
Correction .................................................... 78
8.3.2 Registering Spectrum for Mass Correction to Spectrum
Processing Table ............................................... 80

8.4 Checking Mass Correction Results ....................... 86
9 Exiting
LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF) vii

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1 Starting Up
1
1 Switch ON the power of each LC unit and Q-TOF instrument.
The POWER indicator lamp on the front face of the LCMS Q-TOF lights in green and the
STATUS indicator lamp flashes in green.
2 Confirm that the gases are supplied normally.
3 Switch ON the PC.
4 Confirm that the [LabSolutions Service] icon is displayed in green.
Color of Icon LabSolutions Status Action

Green Normal
Yellow Starting up Wait for a while.
An error has
Red Reboot the PC.
occurred.
5 Click (LabSolutions) on the desktop.
LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF) 1

1 Starting Up
6 Log in.
7 Double-click the icon for the instrument to start the [Realtime Analysis] program.
8 On the [Main] assistant bar, click the (System Control) icon.
The [System Control] window appears.
2 LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF)

9 Click [Auto Startup].
After approximately 10 hours of TOF preliminary temperature control, the rotary pump
starts up. The turbo molecular pump (QP) and turbo molecular pump (TOF) then start
up sequentially. 1
After the rotary pump starts up, the vacuum system, temperature control, and high
voltage power supply become ready, the indicator lamp in the [System Control] window
lights up in green, and then the instrument becomes ready for measurement.
When the vacuum system has not been used for a long period of time, it takes
approximately two days for the system to stabilize.
10 Click [Close].

2 Preparing for Analysis
Before starting analysis, perform tuning to optimize the control parameters for the QP
and TOF sections.
There are two tuning methods: auto tuning and manual tuning.
This section describes the operations in "full mode," in which the instrument sensitivity
and resolution, and mass are calibrated, and the operations for "TOF calibration only,"
in which only mass calibration is performed.
2.1 Auto Tuning (Full Mode)

In auto tuning, control parameters for the QP and TOF sections are automatically
optimized based on the specified auto tuning conditions so that the preferred mass
spectrum peaks can be acquired.
Auto tuning takes approximately 60 minutes to complete because it searches for

the optimum parameters.
1 Prepare a standard sample.
1 Open the front door and pour a standard sample into a standard sample vial.
2 Connect the standard sample vial to port No. 5 of the calibrant delivery system
(CDS) valve.
Refer to 3.8.1 Preparing the Standard Sample in the LCMS-9030 Instruction
Manual.
2 Start the [RealtimeAnalysis] program and click the (Tuning) icon on the
[Main] assistant bar.

The [MS Tuning] window appears.
3 Click (New) on the toolbar.

A new tuning file is created.
4 On the [Tuning] menu, click [Actions After Auto Tuning] - [Print Result] to select
it.

5 Configure the tuning conditions.
1 Click the (Auto Tuning Condition) icon on the [Tuning] assistant bar.
The [Auto Tuning Condition] window appears.
2 Select the polarity to perform tuning and then select [Full Tuning].
For TOF calibration, see "2.2 Auto Tuning (TOF Calibration Only)".
3 Click [OK].
6 On the [Tuning] assistant bar, click the (Auto Tuning Start) icon.
Confirm that the DL plug has been removed.
The [Progress of Auto Tuning] window appears and auto tuning starts. In the [Progress
of Auto Tuning] window, the tuning status can be checked.
After auto tuning is finished, a report is output.

n Example of the Output Report

7 Save the tuning file under a new name.
1 On the [File] menu, click [Save Tuning FIle As].
2 Enter the tuning file name and click [Save].
When saving a tuning file, a confirmation message appears to check

if the file should be used as the default tuning file. If specified as
the default tuning file, this file will be used as the tuning file when
a tuning file is not specified in single analysis or batch analysis.

2.2 Auto Tuning (TOF Calibration Only)

TOF type mass spectrometers can acquire spectra of time of flight (horizontal axis) and
ion intensity (vertical axis). To acquire MS spectra, the horizontal axis of the spectra needs
to be converted from time of flight to mass.
In the most simplified form, the mass is proportional to the square of the time of flight.
However, since offsets and distortions are generated for various reasons in actual
measurements, a mass calibration table is created from the precise ion mass of the
standard sample and its measured time of flight values (up to 32 points) and then the
mass calibration curve is calculated using the table.
For unknown ions, time of flight is converted to mass or mass is converted to time of
flight using this mass calibration curve.
This section describes the operation to calibrate the mass using auto tuning. Perform the
procedure before analysis that requires accurate mass.
Mass calibration results are saved in the tuning file. The results are also saved in the file
containing data acquired using the tuning file so that they can be used to display mass
spectra.
Mass calibration takes approximately 3 minutes when gas flowrate and

temperature are controlled and stabilized.
2.2.1 Preparing Standard Sample
1 Prepare a standard sample.
1 Open the front door and pour a standard sample into a standard sample vial.
2 Connect the standard sample vial to port No. 5 of the CDS valve.
Refer to 3.8.1 Preparing the Standard Sample in the LCMS-9030 Instruction
Manual.
2 Start the [Realtime Analysis] program and click the (Tuning) icon on the
[Main] assistant bar.

The [MS Tuning] window appears.
3 Click (Open) on the toolbar.
4 Specify an existing tuning file name and click [Open].

5 On the [Tuning] menu, click [Actions After Auto Tuning] - [Print Result] to select
it.
6 Configure the tuning conditions.
1 Click the (Auto Tuning Condition) icon on the [Tuning] assistant bar.
The [Auto Tuning Condition] window appears.
2 Select the polarity to perform mass calibration by tuning and then select [TOF
Calibration].
3 Click [OK].
7 On the [Tuning] assistant bar, click the (Auto Tuning Start) icon.

8 Click [TOF Cal.] in the upper area of the Tuning Results window.
The [TOF Calibration] window appears.
No. Item Description

1 Enter TOF value Disabled for auto tuning results.
Recalculate
2 Calibration Disabled for auto tuning results.
Curve
Displays the compounds listed in [Standard Sample Table] in the
3 Compound [MS Sample Table] window in the [System Configuration]
window.
Displays the theoretical m/z values in [Standard Sample Table]
4 m/z in the [MS Sample Table] window in the [System Configuration]
window.
Displays the time of flight (measured value) of the ions in the
5 TOF
standard sample.
Displays the result of "(measured TOF value - TOF value of
6 dTOF/TOF(ppm)
calibration curve) / TOF value curve of calibration curve."
Displays an enlarged MS spectrum close to the m/z of the line
(MS spectrum
7 selected in the TOF calibration table.
graph)
”No Data” is displayed when the target spectrum does not exist.
1 Click [Close].

9 Save the tuning file under a new name.
1 On the [File] menu, click [Save Tuning File As].
2 Enter the tuning file name and click [Save].
When saving a tuning file, a confirmation message appears to check

if the file should be used as the default tuning file. If specified as
the default tuning file, this file will be used as the tuning file when
a tuning file name is not specified in single analysis or batch analysis.

3 Performing Single Analysis in MS/MS (DDA) Analysis Mode
3.1 Creating a New Method File
1 On the [Main] assistant bar, click (Data Acquisition).
The [Data Acquisition] window appears.
2 On the toolbar, click (New).

A new method file is created.
3.2 Setting Parameters to Perform Single Analysis
3.2.1 Setting LC Instrument Parameters
1 Click the [Simple Settings] tab and configure the analysis conditions.
1 Specify the time to finish analysis in [LC Stop Time].
2 Specify the pump flowrate and initial concentration.
3 If the oven will not be used, clear the [Temperature] checkbox.
When creating a new method file, be sure that the rack specified in
[Sample Rack] on the [Autosampler] tab page matches the rack
actually used. If it does not, an error message is displayed and analysis
cannot be started.
In this case, click [Advanced], click [Detect Rack] on the [Autosampler]
tab page, and specify the correct rack.

2 Click the [LC Time Prog.] tab and configure the concentration gradient conditions
and other settings.
For the [Time] column of the time program, specify the elapsed time after the
start of analysis. Be sure to specify 0.01 min or more.
3.2.2 Setting MS Analysis Condition Parameters - MS/MS (DDA) Mode
Set the parameters to automatically select the precursor ion according to the specified
standard and perform MS/MS analysis.
Specify the parent event (survey event) in the MS analysis mode and child event
(dependent event) in the MS/MS (DDA) analysis mode.
1 Click the [MS] tab.
2 Select the polarity and click to select the MS analysis mode.

A survey event is added to the event table.
Set events with different polarities at the different measurement time.

3 Click to select the MS/MS (DDA) analysis mode.

A dependent event is added under the survey event.
4 Add dependent events by the number of dependent spectra to acquire.
Up to 100 dependent events can be set for one survey event.
5 Specify the analysis time, m/z range for TOF, CE, and event time for the survey
events and dependent events.
In the setting above, measurement is performed by changing the analysis

condition sequentially for the specified analysis time (0.00 to 35.00 min) in the
figure below, event 1 → event 2 → event 3 → event 4 → ... event 7 → event
1→ event 2 → ...
After the “event time” specified in event 1 elapses, event 2 starts. The time
spent on one cycle from the start of event 1 to the completion of event 7 is
called [Loop Time]. To check the loop time, click to display the [Loop
Time] window.

6 Specify the precursor ion selection standard.

When a peak that satisfies the precursor ion selection condition specified in this step is
found in the spectra of the survey event, the system searches for the precursor ion.
1 Click [MS] for the survey event.
The [Execution Condition Settings of Dependent Events] window appears.

3
2 Specify the minimum BPC intensity value.
Precursor ion is searched when the maximum centroid peak intensity (BPC) within
the m/z range for searching the precursor ion exceeds the threshold value specified
in this step.

3 Click [Exclusion Settings of Precursor Ions in Detail].
The [Exclusion Settings of Precursor Ions in Detail] window appears.
4 Specify the period not to select the m/z that has once been selected for the
precursor ion.
5 The mass range and analysis time range to be excluded from the selection of the
precursor ion can be specified.
6 Click [OK].
For other parameters, see "3.5 Setting Parameters for Each Analysis Mode".

3.2.3 Specifying Temperature, Gas Flowrate, and Other Items for Interface and Ion Introduction Sections
1 Click the [Interface] tab.
2 Set the parameters.

Specify the gas flowrate and temperature for the main
1 Main-Interface
interface.
Specify the voltage and gas flowrate for the sub interface.
2 Sub-Interface
* These items can be specified when a sub interface is installed.
A 6-port 2-position valve for switching the channels from the

3 Diverter Valve
LC unit. Specify the position at the start and end of analysis.
Specify the gas flowrate and temperature for the ion
4 Ion Guide
introduction section.
5 CDS Specify the initial setting for the position of the CDS valve.

3.3 Saving a Method File
1 On the [File] menu, click [Save Method File As].
2 Enter the file name and click [Save].
3.4 Performing Single Analysis
1 Place the sample on the autosampler.

2 Click (Instrument On/Off) on the toolbar.

The pump starts to deliver the solvent and the temperature control operation for the
oven starts.
3 Click (MS Instrument On/Off) on the toolbar.

It turns ON/OFF the heater, gas, and high voltage power supply collectively.
4 On the [Acquisition] assistant bar, click (Start Single Run).
The [Single Run] window appears.

3
5 Configure the single analysis conditions.
1 Enter the data file name.
2 Specify the vial number, tray number, and injection volume.
3 Click [OK].
Single analysis starts.

To change the chromatogram displayed in the [Acquisition] window during

measurement, right-click the mouse on the chromatogram and select [Display
Settings].
The m/z of the chromatogram to be displayed and magnification can be
specified on the [MS] tab page.
Select the [Auto scale] checkbox.

3.5 Setting Parameters for Each Analysis Mode

Q-TOF analyzers provide both high sensitivity and high resolution through its
configuration in which a quadrupole mass filter (Q1) and TOF section are connected.
Specifying a suitable analysis mode draws out the instrument’s maximum performance.
Five types of analysis modes are available: MS mode, MS/MS mode, MRM mode, MS/MS
(DDA) mode, and SIM mode.
3.5.1 MS Mode
In the MS analysis mode, the Q1 lets ions of all m/z values pass and the TOF section
measures the time of flight of the ions.

3
Start(min)
1 Specify the measurement time range for an event.
End(min)
Specify the m/z of the ion to be measured in the TOF section.
TOF Start m/z
2 * Specify the required m/z range as specifying a wide range increases
TOF End m/z
data volume.
Specify the time required for a single event.

To improve the chromatogram shape, specify a shorter event
3 Event Time(s)
time. To improve sensitivity and repeatability, specify a longer
event time.
When this is selected, the profile spectrum is saved in addition
4 Save Profile
to the centroid spectrum.
3.5.2 MS/MS Mode
In the MS/MS analysis mode, the Q1 screens ions and let ions of a particular m/z pass.
The selected ions are called precursor ions. Precursor ions collide with an inert gas in the
Q2 collision cell, producing product ions. The TOF section then measures the time of
flight of the product ions. Measurement of the product ions provides information that
reflects the structure of the precursor ions.


Start(min)
End(min)
Precursor Ion
2 Specify the m/z of the ion to be selected as the precursor ion.
m/z
Specify the m/z of the ion to be measured in the TOF section
TOF Start m/z as the product ion.
3
TOF End m/z * Specify the required m/z range as specifying a wide range increases
data volume.
4 CE Specify the collision energy value.

Specify the range from the center value specified in [CE] to
acquire spectra while gradually changing the CE value. Enter 0
5 CE Spread(+/-) to fix the CE value.
The CE step value is automatically calculated based on the
injection count and other settings.
6 Event Time(s)
event time.
7 Save Profile
3.5.3 MRM Mode
In the MRM analysis mode, the Q1 screens ions and let ions of a particular m/z pass. The
selected ions are called precursor ions. Precursor ions collide with an inert gas in the Q2
collision cell, producing product ions. The TOF section then measures the time of flight
of the product ions of a particular m/z.

Start(min)
End(min)
Precursor Ion
2 Specify the m/z of the ion to be selected as the precursor ion.
m/z
3 Product Ion m/z
as the product ion.
5 CE Spread(+/-)
to fix the CE value. The CE step value is automatically calculated
based on the injection count and other settings.
Specify the measurement time. Specify the time required for a
single event.
6 Event Time(s) To improve the chromatogram shape, specify a shorter event
event time.

3.5.4 MS/MS (DDA) Mode
Use the MS/MS (DDA) analysis mode when the ion to be observed is unknown. Precursor
ions are automatically selected according to the specified standard. They collide with an
inert gas in the Q2 collision cell, producing product ions. The TOF section then measures
the time of flight of the product ions. The event recognized as the parent in this state
is called survey event and the event recognized as the child event is called dependent
event.
Specify the survey event in the MS analysis mode and dependent event in the MS/MS
(DDA) analysis mode.
Up to 100 dependent events can be set for one survey event. Up to 16 survey events
can be set for one method.

3
Start(min)
1 Measurement time range same as the survey event.
End(min)
TOF Start m/z as the product ion.
2
TOF End m/z * Specify the required m/z range as specifying a wide range increases
data volume.

5 CE Spread(+/-) to fix the CE value.
The CE step value is automatically calculated based on the
injection count and other settings.
6 Event Time(s)
event time.
7 Save Profile

n [Execution Condition Settings of Dependent Events] Window

Number of
Displays the number of dependent events. This is synchronized
1 Dependent
with the number of dependent events on the [MS] tab page.
Events
Int. Threshold of Precursor ion is searched when the maximum centroid peak
2 BPC Starting intensity (BPC) within the m/z range for searching the precursor
DDA ion exceeds the threshold value specified in this step.
The operation pauses for the period of time specified in this
Starting Delay item after the BPC intensity exceeds the threshold value. The
3
Time precursor ion is searched for when the BPC intensity exceeds
the threshold value again.
Search m/z of Specify the m/z range of the ion to be selected as the precursor
4
Precursor Ion ion.
Exclusion
Settings of The [Exclusion Settings of Precursor Ions in Detail] window
5
Precursor Ions in opens.
Detail


Specify the minimum repeat count (the count to repeat even
when the survey event result become less prominent) for the
dependent event to perform MS/MS analysis using the same
Iteration Count
6 precursor ion m/z.
of Measurement
After MS/MS analysis is performed by up to the specified repeat
count using the same precursor ion m/z, the precursor ion m/z
changes.
Search for
7 -
Precursor Ions
Enter the m/z to preferentially select as the precursor ion. This
setting has priority over other settings.
8 Prior Ions When [Int. Order] is selected in [Search Order], the value
exceeding the setting specified in [Int. Thereshold of BPC
Starting DDA] is selected as the precursor ion.
Specify the spectrum pattern to be recognized as the isotope 3
of the precursor ion. Specify the mass difference with the
acquired mass and its acceptable range as well as the intensity
difference and its acceptable range.
Spectrum
9 When [Int. Order] is selected in [Search Order], the value
Patterns
exceeding the setting specified in [[Int. Thereshold of BPC
Starting DDA] is selected as the precursor ion.
* Using spectrum patterns, an ion with unknown valence is not
selected as the precursor ion.
10 Int. Order Stronger intensities are selected as the precursor ion in order.
11 Filter -
Select whether to specify the valence of the ion when selecting
12 Charge State
the precursor ion and also specify the valence.
Select Unknown
Select whether to select ions whose valence is unknown as the
13 Charge State
precursor ion.
Ions
Select Only Select whether to target only on mono-isotopic ions when
14
Monoisotopic selecting the precursor ion.
Select
Select whether to select mono-isotopic ions whose valence is
15 Indeterminable
unknown as the precursor ion.
Ions

n [Exclusion Settings of Precursor Ions in Detail] Window

Automatic When this is selected, m/z values that have been once selected
1 Exclude Ions as the precursor ion are listed and they are not selected as the
Once Selected precursor ion again.
Valid Period of
The time specified in this item is not selected as the precursor
2 Automatic
ion.
Exclude Ions
3 Exclude Isotopes Precursor ion isotopes are also excluded.
Exclude Ions of
Ions whose component is the same as the precursor ion are
4 other Charge
excluded even when they are observed with a different valence.
State
When excluding other valences, other valencies are searched
Supposable based on the adduct ion value specified in this item.
5
Adduct Ion Positive: H+ / Na+ / K+ / NH4+ / Others
Negative: -(H+) / Cl- / Br- / Others
Specify the mass when "Others” is selected in [Supposable
6 Mass
Adduct Ion].
Enter the m/z range and measurement time of the ions to be
excluded from the selection of the precursor ion. This is useful
7 Exclude Ions List
when removing the ions that are always observed as
background from the scope of MS/MS analysis target.

n [Setting of Prior Ions List in Detail] Window

When [Int. Order] is selected, selects items as the precursor ions
in order from the one with the strongest intensity.
1 Search Order
When [List Order] is selected, selects items as the precursor ions
in order from the top of the list.
Set the allowable range to be regarded as the same mass as
2 Tolerance m/z
the prior ions acquired.
3 m/z Set the prior ion m/z.
Set the time at which data acquisition for the prior ions is
4 Start Time(min)
started.
Set the time at which data acquisition for the prior ions is
5 End Time(min)
ended.

n [Settings of Spectrum Patterns Lists in Detail] Window

When [Int. Order] is selected, selects items as the precursor
ions in order from the one with the strongest intensity.
1 Search Order
When [List Order] is selected, selects items as the precursor
ions in order from the top of the list.
2 Spectrum Pattern Switches to the spectral list to edit.
Set the mass difference from the spectrum recognized as
3 m/z diff. (u)
an isotope.
4 Tolerance(+/-)(ppm) Set the allowable range of the mass difference.
Set the intensity ratio with the spectrum recognized as an
5 Int. Ratio(%)
isotope.
6 Tolerance(%) Set the allowable range of the intensity ratio.
3.5.5 MS/MS (DIA) Mode
n MS/MS (DIA) Mode Analysis Image

The MS/MS (DIA) Mode applies the MS/MS Mode and is suited to the comprehensive
analysis of complex samples. It passes ions through while displacing them in order
according to the Q1 Transmission m/z Width within the precursor ion range (for example,
when the Q1 Transmission m/z Width is 10, the mode performs the analysis while
displacing the ions according to an m/z of 100-110, 110-120...).
The ions that pass through collide with an inert gas in the Q2 collision cell to generate
product ions and obtain a mass spectrum of the product ions in the TOF section. This
allows you to obtain a mass spectrum of the product ions across the entire precursor ion
range.
n [DIA Parameter Settings] Window
Select the MS/MS (DIA) analysis mode and then just set the precursor ion range and Q1
Transmission m/z Width, Loop Time, and other items to automatically create the DIA
analysis method.
3

Precursor Ion
1 Specify the m/z of the ion selected as the precursor ion.
m/z
Q1 Transmission Specify the ion width within the precursor ion range which is
2
m/z Width passed through during one event.
Specify the Loop Time for one loop (see the "MS/MS (DIA)
3 Loop Time
Mode Analysis Image").
Automatically calculated from the Precursor Ion m/z and the Q1
4 Event Number
Transmission m/z Width.
Automatically calculated from the Loop Time and Event
5 Event Time
Number.


Specify the central value of the collision energy. You can select
a fixed value or a calculated value. In the case of a calculated
value, it automatically sets a CE value calculated from the Q1
6 CE
Transmission m/z Width (central value of the transmission
width), inclination, and segment. A CE of -0.5082+0.04 x m/z is
recommended when analyzing peptides.
7 CE Spread (±) Specify the width from the central value of the collision energy.
8 Start-End Time Specify the data retrieval start time and end time.
Specify the m/z (TOF start m/z - TOF end m/z) of the product
9 Product Ion m/z
ions.
Specify the necessary values in the [DIA Parameter Settings] window to automatically
generate events as shown below.
When using the [DIA Parameter Settings] window, [Center] (setting to pass
through ions with an m/z width centered around the precursor ion m/z) is
automatically turned on. You can check the [Center] setting from the [Event
Detail Settings] button in the Instrument Parameters View.

3.5.6 SIM Mode
In the SIM analysis mode, the Q1 lets ions of all m/z values pass and the TOF section
measures the time of flight of the ions. Compared with scan analysis mode, SIM enables
highly sensitive analysis without wasting time on detecting unnecessary ions.

Start(min)
End(min)
Precursor Ion
2 Specify the m/z of the ion to be measured in the TOF section.
m/z
3 Event Time(s)
event time. 3

4 Checking Results of Single Analysis
4.1 Opening Results of Single Analysis in the [MS Data Analysis] Window
Display the results of single analysis in the [MS Data Analysis] window.
Do not open any other data files than the ones acquired by LCMS Q-TOF during
acquisition.
1 In the [LabSolutions Main] window, click the [Postrun] icon.
2 Click (Postrun).
The single analysis data file is loaded in the [MS Data Analysis] window.

4.2 Displaying Chromatograms
4.2 Displaying Chromatograms

Chromatograms may be plotted in several different ways. This section describes two types
of procedures.
Chromatogram View
Resolving-to-spec
Click [Peak] or double-click a point on the chromatogram to 4
1 move the line. The MS spectrum at the retention time of the
trum line
position is generated and displayed in [Spectrum View].
2 Highlight Highlights the line of the chromatogram displayed.
The resolving-to-spectrum line on the active chromatogram
moves to the retention time (peak top time) of the detected
Peak selection peak and the spectrum of the peak is displayed in [Spectrum
Scan selection View].
3
Segment The spectrum acquired in the previous or latter scan is displayed
selection in [Spectrum View].
The chromatogram of the previous or latter segment is
displayed.
The range that the spectrum was averaged in [Spectrum View]
Spectrum is indicated by black. The subtraction range is indicated by gray.
4
processing bar When the averaged range and subtraction range overlap, the
area is indicated by dark gray.
5 Active mark Indicates the active chromatogram.

n Place the Cursor on a Peak of the Spectrum and Double-Click the Mouse
1 Place the cursor on a peak of the spectrum and double-click the mouse.
The mass chromatogram at the cursor position is displayed.
n Specify in the Chromatogram Table
1 Right-click the mouse on [Chromatogram View] and click [MS Data View
Parameters].
The [MS Data View Parameters] window appears.
2 Click the [Chromatogram Table] tab.
3 Select the [Disp.] checkbox for the chromatogram to display in the MC table and
specify the event number and m/z.
4 Click [OK].

4.3 Displaying Mass Spectra

Mass spectra may be displayed in several different ways. This section describes three types
of procedures.
Spectrum View

Spectrum tab 4
1 Configure settings for the spectrum displayed in spectrum view.
area
Displays the spectrum of the specified peak or retention time.
Spectrum graph When analysis is performed on multiple events, the spectra of
2
area all events that belong to the same loop are displayed in stacked
form.
Switches the way to display the spectra of multiple events
3 Stack / Overlay
between stack and overlay.
4 Scroll bar Scrolls the spectrum view.
5 Active mark Indicates the active spectrum.

n Selecting a Spectrum to Display from the Spectrum Tree (MS/MS (DDA) Analysis Mode)
1 In [Spectrum View], click the [Tree] tab.

The selected precursor ions are displayed on the [Tree] tab page in [Spectrum View]
by order of mass.
2 In the list on the tree, click the precursor ion to check the spectrum.
The spectra of the survey and dependent events are displayed in [Spectrum View].
Spectrum tab area

A tree of survey and dependent events is displayed.
Click a dependent event on the tree to display the spectra of
1 Spectrum tree
the survey and dependent events in stacked form in [Spectrum
View].
2 Filter Switches ON/OFF the filter for the spectrum tree.
Displays the [Spectrum Tree] tab page.
3 Settings Settings for the method to sort and filter settings of the
spectrum tree can be configured.

[Spectrum Tree] tab page
No. Item Description 4

1 ［Sort］ tab Specify the conditions to sort the items displayed on the tree.
［Precursor
2 Specify the precursor ion extraction standard.
Extract］ tab
Edit precursor mass. Precursor ions to be displayed on the tree
3 ［MS/MS］ tab
can be precisely filtered.
When MS/MS analysis has been performed on a single precursor ion multiple
times, select either to average the results or display the individual results.
Click the [Precursor Extract] tab and change the [Maximum number of
intermediate loops] setting.
When the Maximum number of intermediate loops is increased, the same m/z
value is recognized as the same one and the values are averaged even when
the times for which the value is used as the precursor are separate. As a
result,the number of items listed in the tree decreases.
When the number of spectra that exist is equal to the value specified in
[Manimum number of scans in a group], they are regarded as identical and
averaged.
The change can be confirmed on the spectrum processing bar under the
chromatogram.

Precursor ions to be displayed on the tree can be precisely filtered on the

[MS/MS] tab page. [Precursor m/z] is a convenient function when the target mass
and range are known.
n Displaying Spectrum from Chromatogram (1 Scan Only)
1 In [Chromatogram View], double-click the mouse on the time position to generate

a spectrum.
The resolving-to-spectrum line moves and the spectrum of the time position is
displayed in [Spectrum View].
• Click the [Peak] button in the upper area of [Chromatogram View]

to move the resolving-to-spectrum line to the retention time of each
detected peak of the active chromatogram and display the spectrum
at the position of the resolving-to-spectrum line in [Spectrum View].
• Click the [Scan] button in the upper area of [Chromatogram View]
to move the resolving-to-spectrum line by scan.

4.4 Performing Background Subtraction
n Displaying Spectrum from Chromatogram (Averaged Spectrum)
1 Click (Average Spectrum) on the toolbar.
2 In [Chromatogram View], point the time to start averaging and drag the mouse
to the time to end averaging.
[Spectrum View] displays the averaged spectrum.
The averaged range is indicated by black in [Spectrum ProcessBar] under the
chromatogram.
4
4.4 Performing Background Subtraction
When spectra are displayed, background spectra are subtracted according to the spectrum
processing parameters.
1 Set the spectrum processing parameters.
1 In [Method View], click the (Edit Mode) icon.
2 Click the [Spectrum] tab and specify the parameters.
3 In [Method View], click the (View Mode) icon.

2 Manually specify the subtraction range.
1 Click (Subtract Spectrum) on the toolbar.
2 In [Chromatogram View], drag the time range to subtract using the mouse.
[Spectrum View] displays the spectrum in which the spectrum in the dragged time
range has been subtracted as background.
The time range averaged for subtraction is indicated by gray in the spectrum
processing bar below [Chromatogram View].

4.5 Printing Analysis Results
4.5 Printing Analysis Results

The information displayed in the [MS Data Analysis] window can be printed.
1 On the [File] menu, click [Print Graph Image] -[Print].
n Example of the Output Report

4.6 Export Data in mzXML or mzML Format
1 On the [File] menu, click [Export Data] - [Export Data as mzXML] (or [Export Data
as mzML]).
2 Specify the destination folder, unit for outputting, and spectrum type.
3 Click [OK].
The data file is exported to the specified folder.

5 Batch Analysis
5.1 Creating a Batch Table
Create a batch table using the created method file in order to perform batch analysis
(sequential analysis).
1 On the [Main] assistant bar, click the (Realtime Batch) icon.
The [Realtime Batch] window appears.
2 On the [Edit] menu, select [Table Easy Settings].
3 Configure settings in the [Table Easy Settings] window.

As an example, this section describes the process to create a batch table to perform
analysis on five unknown samples.
1 Select [New].
2 Select the [Unknown] checkbox and specify the vial number, tray number,
repetitions, and injection volume.
4 Click [OK].

5 Batch Analysis
4 Edit the batch table.
1 To output a report after analysis, select the [Report Output] checkbox and specify
the report format file name.
To specify the items to display on the batch table, right-click the

mouse on the batch table, select [Table Style] on the menu displayed,
and specify the items in the [Table Style] window displayed.
To add rows, right-click the mouse on the batch table and then click
[Add Row] on the menu displayed.
To apply settings on the entire column in sequential numbers or copy settings,

right-click the mouse on the batch table and select [Fill Series] or [Fill Down]
on the menu displayed. Using this procedure, settings can be applied on the
entire column in sequential numbers or the settings of a cell can be copied
easily.
・ To apply settings in sequential numbers,
enter “Std01.lcd” in the top row in [Data File], right-click the mouse, and click
[Fill Series]. [Std01.lcd] to [Std04.lcd] will be set on each cell.
・ To copy settings,
enter “Method1.lcm” in the top row in [Method File], right-click the mouse, and
click [Fill Down]. [Method1.lcm] will be copied to all cells in [Method File].

5.2 Performing Batch Analysis
5 Click (Save) on the toolbar and save the batch file under a new name.
5.2 Performing Batch Analysis

Perform batch processing.
2 When performing auto tuning before analysis, place a standard sample.

For details, see "2.2.1 Preparing Standard Sample".

5 Batch Analysis
3 On the [Realtime Batch] assistant bar, click (Start Realtime Batch).
During batch analysis, the [Realtime Batch] window and [Data Acquisition] window are
displayed at the same time on the split screen.
• To stop batch processing, click (Stop).
• By pausing, subsequent batch tables can be changed while continuing the

analysis currently running.

This section describes the settings for exporting data to a mzXML or mzML format file
in batch postrun analysis using a batch file used in batch analysis.
1 Start the [Postrun Analysis] program.
2 On the [Main] assistant bar, click the (Postrun Batch) icon.
The [Postrun Batch] window appears.

3 Open the batch file used in batch analysis.
1 On the [File] menu, click [Open Batch File].
2 Enter the batch file name and click [Open].
5
4 Click the [Analysis Type] cell.
The [Analysis Type] window appears.
1 Clear all items when there is no need to perform peak integration or quantitative
calculation again.
2 Click [OK].

5 Batch Analysis
5 On the [Postrun Batch] assistant bar, click (Settings).
The [Settings] window appears.
6 Click the [File Conversion] tab.
7 Configure settings to export data to a mzXML or mzML file.
1 Select the checkbox for the file format to export data.
2 Specify the unit for outputting and spectrum type.
8 Click [OK].
The batch table is displayed again.
9 On the [Postrun Batch] assistant bar, click the (Start Postrun Batch) icon.
The data file is exported in the specified file format.

6 Performing Single Analysis in MRM Analysis Mode
This section describes the procedure to configure analysis conditions for a target and
perform single analysis. It also describes the procedure to introduce a mass correction
sample during measurement to correct the mass axis.
6.1 Opening a Method File
2 Click (New) on the toolbar and create a new method file.
cannot be started.

and other settings.
6.2.2 Configuring Analysis Conditions for a Target - MRM Analysis Mode
In this process, select the precursor ion of a particular m/z and perform MS/MS analysis
to measure the product ion of a particular m/z.

2 Add the event to measure the target spectrum.
1 Select the polarity and click to select the MRM analysis mode.
An MRM event is added to the event table.
2 Specify the analysis time, m/z of the precursor ion, m/z of the product ion,
compound name, CE, and event time.
3 To measure the reference ion, add a channel.
1 Click [MRM Ch2].

An event whose [Type] is set to [MRM(Ch2)] is added.
2 Specify the parameters.
Up to 6 channels can be set for one event.
4 To measure a different compound, add an event.
Up to 1000 rows can be set.

6.2.3 Configuring Analysis Conditions for Mass Correction - MS Analysis Mode
1 Add an event to measure the spectrum for mass correction.
1 Select the polarity and click to select the MS analysis mode.

An MS event is added to the event table.
2 Specify the analysis time, m/z range, and event time.

2 Configure a MS program to introduce a sample for mass correction.

Specify the time to introduce the sample for mass correction while avoiding allowing its
peak to overlap with the target’s peak.
1 Click [MS Program].

The [MS Program] window appears.
2 Select the [MS Program] checkbox.
3 Specify the time to introduce the sample in [Time(min)], set the activation of the
CDS to ON in [Command], and specify the sample vial position to which to switch
the valve.
4 Switch the valve to the home position and configure settings to turn OFF the
activation of the CDS.
5 Click [OK].
• Depending on the instrument configuration, it takes approximately

7 seconds to 1 minute from when the CDS valve is turned ON until
the sample for mass correction reaches the interface and ionization
starts.
• Specify the initial position on the [Interface] tab page.

3 Setting Mass Correction Parameters
1 On the [Method] menu, click [Mass Correction Parameter].
The [Mass Correction Parameter] window opens.
2 For the polarity to analyze, select the [External Standard(Standard Spectra in the
same file)] correction mode.
3 In [Edit Correction Points], select the polarity to edit the correction point.
4 Click [Add Correction Point].
The [Add Correction Point] window appears.

5 Select the [Select] checkbox for the compound to set correction points.
Specify the correction points between which to contain the measured

m/z of the target ion.
6 Click [OK].
The compounds are added to the correction point list in the [Mass Correction
Parameter] window.

In this window, the theoretical m/z, m/z tolerance in ppm (+/-),

intensity threshold value, and compound name can be edited.
For each correction point with the [Select] checkbox selected, the
correction peaks that satisfy the conditions are searched for in the
actual spectrum.
If one or more correction peaks are found, the m/z is corrected so as
to match the theoretical m/z of the correction points and the actual
m/z of the correction peaks.
If a peak that corresponds to a correction point is not found, the
correction fails.
7 Click [Peaks for Mass Correction Setting].
The [Peaks for Mass Correction Setting] window opens.
8 Select [Ret. Time, and # of Event].

The upper level displays the MS program settings.
9 Specify the measurement event number for the spectrum for correction in [Event
#].
10 Specify the sufficient time for the spectrum for mass correction to appear in [Ret.
Time].
11 Click [OK].
The [Mass Correction Parameter] window appears again.
12 Click [OK].

1 Click the [Interface] tab.
2 Set the parameters.

Specify the gas flowrate and temperature for the main
1 Main-Interface
interface.
6
Specify the voltage and gas flowrate for the sub interface.
2 Sub-Interface
* These items can be specified when a sub interface is installed.
A 6-port 2-position valve for switching the channels from the

3 Diverter Valve
LC unit. Specify the position at the start and end of analysis.
Specify the gas flowrate and temperature for the ion
4 Ion Guide
introduction section.
5 CDS Specify the initial setting for the position of the CDS valve.

6.2.5 Saving a Method File

2 Click (Instrument On/Off) on the toolbar.

The pump starts to deliver the solvent and the temperature control operation for the
oven starts.
3 Click (MS Instrument On/Off) on the toolbar.

It turns ON/OFF the heater, gas, and high voltage power supply collectively.
4 On the [Acquisition] assistant bar, click (Start Single Run).
The [Single Run] window appears.
5 Configure the single analysis conditions.
6
2 Specify the vial number, tray number, and injection volume.
3 Click [OK].
Single analysis starts.

To change the chromatogram displayed in the [Data Acquisition] window during

measurement, right-click the mouse on the chromatogram and select [Display
Settings].
The m/z of the chromatogram to be displayed and magnification can be
specified on the [MS] tab page.
Select the [Auto scale] checkbox.
6 Check the results of single analysis.

For details, see "4 Checking Results of Single Analysis".

7 Performing Single Analysis in SIM Analysis Mode
This section describes the procedure to configure analysis conditions for a target and
perform single analysis. It also describes the procedure to introduce a mass correction
sample during measurement to correct the mass axis.
7.1 Opening a Method File
7
cannot be started.

and other settings.
7.2.2 Configuring Analysis Conditions for a Target - SIM Analysis Mode
In this process, select the ion of a particular m/z and perform analysis.

2 Add the event to measure the target spectrum.
1 Select the polarity and click to select the SIM analysis mode.
An SIM event is added to the event table.
2 Specify the analysis time, m/z of the ion, compound name, and event time.
3 To measure the reference ion, add a channel.
1 Click [SIM Ch2].

An event whose [Type] is set to [SIM(Ch2)] is added.
2 Specify the parameters.
7
Up to 6 channels can be set for one event.
4 To measure a different compound, add an event.
Up to 1000 rows can be set.
7.2.3 Configuring Analysis Conditions for Mass Correction - MS Analysis Mode
For details, see "6.2.3 Configuring Analysis Conditions for Mass Correction - MS Analysis
Mode".

For details, see "6.2.4 Specifying Temperature, Gas Flowrate, and Other Items for Interface
and Ion Introduction Sections ".

For details, see "6.3 Performing Single Analysis".

8 Mass Correction
Mass correction is a function to correct the systematic error of m/z in measured data,
using the peak of the standard sample with a known m/z.
Perform mass correction before performing precision mass spectrometry.
There are three ways to perform mass correction: internal standard that introduces a
sample for mass correction and uses an ion constantly observed as the peak for correction,
external standard that uses an ion in the same data file, and external standard that uses
an ion in a different data file.
Results of mass calibration by tuning stored in the data file are not overwritten. The
mass axis is corrected each time the spectrum is loaded.
For details of mass calibration, see "2.2 Auto Tuning (TOF Calibration Only)".
8.1 Internal Standard

This section describes parameter settings to introduce a sample for mass correction during
analysis of a target sample, use an ion constantly observed as the peak for correction,
and correct the mass axis.
8.1.1 Preparing Sample for Mass Correction
1 Prepare a sample for mass correction.
1 Open the front door, pour the sample for mass correction in a sample vial, and
connect it to the CDS valve.
Refer to 8.4 Sample for Mass Correction in the LCMS-9030 Instruction Manual.
2 On the [Main] assistant bar, click the (System Configuration) icon.
3 In the [System Configuration] window, double-click [LCMS].

8 Mass Correction
4 Select the name of the sample for mass correction in [Sample Bottle 1] to [Sample
Bottle4].
To add a new sample name, click [MS Sample Table] and register it to
[Supplementary Sample Table] in the [MS Sample Table] window.
5 Click [OK].
The [System Configuration] window appears again.
6 Click [OK] to close the [System Configuration] window.

8.1.2 Setting MS Instrument Parameters
1 On the [Main] assistant bar, click the (Data Acquisition) icon.
1 On the [MS] tab page in [Instrument Parameters View], click [MS Program].
the valve.
5 Click [OK].
• It takes approximately 7 seconds to ionize the sample or stop

ionization of the sample after the specified time.

8 Mass Correction
8.1.3 Setting Mass Correction Parameters
2 For the polarity to analyze, select the [Internal Standard] correction mode.

4 Set the correction point list.

A peak for correction is detected when ions selected in the correction point list are in
the vicinity of the time of flight obtained by automatic calibration.


8 Mass Correction
3 Click [OK].
Parameter] window.

actual spectrum.
correction fails.


8 Mass Correction
8.2 External Standard (Using a Spectrum in the Same File as the Standard)
This section describes parameter settings to correct the mass axis using the spectrum for
mass correction in the same data file.
Specify events for mass correction and target separately in MS instrument parameters to
acquire data.
8.2.1 Preparing Sample for Mass Correction
For details, see "8.1.1 Preparing Sample for Mass Correction".
8.2.2 Setting MS Instrument Parameters
3 Add the event to measure the target.
1 On the [MS] tab page in [Instrument Parameters View], select the polarity and click
the analysis mode button.
An event is added to the event table.
2 Specify the analysis time, measured m/z, compound name, event time, and other
items.

To measure the target sample and sample for correction using different events, add an
event to measure the sample for correction.
The target sample and sample for correction can be measured in a single event
in the MS analysis mode. However, the measurement should be separated into
different events if their peaks overlap.
1 Select the polarity and click the analysis mode button.

items.


Specify the time to introduce the sample for mass correction while avoiding allowing its
peak to overlap with the target’s peak.

the valve.
5 Click [OK].
• It takes approximately 7 seconds to ionize the sample or stop


8 Mass Correction
The [Mass Correction Parameters] window opens.
2 For the polarity to analyze, select the [External Standard(Standardize Spectra in

the same file)] correction mode.




8 Mass Correction
3 Click [OK].
Parameter] window.

actual spectrum.
correction fails.
5 Click [Peaks for Mass Correction Settings].
The [Peaks for Mass Correction Settings] window opens.

6 Specify the peak for mass correction.
1 Select [Ret. Time, and # of Event].
2 Specify the measurement event number for the spectrum for correction in [Event
#].
3 Specify the time in which the peak appears in [Ret. Time].
4 Click [OK].
7 Click [OK].

8 Mass Correction
8.3 External Standard (Using a Spectrum in a Different File as the Standard)

This section describes parameter settings to analyze the sample for mass correction in
advance and correct the mass axis using the spectrum stored in the data file.
8.3.1 Performing Single Analysis on Sample for Mass Correction
1 On the [MS] tab page in [Instrument Parameters View], select the polarity and click
the analysis mode button.
items.

Specify the time to introduce the sample for mass correction while avoiding
allowing its peak to overlap with the target’s peak.

the valve.
5 Click [OK].
It takes approximately 7 seconds to ionize the sample or stop

Specify the initial position on the [Interrace] tab page. 8
5 Perform single analysis.

For details of single analysis, see "3.4 Performing Single Analysis".

8 Mass Correction
8.3.2 Registering Spectrum for Mass Correction to Spectrum Processing Table
1 On the [Acquisition] assistant bar, click [Data Analysis].
The mass axis of [Spectrum View] is displayed using the time of flight obtained by
automatic calibration.
2 Click (Average Spectrum) on the toolbar to average the spectra in the vicinity
of the applicable peak top on the chromatogram of the measurement event for
mass correction in [Chromatogram View].
For averaging spectra, see "4.3 Displaying Mass Spectra".
3 In [Spectrum View], select the averaged spectrum of an event for mass correction
and then click (Register Spectrum Process Table) on the toolbar.
The spectrum is registered to the spectrum processing table.
4 Click (Save) on the toolbar and save the data file.

4 For the polarity to analyze, select the [External Standard(Standardize Spectra in

another file)] correction mode.

8 Mass Correction



3 Click [OK].
Parameter] window.

actual spectrum.
correction fails.
7 Click [Peaks for Mass Correction Setting].
The [Peaks for Mass Correction Setting] window opens.

8 Mass Correction
8 Specify the peak for mass correction.
1 Specify the name of the data file for the sample for mass correction in [Standard
Sample Data File].
2 Select [# of Spectrum Processing Table].

The spectrum processing table saved in the data file is displayed.
3 Specify the spectrum processing table number for the spectrum for correction in [#].
4 Click [OK].
9 Click [OK].


8 Mass Correction
8.4 Checking Mass Correction Results

To check the mass correction results, see spectrum information in [Spectrum View] in the
[MS Data Analysis] window.
In the [Internal Standard] correction mode, the mass calibration table is corrected to
calculate the mass calibration curve and the mass axis of the spectrum is corrected each
time a spectrum is loaded.
Type Format to Display Spectrum Information

When mass correction (all)
has been completed “Event#: Ret. Time: Scan#: Correction: Success”
successfully
When part of the mass
correction has been
completed successfully “Event#: Ret. Time: Scan#: Correction: Partial Success”
during averaging or
subtraction of spectra.
When mass correction (all)
“Event#: Ret. Time: Scan#: Correction: Failure”
has failed
When data not
supporting mass
correction is used
“Event#: Ret. Time: Scan#: “
In a mode in which mass
correction is not
performed
When spectrum arithmetic processing (averaging, subtraction) has been

performed, the information about it is indicated with the retention time and
scan no.

8.4 Checking Mass Correction Results
Right-click the mouse on the spectrum and display [Mass Table] to check detailed mass
correction results.

When no subtraction has
been performed on the
unprocessed spectrum
“Internal Standard (m/z of Correction Point: , , … Scan No.:)”
When the internal
* The scan no. of the spectrum for correction is indicated.
standard correction has
been completed
successfully
unprocessed spectrum “Internal Standard (m/z of Correction Point: None)”
When internal standard
correction has failed
unprocessed spectrum
When the external “External Standard (m/z of Correction Point: , , …)”
standard correction has
been completed
successfully
unprocessed spectrum “External Standard (m/z of Correction Point: None)” 8
When external standard
When averaging or
subtraction has been
performed on the
spectrum and “Internal Standard (Success)”
all of internal standard
correction has been
completed successfully

8 Mass Correction

When averaging or
performed on the
spectrum and “Internal Standard (Partial Success)”
part of internal standard
correction has been
When averaging or
performed on the
“Internal Standard (Fail)”
spectrum and
internal standard
When averaging or
performed on the
spectrum and “External Standard (Success)”
external standard
correction has been
When averaging or
performed on the
“External Standard (Fail)”
spectrum and
external standard
In a mode in which mass
correction is not “None”
performed

9 Exiting
9
1 Close the [Realtime Analysis] program.
This window opens if there are unsaved files.
2 Stop the operation of the pump and heater and shut off the gas in the
[Shutdown] window.
1 Select the items to stop and click [OK].

9 Exiting
3 Exit LabSolutions.
4 Switch OFF the power of the LC unit.
Do not switch OFF the power of the LCMS Q-TOF in regular operation.
5 Shut off the nitrogen gas supply and insert the DL plug.

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LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF) i

Indications Used in Instruction Manuals

The following symbols are used in this manual.

Indicates information provided to improve product performance.

Indicates the location of related reference information.

ii LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF)

Shimadzu provides the following warranty for this product.

(1) Improper product handling

(7) Reasons unrelated to the product itself

(10) Product movement or transportation after installation

(11) Consumables and equivalent items

LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF) iii

* If there is a document such as a warranty provided with the product, or there is a

iv LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF)

2.2 Auto Tuning (TOF Calibration Only) ..................... 8

Performing Single Analysis in 12

3.2 Setting Parameters to Perform Single Analysis ..... 12

3.3 Saving a Method File ........................................ 18

3.5.2 MS/MS Mode .................................................. 21

3.5.3 MRM Mode ................................................... 22

Checking Results of 4.1 Opening Results of Single Analysis in the [MS

LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF) v

4.4 Performing Background Subtraction .................... 39

5 Batch Analysis 5.1 Creating a Batch Table ...................................... 43

Performing Single Analysis 49

6.2 Setting Parameters to Perform Single Analysis ..... 49

6.2.5 Saving a Method File ......................................... 58

Performing Single Analysis 61

7.2 Setting Parameters to Perform Single Analysis ..... 61

7.2.5 Saving a Method File ......................................... 64

vi LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF)

8 Mass Correction 8.1 Internal Standard .............................................. 65

8.1.4 Saving a Method File ......................................... 71

8.2.4 Saving a Method File ......................................... 77

8.3.3 Setting Mass Correction Parameters .......................... 80

8.3.4 Saving a Method File ......................................... 85

LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF) vii

2 Confirm that the gases are supplied normally.

3 Switch ON the PC.

4 Confirm that the [LabSolutions Service] icon is displayed in green.

Color of Icon LabSolutions Status Action

5 Click (LabSolutions) on the desktop.

LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF) 1

8 On the [Main] assistant bar, click the (System Control) icon.

The [System Control] window appears.

2 LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF)

LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF) 3

2.1 Auto Tuning (Full Mode)

Auto tuning takes approximately 60 minutes to complete because it searches for

1 Prepare a standard sample.

[Main] assistant bar.

3 Click (New) on the toolbar.

4 LabSolutions™ LCMS Quick Reference (for LCMS Q-TOF)

5 Configure the tuning conditions.

The [Auto Tuning Condition] window appears.

Confirm that the DL plug has been removed.