Introduction to

Varian MS Workstation v.6.5

Qualitative Data Review
August 2005
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Main Menu - Qualitative Analysis

MS Workstation Toolbar

MS Data Review Menu and Toolbar

New MSWS Descriptors Explained

Display of Plots

Preferences

Creating a Spectrum

Spectral Search

Spectrum List

Click on any topic to

hyperlink to those slides
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The Varian MS Workstation Toolbar

Quick Start
Active Compound Set

File Converters
Security
Custom Reports
Standard Reports
Data Review
The Data Review section is
Automation
the one new section in v.6.5
Method Editor compared to v.6.3 & 6.42
System Control
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The Varian MS Workstation Toolbar

Right-click on an open
area (not on an icon) in
the Toolbar to open the
toolbar menu

Use the Show/Hide

Applications item to tailor
the Toolbar to your
individual requirements
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MS Data Review
Drop-down Menu

Menus have been consolidated and simplified

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MS Data Review
Drop-down Menu

Menus have been consolidated and simplified

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MS Data Review
New Help Menu Topics
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MS Data Review
New Help Menu Topics (cont.)
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MS Data Review Toolbar Icons

Select Chromatogram Plot Chromatograms

Data to Plot and Spectra

Print Chromatograms
Search Options
and Spectra Reports

Export Chromatograms
Process Data
and Spectra

Review Data and

Calibration
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MS Data Review Toolbar Icons

Export Spectrum to NIST Help

Export Chromatogram
to AMDIS

Show/Hide Selection
Panes

Rotate Plots
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3 Views for Data Review

Data may now be reviewed,

quantitated, and/or reported using
any one of three icons

Plot Chromatograms
and Spectra

Process Data

Review Data and

Calibration
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Start MS Data Review

As with earlier versions of

MSWS 6.x, open a file
either the menu or icon

New options for

opening files are
shown on several
following slides
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New Terms in MSWS

The Varian MS Workstation uses the following
terms to describe different types of data used.
A SCAN DESCRIPTOR is used to describe what data was collected from the mass
spectrometer. Some examples of scan descriptors are:
a. 40:450(2): A full scan analysis over the range of 40 m/z to 450 m/z in time segment 2.
b. 272>: SIS of 272 ion using Q1 of a triple quadrapole MS
c. 272>50:250(4): MS/MS of with a precursor ion of 272 and scanning the product ions formed
within the range of 50 m/z to 250 m/z
A scan descriptor is determined by the data acquisition method.

A COMPOUND DESCRIPTOR is used to describe the properties of a compound analysis,

such as:
• quantitation ion(s),

• qualifier ions , or

• the conditions of which unknown compounds are analyzed.

Compound descriptors are determined by the quantitation method.

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New Terms in MSWS (cont.)

The Varian MS Workstation uses the following
terms to describe different types of data used.
A USER DESCRIPTOR is user defined information that is stored with the data file. There are
two types of user descriptor:
• User Plot - a saved combination of ions and scan descriptors that can indicate the presence
of selected classes of compounds, for example phthalates, from distinctive ions;

• User Trace - information from the analysis equipment, such as flow rate, temperature, or
pressure, which is saved with the data file during acquisition.

A PLOT DESCRIPTOR is a Scan Descriptor, Compound Descriptor, or User Descriptor

used to create a chromatogram (or other trace) within MS Data Review. There are two
general classes:
• Data File Descriptor – any descriptor that was specified in the acquisition method (e.g.
Scan Descriptor and User Trace)
• Method Descriptor – a descriptor that was applied to the data after acquisition occurred,
either through quantitation or by the user in MS Data Review (e.g. Compound
Descriptors and User Plots)

Examples of these descriptors can seen on the next slide

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Chromatogram & Plot View

Click here for the Chromatogram & Plot view

Data files, recalc list, and/or scan

descriptors may be selected to
view chromatograms and spectra

Note examples of different descriptors in Selection Pane

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Process Data View

Click here for the Process Data view

Methods and data files or recalc lists

may be selected to process data
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View Results View

Click here for the Results view

Data files or compounds may

be selected to view results
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Plot Displays

Chromatogram
Pane
Plot descriptor
Pane

Directory Pane

Spectrum
Pane
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Selecting Files from the directory pane

Individual files can be added clicking on the files in the

directory pane. The fie name will be shown in bold
letters

Additional files can be added by holding the “Ctrl” key
down while clocking on the files in the directory pane,
again showing the added files in bold font. Clicking again
on a file while the “Ctrl” key is pressed will remove that
file from the list, it will turn non-bold.

All files in a Recalc list can be added by right clicking on
the directory file and selecting the “Add files in recalc
list”. To view the added files in the directory pane, the
Recalc list file must be shown in extended form.
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Selecting individual files

Individual files can be added clicking on

the files in the directory pane. The file
name will be shown in bold letters.

The Recent button also can be used to

add either data file or Recalc List file to
the plot display
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Options of the data file

Right Click on a data

file, and the menu
above will show up
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Options of the data file

Right Click on a data file, and the menu

below will show up allowing quick
access to create/edit Recalc lists.
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Creating reference file

A data file can be

designated as reference to
offer easy comparison to
Right Click on a
following analysis files. The
data file, and the
Reference file will be shown
menu above will
on top until removed
show up
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Creating reference file

Reference chromatogram also

can be created by right clicking
on a plot and selecting that file
as a reference file
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Selecting multiple files

Additional files can be

added by holding the
“Ctrl” key down while
clicking on the files in the
directory pane. The added
files will be shown in bold
font. The chromatograms
will be shown (governed
by the plot preference
settings).

Clicking again on a
selected file while the
“Ctrl” key is pressed will
remove that file from the
list, it will turn non-bold.
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Selecting a Recalc List

All files in a Recalc List can be added by

right clicking on the Recalc List file name in the
directory pane. It will open a menu allowing the
selection of “Add files in Recalc List” or “Replace
with Files in Recalc List”. It also will give
access to that Recalc list file.
The files will be shown in the plot pane governed
by the set preferences.
To view the added files in the directory pane, the
Recalc list file must be shown in extended form.
Note: The file paths in the Recalc list and the
current location of the files must match
otherwise the peaks will be marked as
“MISSING”.
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Adding Ion Traces

Additional ion chromatogram

displays can be generated from
the active file (solid color marker)
just by entering the desired mass
value and pressing enter as
shown here for ions 85 and 91
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Preferences for Plot displays; Descriptor,

Chromatogram and Spectrum Panes
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Descriptor Pane Preferences

Data file only descriptors reflect

acquisition (raw data) scan
information
Method only descriptors reflect
post acquisition information
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Descriptor Pane Preferences

User Plot and the User Trace. The

User Plot is a saved combination
of ions and scan descriptors that
can indicate the presence of
selected classes of compounds,
for example phthalates, from
distinctive ions. A User Trace is
information from the analysis
equipment, such as flow rate,
,
temperature, or pressure, which is
saved with the data file during
acquisition.

If the Qualifiers option is

selected, both the
Quan ions and Qualifier
ions will be shown in the
descriptor plot
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Descriptor Pane Preferences

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Selecting Plot Descriptors

Right clicking on a plot descriptor will

open up the menu above. This
overrides the preferences set in the
Plot View selection, although not all
options can be specified in the right
click menu. For example the qualifier
display can not be specified.
Note: Use “Replace” when it is
appropriate instead of “Add” to avoid
very long list
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Creating User Traces

A user defined trace can be created by

selecting one or more traces. By right
clicking on the peak a user trace can
be created from it and saved under the
desired name
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User trace is saved only to the

datafile
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Chromatogram Plot Options

Maximum 20 plots can be shown at a time,

but even with large monitors lower
numbers are desirable for better viewing.
If more traces are present than what can
be shown in one instance, the selected
number of plots can be replaced in one
action.
We selected 6 traces to be shown and 6 to
be replaced.
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Spectral Preference
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Navigating the display

One compound, multiple files

The plotting of the Quan

ion (160) for one analyte
is specified.
The plot is for ion 160,
but the information
shows what qualifiers
would be also available
for this compound

In this case, 11 files

were selected with
6 plots … 15 to…20
showing at a time.
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One compound, multiple files

The first 6 files,

(…15.xms to …20.xms)
are displayed with
information for the
selected compound

By Selecting
FILE
And pressing
the > key will
display the
next 6 files.
See next slide
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One compound, multiple files

By clicking the 1 (first

entry, in our case file
#15) or typing in any
Now files 20 to 25 number associated
are shown for the with the selected
selected compound files/plot descriptors)
will make that plot the
starting plot in the
display.
By clicking on 11 (the
last entry in our case)
will make that entry the
last display in the plot.
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One file, multiple Compounds

Information of for a single

data file with all entires is
included. Navigation as in
the previous slide, but at
this point the Plot
Descriptors will be changing
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Multiple files and Multiple compounds,

File is Primary

Display the same file for all plot

descriptors (in our case
compounds) before switching to
the next file

File is fixed, Plot descriptors are

“rolling” until all descriptors were
shown and the system switches to
the next file.
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Multiple files and Multiple compounds,

Plot descriptor is Primary

Display the same plot descriptor

(compounds in our case) for all files
before switching to the next
compound.
Plot descriptor (PD) is fixed, files are
“rolling” until all files were shown for
the given compound. Then the system
switches to the next compound.
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Preferences

All global preferences in MS

Workstation, version 6.5 are now
consolidated in one drop-down
menu location
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Preferences – Plots View Chromat.

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Preferences – Plots View Spectra

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Preferences – Plots View

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Preferences – Results View

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Preferences - Reports
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Preferences - General
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Preferences - Applications Start Up

View Displayed at Start Up

File Displayed at Start Up

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Preferences - Start Up View (cont.)

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Hiding Selection Panes

Click this icon hide Selection Pane

Selection Pane
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Showing Selection Panes

Click this icon show Selection Pane

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Hiding Toolbars

Click these icons to hide Toolbars

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Unhiding Toolbars

Click here to unhide Toolbars

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Maximizing a Window

Click this icon

maximize the window
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Returning to the Original Layout

Click this icon to unmaximize

the window and return to the
previous configuration
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Closing Windows
Click here to close any Plot
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Rotating Plots

Click this icon to rotate plots

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Creating a Spectrum (Option 1)

With “Display Spectrum” “Set Spectrum Selection”

checked, a mouse click will determines is the spectrum
generate an active spectrum is taken at the peak apex or
the nearest point

This opens only one spectrum

window; additional mouse clicks on
other peaks in the chromatogram will
update the displayed spectrum for
that peak
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Creating a Spectrum (Option 2)

If a different single-click
mouse function has been
selected . . .
. . . use the “S” hot key to
temporarily change the
mouse function to display
a spectrum (press “S” and
click simultaneously on the
peak)
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Creating a Spectrum (Option 3)

A right-click anywhere on
the Chromatogram
Window is the most
flexible way to display This powerful tool for
one or more spectra from spectral comparison will
one or more be explained in detail on
chromatograms several following slides

This menu will change

slightly as the number of
plots and spectra change
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Spectrum Windows

Up to four Spectrum Each Spectrum Window can

Windows can be created display A and B spectra plus the
from the displayed plots difference spectrum
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Adding a Second Spectrum

Selecting
“New
Spectrum
Window” on
the menu will
add the
second
spectrum (2A)
A right-click anywhere into a new
near this peak will spectrum
open the menu window

See next slide

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Second Spectrum from Plot 1

Mouse click on the plot Spectra 1A and 2A are

will update the 2A active shown in separate windows
spectrum window

“Filled” color indicates the

No “fill” indicates inactive
active spectrum
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Adding Spectrum 3 from Plot 2

Right-click near this

peak on plot 2 will Selecting “Update Spectrum Plot”
open the menu for and plot 1B from the menu will add
plot 2 the spectrum in Window 1 and
generate a difference spectrum

See next slide

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Two Plots and Four Spectra

Delete spectra
Active plot and spectrum are by clicking on
identified by the “Fill” color the “X”
and the Segment bar
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Spectral View Icons

Icons explained
on next 2 slides
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Spectral View Icons (cont.)

Set mass range

Set vertical scale

Click & drag actions

Single click actions

Returns spectrum window to previous scale

Returns spectrum window to full scale (X and Y)
Hides toolbar for more space on spectral window
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Spectral View Icons (cont.)

Set spectrum display

Background correct spectra

Select mass for chromatogram plot

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Spectral Search

Spectral searches have been

consolidated into one icon
and two drop-down menus
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Spectral Search (cont.)

Spectral searches have been

consolidated into one icon and
two drop-down menus

Menu commands are shown

in the next few slides
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Library Search Active Spectrum

Example of a library
search of a spectrum
using the Spectrum
drop-down menu
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Library Search Toolbar

Library Search toolbar icons are the

same as in MSWS version 6.2-6.4x

NIST search Page Mode

New Search Spectrum

Edit Search Spectrum

Move Difference to Search Rotate Plots

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Target List Search

Target List Search

of Active Spectrum
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Edit Active Spectrum

Example of the fields that
can be edit in the spectrum
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Edit Spectrum List

Example of a spectrum
list that can be edited
using the Spectrum List
drop-down menu
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Spectrum List Toolbar

Spectrum List toolbar icons are the
same as in MSWS version 6.2-6.4x

Select spectrum list Library search spectrum list

Edit spectrum Import from spectrum list

Delete spectra Library search spectrum list

Library search spectrum Page mode

Target list spectrum search Rotate plots