Basic Operation of the TRACE MS PLUS for Engineers

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1. Basic Operation of the TRACE MS

PLUS for Engineers

Introduction
This document assumes the reader already has a working familiarity with
TRACE MS/Voyager/MD800 control via the Xcalibur data system.
TRACE MS Plus requires Xcalibur 1.3.

Configuring TRACE MS Plus

Run the Xcalibur Instrument Configurator.

Select Instrument Configurator from the Windows Start menu.

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Double-click the TRACE MS Plus button that appears in the instruments

list on the right-hand-side of the dialog.

At time of writing, there were no configurational settings for TRACE MS

Plus. It can be anticipated that there will be some adjustable parameters in a
later release version, to enable such options as 800amu (for ToxLab) and CI
capability.

Launching the Server

The Server can be launched in 2 ways:

1. Running the Tuning application for TRACE MS Plus.

2. Launching Xcalibur.

If Xcalibur is launched, it is assumed that the instrument configuration has

declared the TRACE MS Plus as selected.

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When the Server is running, there will be an icon in the Windows Start
menu, as shown below.

The Icon changes colour depending on the state of the MS.

Yellow indicates Pumped Down and in Standby.

Green Indicates the MS is in Operate.

Red indicates the system is Vented, and therefore in Standby.

Perform a right-click on the icon to open the Server menu.

It is possible to access the Manual Tune dialog from here if it is not already
open.

Other operations that are possible from this menu are:

Automated Tuning and/or Automated Mass Axis Calibration

Manual Mass Calibration, via the Instrument Tune and Calibration…

menu item

Reconfiguration of the MS Inlet (GC, DIP or DCI)

Venting/Pump-down operations

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Tune Dialog

Opening the Tune dialog

Tune can be launched from its Shortcut on the Windows Desktop, or if not
visible, through the Start Menu, as shown below.

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Default Tune dialog

The Tune dialog represents a radical departure from earlier generation user
interfaces. When it first launches the display is seen to be organised into
two regions.

Graphical Display

The top of the dialog is occupied by one or more mass range graphical
displays - dependent on how many have been specified/activated – and each
will have annotation indicating Absolute Intensity, Centroided Mass
Measurement and Display Gain (Zoom) of the individual mass selection.

Tabular Display

The bottom region of the dialog is composed of a table of Scan Functions.

Each entry (row) describes a mass with defined mass span, scan time,

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detector voltage setting and peak format and each may be selected in the
graphical region above.

In the example caption, it will be evident that a level of customisation is

possible. Each Scan Function can have an alias name applied to it, for
familiarity. The total number of rows visible on-screen is defined in a
configurational dialog that opens from the View | Options… menu item. It
will be discussed later.

The example shows 7 Scan Functions that have been compiled and together
these define the most routine interactive procedures associated with
maintenance of a MS.

FS1 through FS3 show individual ions from the spectrum of PFTBA
(Heptacosa); these would be used to review sensitivity and mass resolution
for routine analysis.

FS4 has been designed to show a wide mass range and therefore allowing
inspection of the instrument ion background; this would be useful to monitor
contaminants such as column and septum bleeds, hydrocarbon background
from dirty samples and plasticizer ions that could potentially be introduced
during column installations and/or source cleaning.

FS5 through FS7 have been set up to monitor for potential air leaks,
referenced against Helium carrier gas.

Collectively, the table of Scan Functions replaces the earlier technique of

swapping saved parameter display files to accomplish these fundamental
tasks.

The table also permits time windows to be applied to any or all Scan
Functions. Although the default setting is zero, a time range, say 0.00min to
1.00min would enable an acquisition to be performed from the tune dialog,
independent of Xcalibur. This is useful for performing diagnostic manual
mass calibrations very rapidly.

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Displaying Tune Parameters

The Windows slider control marked Show Per Method Parameters, at top
right of the dialog will reveal the tune parameters, as shown below.

These parameters are global to all Scan Functions.

Method Editor dialog

The Method Editor dialog for TRACE MS Plus is launched from

Xcalibur’s Instrument Setup dialog

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Pumping Down and Venting

This is achieved by right-clicking the Server icon at the right hand side of
the Windows taskbar.

Pumping Down

When the instrument is vented, the Server icon will be red (Vented).

To pump down, perform a right-click on the icon to display its menu.

Select the Pump menu item to start the pump down procedure. The Server
icon will flash yellow until high vacuum has been achieved AND
turbomolecular pumps achieve adequate frequency of rotation, where after it
will stop flashing and adopt a continuous yellow appearance.

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Venting

When the instrument is pumped down, the Server icon will be yellow
(Operate OFF) or green (Operate ON). The right-click operation will
reveal the following menu:

Selecting the Vent item will display a confirmation prompt, as follows:

Select Yes to Vent the MS, if this is required. Venting will be immediate,
with the deactivation of the Vent Valve solenoid attached to the front (or
only) turbomolecular pump.

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Tuning and Calibrating

Autotuning

Select the Instrument Tune and Calibration menu item from the Server icon.

The following dialog will be displayed:

Select the option for Full System Autotune.

A status dialog will be generated showing a log of events that will

eventually lead to a fully tuned and calibrated instrument.

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The Tune dialog can be seen to update with the Autotune algorithm.

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Ultimately, the log of events can be copied to the clipboard for pasting into a
document. This may be useful for diagnostics, if a problem is suspected, or
as a teaching aid for learning manual tuning.

Eventually, the system will be tuned and calibration will follow:

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The Tune dialog will show a full scan across the reference ions of the
internal tuning compound, PFTBA (FC43).

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And here is the final outcome:

Print the report, if required, otherwise hit the Finish button.

The Reference gas will be turned OFF automatically and Operate will be
set back to its previous state.

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Tuning in Normal Mode

Select the Manual Tune menu item to launch the Tune dialog.

This dialog shows the Standard Tune view. There are no Tune parameters
to adjust. It is assumed that Autotune is used to set up the instrument.

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Selecting Ionisation Mode

Different ionisation modes are selectable from the combo bow as shown
below:

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Tuning in Engineers Mode

To turn ON Engineers Mode, open the Options dialog from the View menu:

The Options dialog will appear as shown:

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Select the radio button marked Engineer to reveal all parameters.

When the Tune page is re-opened you will see additional Per Method
Parameters.

It is possible to view many readbacks, power supply rails and perform

various diagnostic tests.

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Performing Mass Calibration

This can be achieved from the menu attached to the Server icon.

Select the Standard Mass Scale Calibration option and follow the
instructions:

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The dialog will show status information as the instrument is calibrated.

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The Tune dialog will show a scanning acquisition occurring.

Ultimately the process will terminate:

There will be an option to print off a report prior to closing the dialog.

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Manual Mass Calibration

Only necessary for diagnostic purposes. Uses an acquired file, and a
selected calibration reference file:

Follow the instructions in the wizard, as shown below:

The Raw File must contain spectra acquired over an adequate mass range
with satisfactory mass resolution.

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Saving Tune Parameters to a named file

Very straightforward, merely open the File | Save As… menu item and
name your tune file.

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Setting up MS-only acquisition

Acquiring from Tune Dialog

Need a scan function defining an adequate mass range, as in example below:

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Specify a file name and location in the options dialog:

Use the File | Start Acquiring menu item to commence:

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You will be able to monitor the elapsed time.

Acquiring from Xcalibur

This is same as with previous systems. Define parameters in Instrument
Method Editor and run from a Sample Sequence in Home Page.

Performing GC/MS acquisitions

Solvent Delays

There is no longer a limit on the positioning or number of solvent delays

within an acquisition.

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Scanning acquisition
This is the default mode of acquisition. To add a scan function, literally hit
the Add Full command.

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SIM acquisition
There are no constraints on how many ions get acquired in a data file. In
reality, there is an upper limit of 511 individual ions which may be grouped
into any number of SIM groups.

The start and end times can be defined in the table or by moving the
graphical bars with the mouse.

At the time of writing, the grouping control was unfinished for TRACE MS
Plus.

Mixed Scan and SIM acquisition

TRACE MS Plus can be used analytically to perform scanning acquisitions
as well as SIM. There is complete freedom of overlap, simultaneous or
discreet groupings.

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Use the Add Full and Add SIM HTML links to add Scan Functions:

Now use the Preview | All Scans to view all Scan Functions.

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They may be edited as needed. There are no constraint on start and end
times, and Scan Functions can overlap.

If the green scan function is clicked-and-dragged, then its position and times
can be varied with the mouse.

Toggle between Scan and SIM functions with the slide controls:

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When you click on any graphical scan function, its properties are shown in a
pop-up window:

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