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ToF-AMS Data Acquisition Software

Joel Kimmel

Univ. of Colorado - Boulder&

Aerodyne Research, Inc

AMS User’s Meeting 2006

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ToF-AMS Web Pagehttp://cires.colorado.edu/jimenez-group/ToFAMSResources/

Includes:• Data Acquisition (DAQ) Software Downloads

• Manual for DAQ Software

• Release Notes

• Supplemental Software tools

• “To Do” list describing planned DAQ development timeline

• Guidelines for making software requests and reporting bugs

Versions

• v1.7, this week.– m/z Calibration and Tuning Window with raw display of

mass spectra and time traces of figures of merit (1 sec auto-refresh)

• v1.8, ~ 1 month.– Refined Threshold Analysis Window. Emphasis on

usability and baseline analysis.

• v2.0, ~ 2 months.– Restructured Menu Files and HDF format. New

“paradigm” of experiment design through custom menu switching sequences.

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Menu Parameter FilesMenu Parameter Files save all adjustable parameters relevant to the operation of the instrument, e.g., timing and saving controls.

Parameter values are updated via:

•ToF-AMS Menu Window

•Default Parameter Window

•Real time (e.g., Run Number)

•Text Editor (Not encouraged)

Values archived in two ways:

•ParVal and ParStr waves written to all data files (HDF and itx)

•Copies saved at load of software C:\ToFAMS\ToFAMSData\LogFiles\MenuCopies

Defining A RunA RUN: A user defined duration of data averaging, having operating

parameters determined by the active menu file

• A unique data set is saved at the completion of each run

• A run can be have a fixed acquisition mode (MS, PTOF, or BFSP) or

Alternate acquisition modes across its duration (General Alternation, GenAlt)

• For General Alternation– The user must:

• Define which acquisition modes are active• Define the amount of time to spend in each mode, called the

dwell time.– The system will continuously cycle through active modes until the

defined averaging time of the run is reached.

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Defining a Sequence of Runs• In typical operation, one collects a continuous sequence of

runs with identical operating parameters (i.e., a fixed menu file).

• Menu Switching allows the user to define a sequence of runs that alternates between unique menu files. – Most commonly applied to “V/W Switching” with HR-

ToFMS.

• Any change between menus that depend on different TOFMS voltages requires TPS Remote Control and computer control of heater bias

Note: TPS remote control is available for all TOF types, but requires recent firmware and software versions

Data SavesIgor text files saved for ALL runs

•One run per file

•MS and PTOF in separate files

•PTOF and BFSP binary optional

HDF saves are optional •HDF necessary for use of SQUIRREL

•Raw MS, MS Stick, PTOF stick, ParVal, InfoValare datasets within “Main” (_m) HDF file

•Raw PTOF written to _p (optional)

•No BFSP data

•For _m and _p, Runs are layers of datasets

•RunInfo dataset provides a summary of file

•HDF files can be browsed in IGOR

•HDF files can be generated from existing Igor data using HieDI

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ToF-AMS Menu Window Demo

Voltage Control• Voltages cannot (yet) be tuned

directly from DAQ

• Instead, setting files are created in TPS control software and loaded to DAQ

• During acquisition, the DAQ writes a setting file, and points the TPS Control Software to this active file.

• The DAQ ALWAYS follows these protocols – but remote control commands are ignored by the TPS Control Software functionality is turned on there.

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Glimpse of 2.0Version 2 will represent a fundamental change in the menu and data structure.

• Menu switching has primarily been used for(1) ToF Type: V-W-V-W-V …(2) Averaging Times: 10sec-1min-10sec ..

• The HDF data structure has transparent “masks” for ToF-type (e.g., V or W). SQUIRREL makes clear distinction between data based on ToF-type.

• New HDF data structure designed for scenarios where menus are used to vary multiple significant parameters during course of continuous experiment. (ToF-Type, Ion Type, and Sampling Type)

• Transparent mask in files (and SQUIRREL) corresponding to menu number.

• New menu structure divides parameters into “Common parameters” and “Acquisition Parameters.” The former is the same for all menus, the latter is independently controlled across files.

Demo of 2.0 Menu Summary-Multiple Menus-ToF Type-Ion Type-Sampling Type-Calibration Group

AP240 Parameters

…Defer discussion of thresholding etc until later today …

For use of DAQ Software, one should understand:Full Scale

Offset / BaselineThreshold

255

0 +1V

-1V

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Full Scale

255

0 +1V

-1V 255

0 +0.25V

-0.25V

2 Volt 500 mV

Board has 256 bit full scale.

User defines a voltage full scale to accommodate the largest signals.

- Avoid saturation

- Maximize bit resolution

For ToF-AMS, this value depends primarily on pre-amp

Offset• For any full scale, the board defaults to a position

centered around 0 V.• Changing offset allows the user to shift this window• For our negative (inverted) signals, we apply positive

offsets that are ~45% of full scale.

255

0 +1V

-1V

0.9 V Offset

255

0 +0.1V

-1.9V

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Fine Adjust

Fine Adjust

255

0 +0.09V

-1.91V

User defines Baseline in volts. This is the zero point, from which signals originate.

For acquisition, the board requires that the baseline voltage has an integer bit equivalent.

If this condition not satisfied, the board will “force” the baseline voltage to nearest bit. i.e., the board will determine your zero!

To avoid this systematic error, we fine adjust the offset in order to meet condition

255

0

-1.9V

+0.1V

Threshold

B

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With thresholding applied:

AP240 records signal intensities as bits relative to the baseline bit value

All elements with intensity less than threshold are recorded as 0 bits

Note that:

Multiple TOFMS extractions are averaged on the AP240 before transfer to the PC

Each extraction is thresholded before averaging

The thresholding processing cannot be undone

Likewise, the effects cannot be achieve by post-processing

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B

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B

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B

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0

Threshold EffectsThresh=3

Thresh=1

Thresh=4

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Discard noise, maintain signal

DEMO

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1. Identification of three know peaks for m/z calibration

• User defines exact m/z and center

• Grey box shows integration area

• Parabolic fit determines non-integer center

2. Display of LSF and mass accuracy

3. Raw display of mass spectrum

• Zoom and scroll

• Mouse over data values

• Display of nominal m/zpositions

4. Tuning Scans• Conitnuous auto-refesh

• 4 figures of merits (more to come)

• Scroll through time

m/z Calibration & Tuning

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Example: Tune Reflectron

Example: Tuning HB

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Example: Zoom Raw Display

Threshold window looks at effects on single ion signals

Ration window looks at how these effects manifest in averaged data AND detects ADC saturation by large signal

As will be discussed later, these windows should be used together.

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Baseline: Quantify effect of thresholding on electronic noise

Baseline: Determination of baseline position

Peak: Determination of shape and area of raw (un-thresholded) single ion signal

Peak: Calculation of effect of thresholding on single ion signal(Glimpse of next version)

Threshold Analysis Window

Servo Diagnostics

Top Hat: Record PTOF AB as a function of servo position. Maximum at positions where servo is chopping beam. Effectively zero at points where beam is completely transmitted or blocked.

Wait Time: Record MS AB as a function of “wait after servo movement.”

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DEMO

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Time Trace

TimeTrace.txt is an “optional,” tab delim text file that can be used for quick views of data in real time.

In addition to key diagnostics, user can define up to 10 m/z values to track

Igor template for viewing is available on ToF-AMS Software Page