UsersMeeting 2007 ppt - welcome |...

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Joel Kimmel, 8th Aerodyne AMS Users Meeting, Reno, NV, Sept 28 – Oct 1, 2007

ToF-AMS DAQ

Joel KimmelUniv. of Colorado at Boulder

&Aerodyne Research, Inc

AMS Users’ Meeting 2007


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Web Resources

http://cires.colorado.edu/jimenez-group/ToFAMSResources/ToFSoftware/

Downloads

Release Notes

Supplemental Files

Directions for New Features

[email protected]

Questions

Requests

Problems / Bugs


Reporting Problems

[email protected]

Copies of Menu Files

PowerPoint File with Screenshots

Text from Error Message (If Bug)

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Outline

• Function and Structure of Code• Configuring Acquisition Parameters• Structure of Data Files

• V2.1

• Tuning Window– Fundamental of TOFMS calibration and tuning

• BitWise– Fundamentals of ion detection

• Looking Ahead to V2.2


ToF-AMS DAQ

Data Averaging (AP240 + RAM)

Sequence of Acquisition

Modes (GenAlt)

Sequence of ToFor Ion Types

(Menu Switching)

Acquisition Timing & Triggering

Data SaveDiagnostics

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Menu parameter files drive the DAQ.

(You define the menu file)


ToF-AMS DAQ

Data Averaging (AP240 + RAM)

Sequence of Acquisition

Modes (GenAlt)

Sequence of ToFor Ion Types

(Menu Switching)

Acquisition Timing & Triggering

Data Save

Menu Parameter

Files

Diagnostics

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Menu Parameter Files

MENU PARAMETER FILES save all adjustable parameters relevant to the operation of the instrument, e.g., timing and saving controls

MenuParameter

Files

Text EditorMenu

Window

ArchiveAt Load

of Software

Auto-SaveChanges During Use of Software

Meta-DataValues for Run included in all AMS data files

(ParVal)

VIEW/UPDATEMenu Values through DAQ or Text Editor

SAVE VALUES in archive, to operating files, and with data


To design an experiment is to configure runs.

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The Run is Our Base Unit

A RUN is a user defined duration of data averaging, having operating parameters determined by the ACTIVE MENU FILE

Run

Unique ID Number

Active Menu File

Hardware Configuration

Acquisition Timing and Triggers

Time to Average (Run Duration) / Synchronization with Clock

Sequence of Acquisition Modes (GenAlt)

Structure for Saved Data


GenAlt allows flexibility within a single run.

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Sequence of Acquisition Modes (GenAlt)

When configuring a run, the user defines ACTIVE ACQUISITION MODES

During a single run acquisitionCYCLES THROUGH ACTIVE MODES

Acquisition in a mode lasts for a user-defined DWELL TIME

Between modes, software checks whether total acquisition time has reached the user-definedSAVE TIME (TSave)

Start New Run, t = 0

PTOF

BFSP MS

Save AMS Data

Acquire

Stop

While

t < Tsave


PTOF 10 s

EXAMPLE GenAlt

Acquisition may run with ANY COMBINATION of PToF, MS, and BFSP

During the run, acquisition CYCLES through active modes, spend the user-definedDWELL TIME in each

The cycle continues until the acquisition time exceeds SAVING TIME

MS 10 s

BFSP 5 s

Start New Run, t = 0

Save Run

While t < 50s

(2 cycles)

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MS 10 s

Avg Data on AP240 for “Time Spent on Board” (2 sec)

Transfer Data AP240 to RAM; Average with

existing Data (Open or Closed)

Move Chopper

If t > TDWELL (10 sec)Stop

CLOSER LOOK AT MS DWELL

User-defined “Time Spent on Board”

Transfer and Chopper Move = DEAD TIME

For MAX DUTY CYCLE , keep ON BOARD high (but less than dwell)

Start


Number of choppers determines the on board averaging time for PToF mode.

This value is an estimate based on input chopper frequency.

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Magnitudes for proper settings:(On Board Time) =< (DWELL)

AND

S(dwell times) <= (Saving Time)


Menu switching allows flexibility in a sequence of runs.

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Sequence of Unique Runs

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 cyclic sequence of menu files to use.

– Allows continuous experiment, with alternating configuration

– Most commonly applied to “V/W SWITCHING” with HR-ToFMS

Run 2n - M2

Run 1n - M1

Run 3n - M3

Run 4n - M4

Run 1

Run 2

Run N

M1


GenAlt + Menu Switching = flexible experiment design.

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V (PM)

V (PM)

W (M)

W (M)

V (MP) 5-min

V (M) 30 sec W (M)

V (M) 30 sec

V (M) 30 sec

EXAMPLE DESIGNS (i) 2 menus; Vary ToF type; Different active modes for each ToF type

(ii) 3 menus; Vary ToF Type; 2 different V-mode configurations

SEQUENCE is DEFINED BY• Active Menu Numbers

• Start Menu• Successive Runs at each menu number

(i) (ii)


Select Menu

Save AMS Data

Update Hardware

and Timers

PTOF

BFSP MS

Acquire & Average AMS

Data

Save Active Menu File

Run Number

+1

AcquireStop

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Menu Summary

V (PM)

V (PM)

W (M)

W (M)


ToF-AMS data are written as HDF files. One file contains all data

from multiple runs.

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HDF File Format

A single HDF FILE can contain multiple DATASETS, each of unique size and dimension (equivalent of an Igor wave)

All datasets have an EXTENDIBLE DIMENSION

An existing dataset is written to by adding a LAYER along the extendible dimension

Dataset 1Dataset 2

Dataset 3

Dataset 4

Layer 1Layer 2

Layer 3Layer 4


ToF-AMS DAQ writes to TWO TYPES of files

The MAIN (_m) file contains MS data and PTOF-stick data.

The PTOF (_p) file contains only raw PTOF data.

Data from each RUN ARE WRITTEN AS LAYERS of the datasets.

Both file types include parameter and “info” values, and a RUNINFO dataset that SQUIRREL uses for indexing of the data.

Run 1000Run 1001

Run 1002Run 1003

070930_001000_m.hdf

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Run as Layer of HDF Datasets

Run

If MS Active If PTOF Active If PTOF Active ANDSave RAW

RunInfo

ParVal

ComParVal

RunInfo

ComParVal

InfoVal

If V If W If V If W

MSSClosed_v

MSSDiff_v

MSClosed_v

MSOpen_v

MSSClosed_w

MSSDiff_w

MSClosed_w

MSOpen_w

ptof_stick_v

ptof_stick_wInfoVal

ParVal

If V If W

ptof_v

ptof_w

The datasets written for a run depend on active modes and save preferences.

Data are sorted as V or W; Menu Number is NOT part of the save structure

RunInfo guides SQUIRREL in indexing of the layers.


Estimating Data Size

Data values are singles (4 Bytes)

MS: Array of length = number of samples

MSS: Array of length = MaxMass – MinMass

PTOF: Matrix of dimension = (ToFperChop/Co-Adds) x (number of sample)

PTOF Stick: Matrix of dimension = (ToFperChop/Co-Adds) x (MaxMass - MinMass)

Example. V-mode Run. 30,000 samples, m/z = 10 to 410 Th 100 Tof/chop, 2 co-adds

MS = 30,000 * 4 = 120 KB

MSS = 400 * 4 = 1.6 KB

PTOF Stick = 50 * 400 * 4 = 80 KB

PTOF = 50 * 30,000 * 4 = 6 MB

_m = 2*120KB + 2*1.6KB + 80KB = 323 KB/Run

_p = 6 MB/Run

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V2.1

• Implementation of Common Menu Structure

• Expanded m/z Calibration and Tuning Window

• BitWise replaced Threshold Analysis and m/z Ratio Windows

Go to DAQ


Calibration and Tuning

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TimeTime--ofof--Flight Mass SpectrometryFlight Mass Spectrometry

To determine m/z valuesA packet of ions is accelerated by a known potential and the flight times

of the ions are measured over a known distance.


Data are collected in time (ns).

User assigns m/z values to known peaks in time spectrum.

Mass Calibration based on LSF allows determination of m/z from time of flight.

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TOFMS

Detector

V

Source, S Drift Region, D

E = V/S E = 0

mqEsD

vD

t

mqEs

v

mvqEs

qEsqVU

aDD

aD

Da

aa

2

221 2

==

=

=

==Ideally U is known exactly, T is exactly predictable.

IN REALITY:

Initial U

And position dependent Va and …

Causes broadening of ToF peak.

a


From: http://www.chemistry.wustl.edu/~msf/damon/reflectrons.html

Series of electrodes, forming a linear field in direction opposite of initial acceleration.

Penetration depth depends on Us, which is function of U0 and acceleration field, E.

Reflectron voltages are tuned to create a SPACE FOCUS at the plane of the detector.

Reflectron

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For ToF-AMSIon source voltages are tuned to maximize

transmission into TOFMS extraction region

Reflectron is tuned to compensated for ?E of accelerated ion beam.

Go to window


BitWise

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Ion Detection

Signals in AVERAGED TOF mass spectra can be divided into two classes:

(i) LOW ABUNDANCE, which have shape and intensity originating from the accumulation of stochastic single ion detection events

(ii) HIGH ABUNDANCE, which have shape and intensity originating from the accumulation of signals generated by the simultaneous detection of multiple ions.


Time-to-Digital Converter (TDC)

Converts a signal of sporadic pulses into a digital representation of their time indices.

Neither the height nor the area of the pulse is recorded.

A TDC usually follows a discriminator, which sets the minimum accepted pulse amplitude.

ToF-MS experiments measuring ONLYLOW ABUNDANCE IONS can use TDC for ION COUNTING

Peaks heights in MS develop through averaging

NOT LINEAR IN HIGH ABUNDANCE REGIME (Saturation)

Time

D

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Analog-to-Digital Converter (ADC)

Demo from Learning by Simulation. By Hans Lohninger(http://www.vias.org/simulations/simusoft_adconversion.html)

Converts continuous signals to discrete digital numbers.

Records time and amplitude of waveform events.

Acqiris AP240 = 8-bit, up to 2 GHz


Particle Detection bursts necessitate ADC.

Quantification relies on

(1) The detector having a response that is proportional to the number of incident ions

(2) The ADC recording the signal waveform with fidelity

(3) Knowledge of the relative detector response in order to calculate the ion count rate.

Measure response of ToF-MS detector for single ion and use this value as the base unit for quantification

Total integrated signal at m/z 30 and 46 for single ammonium nitrate particle detection events. Total recorded signal grows as cube of diameter, indicating that recorded intensity is proportional to the number of ions.

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To determine the SI area in the ToF-AMS we record the average shape of LOW ABUNDANCE m/z PEAK DETECTION EVENTS

0.10 implies that 10% of recorded events will be double ion signals.


Peak height and Areas have broad distributions

Calculate Average Area as sum of average element values

Magnitude of response depends on MCP gain

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Use of the calculated SI value for quantification of AMS data requires that it is not m/z dependent.

Kimmel et al., 2007, In preparation for JASMS


Noise

Noise in the ToF-AMS has ELECTRONICand CHEMICAL components.

Chemical originates from scattered ions, and thus has an intensity equivalent to real, low-intensity signals (i.e., single ion arrival events).

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Threshold

AP240 includes noise rejection thresholding

Any portions of the signal waveform with amplitude greater than a user-defined threshold are recorded relative to a real and exact baseline.

All portions with amplitude below user defined amplitude discarded (i.e., recorded as 0 amplitude).

Choosing the ADC threshold setting is a balance of SNR and dynamic range. The threshold is ideally set at a value where electronic noise is rejected and all ion signal intensity is recorded.

m/z 32


Before determining best threshold, must determine BASELINE

In voltage space, ToF-AMS signals are negative going.

Setting baseline that is MORE POSITIVE than actual INFLATES signals

Setting baseline that is MORE NEGATIVE than actual DEFLATES signals

Sig

nal (

Bits

)

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BASELINE is average value of recorded signal with no detector gain

With baseline set, we can then determine the distribution of intensities of noise signals

FIRST GUESS (ideal) THRESHOLD will be value discards all electronic noise


Affect of threshold on single ions is determined by applying a software threshold to all events used to calculate average shape

AGAIN, setting threshold is a balance of eliminating noise and maintaining AREA OF LOW ABUNDANCE signals.

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To observe effect of threshold on average data, we monitor the relative intensities of HIGH and LOW ABUNDANCE ions

The total area of 40 decreases, while m/z 28 is unaffected until high voltages


Effect of baseline setting on 40/28. Black = Area measured with threshold applied. Grey = Raw Area.

From: Kimmel et al, 2007, In preparation for JASMS

Baseline setting is AS CRITICAL. Inflation and deflation have clear effect on LOW ABUNDANCE signals.

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Use 40/28 to determine degree of degradation at “Ideal Threshold.”

Balance low abundance signals with electronic noise

If not possible, consider raising threshold. (Avoid saturation – more in a couple slides)


1950V 2050V

2150V 2250V

2350V

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ADC saturation can be detected by comparing the signal of ambient O2

+ (m/z 32) to the signal of ambient N2+ (m/z

28) in unthresholded ToF- aerosol mass spectra.

The N2+ signal will saturate at far lower MCP gain than

O2+.

With BitWise, saturation can be identified with the peak analysis routines by watching m/z 28 with the chopper open.


1. Set Baseline2. Measure electronic noise to determine

ideal threshold3. Measure peak shapes to determine

saturation probability and SI Area4. Use m/z ratio to determine if ideal

threshold is detrimental to small peaks

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Peak-to-Noise Ratio compares the probability signal events and noise events within the m/zintegration area at the user-defined peak threshold.

A low value suggests that SI area calculation will include noise events – low bias.

Want to run at lowest


Measured Areas “settle” after 300 PEAKS

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V2.2

• Within the first half of 2008• Emphasis:

– More Accurate Run Timing– LS triggered SP mode– More tuning functionality– Burst Modes (Up to 2 Hz PTOF and MS)

• Suggestions welcome!!

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