SAM SAGE Igor Tool

SAM SAGE - Software for Analysis of GCMS and EGA - was developed to aid in the analysis of SAM flight model data. SAGE will be used to model undersampled GCMS and complicated EGA data, calculate mass spectra based on modeled GCMS data, and determine peak onset temperature, peak maximum temperature, and peak area of modeled EGA data.

Latest

Use the #igorpro channel of the SAM-MSL Slack for help requests and discussion.

Igor 8 requires SAGE 1.8.4 or higher.

Software: SAGE1.8.4.pxp

Documentation/History

Manual: SAGEManualv1.3.pdf

SAGE new features.pptx in 1.7

Selected new features in 1.2, presented at the GCMS focus group meeting: SAGE_update_09_20_12.pptx

SAGE Release History

Archived SAGE Versions

Data Preparation

The data that SAGE requires can be checked out from XINA and takes the form of a file named IGORdata.zip. Use 'Checkout All' or 'Checkout Secondary' to retrieve it. Unzip the archive inside the TID folder, and then load the TID folder from SAGE using the "Macros/Load TID Folder" menu item.

All SAM runs with QMS data should have an IGORdata.zip file generated and available alongside the tm.sam file. If there is one missing let Micah or Anna know. We will run tm2igor.pl and generate one.

You can run tm2igor.pl yourself if you install the Python 3 version of the http://699wiki.com/wiki/index.php/Tm2igor_Quickstart 699 command-line tools.

A minimal set of files can be generated if there is no IGORdata.zip archive available, but the available functionality is reduced. The new overlay feature added in SAGE 1.4 will be mostly unavailable to you if you generate the subset of files this way.

To generate the bare essential data for use with IGOR, run the following commands inside the TID folder:

gcms.py > gcms.txt
gcms.py -b > gcms_b.txt
tmmarker.py > tmmarker.txt

Quickstart

  1. If you don't have IGOR Pro, install it from Wavemetrics
  2. Double-click the .pxp file of the latest version of SAGE
  3. Save the .pxp file with a new name
  4. Under the Macro menu select "Load TID Folder" and navigate to the TID folder you want to look at
  5. Try out SAGE's data processing capabilities
    • Check the TM Msgs to determine which EM was used, in order to select the correct coefficients for deadtime correction (v1.2 only)
    • Optionally display TM markers and other overlay data
    • Drag the vertical lines to set a background region
    • Display different data corrections with the dropdown menu at the top left
    • Use the Plot tab to add/remove bands and masses from the graph
    • Select peak regions in the Peak tab
    • Open Peak Graph window with the Magnify button
      • In Time tab, adjust time range of peak region, if necessary
      • In Mass tab, select set of masses and bands to use in fit
      • In Fit tab, select fit function, choose initial peak parameters, and click Fit
      • Display mass spectra of fitted peaks, with options to output to NIST 11 format text file
      • In Review tab (> tab, v1.2 only), quickly compare the "raw" data to the fitted data of a single mass (or a single band) at a time
    • Export all fitted peaks to a chromatogram (in a .jdx format text file, which is compatible with ACD), with gaps between fitted peaks modeled with either a line fit or a moving average or connect data points.
  6. Send any feedback to Micah Johnson and Anna Brunner

IGOR Tips

Release History

Preview 1

Preview 2

Preview 3

Version 1.0

Version 1.1

Version 1.2

Version 1.3

Version 1.4

Version 1.5

Version 1.6.1

Version 1.7

Version 1.8.1

Version 1.8.3

Version 1.8.4


Revision #1
Created 23 March 2023 14:48:31 by Nick Dobson
Updated 13 April 2023 15:21:48 by Nick Dobson