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audere-labs / pyvalence

python package for processing analytical chemistry data
BSD 3-Clause "New" or "Revised" License
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Agilent DATA.MS Details #2

Closed blakeboswell closed 7 years ago

blakeboswell commented 7 years ago

I need more insight into the DATA.MS file.

  1. Exactly what data is available in this file.
  2. How should the data be grouped ... i.e. does the data consist of 10 series that can go in one table, 10 series that should be split into 2 tables etc.
wilsoa6 commented 7 years ago

  1. So i know there gc chromatogram data is is there. We have plotted it. The MS data is also in there as well. There should be one MS data set for each timepoint from the GC data. I am not sure at all how this is structured, but I am certain it is in there because i can use just he data.ms file in openchrom at it has the MS data and the chromatogram data. Here is what the MS data will look like when plotted (Abundance vs. m/z).

  2. So each MS plot (Ab vs m/z) is associated with a timepoint in from the GCMS. You could make a dic of tuples? where the key is the RT (retention time, i.e. time) from the GC data. The way will want to access the MS data is through retention time if we want to pull out a specific MS plot. This will by typical for the user. How this would work for the user is we would plot the Chromatogram and then the user could double click (or something) on the plot and the MS data would pop up (pretty typical setup for GC and MS data).

From an analysis stand point we will eventually want to guess what the molecule is based on the MS data for each timepoint on the Chromotrogram. Good news is i think we can build a library from open NIST data. May be a little tedious, but we wont have to pay for anything and we can then offer that as a feature which is pretty huge.

blakeboswell commented 7 years ago

combined tme and tic data series into single data frame in a787ea442478d1242ec1eebb453176d70824b749

We should break this issue into multiple issues.

wilsoa6 commented 7 years ago

i think this is sorted out, or at least its clear what is in the .ms files, organizing it may still be up for debate