Differentiating MSe from MS when parsing MassLynx files

starikov
starikov
in Software Products
I work on a product that parses MS files and offers some processing functionality for the data.

I have recently found Waters *.raw file examples where e.g. the 1st and 2nd functions do not seem to have discriminating parameters, but our clients say that the second one is MSe and they prefer then to see it labeled as such.

I see in the ProteoWizard codebase (https://github.com/ProteoWizard/pwiz/blob/master/pwiz/data/vendor_readers/Waters/SpectrumList_Waters.cpp#L183) that they tried to use Collision Energy for determining if the 2nd, 3rd etc. functions are MSe, but then commented that out and essentially are qualifying everything after the 1st function as MSe. In some of the examples that I have the Collision Energy could indeed be used, but not in all cases.

Could you please clarify, is there a criterion or at least a reliable heuristic that can be used for determining if a function is MS or MSe when parsing Waters RAW files?

Thank you!

Answers

  • Dr_Toxic
    Dr_Toxic
    MSe (or HDMSe) acquisitions are Data Independent Acquisition methods that usually only have three channels:
    1. Low collision energy scan, which should be intact molecules/ions.
    2. High collision energy scan, which are fragment ions of the intact molecules/ions from the preceding low energy scan. Fragments in the scan can come from different precursors.
    3. Lock mass scan.
    Data Dependent Acquisitions, or "traditional" MSMS are experiments where an MS scan of the intact molocules/ions occurs and then each ion is sequentially selected for fragmentation. In Waters instruments using MassLynx, channel:
    1. MS scan, with intact molecules/ions.
    2. First MSMS scan of a selected precursor.
    3. Second MSMS scan of next selected precursor.
    Channels 4-11 are subsequent MSMS scans if the number of precursors selected for MSMS in the method is 10. If it's 15, there will be channels up to 16. Not all of these channels will contain MSMS data if the number of selectable precursors is less than the maximum set.

    Channel 12 (or 17) is lock mass.

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