#170 Change MS2 file parsing to read precursor mass from Z line

[Kaipo]

According to the MS2 format specification, it seems that we should still read the precursor from the S line. The problem is that msconvert writes the isolation window to the S line and the M+H+ calculated from precursor to the Z line, but it should be writing the precursor to the S lines (Z line values are correct).

So I think the best solution is to change msconvert to write the precursor to the S line rather than the isolation window, meaning the isolation window information would no longer be in the MS2 file (not sure whether that is a problem or not).

[Jeff Howbert]

For DIA data I think you want the isolation window written the S line. Maybe this is the same as the precursor in DIA - I don't know.

Jeff

On Wed, 25 Jun 2014, Kaipo wrote:

According to the MS2 format specification, it seems that we should still read the precursor from the S line. The problem is that msconvert writes the isolation window to the S line and the M+H+ calculated from precursor to the Z line, but it should be writing the precursor to the S lines (Z line values are correct).

So I think the best solution is to change msconvert to write the precursor to the S line rather than the isolation window, meaning the isolation window information would no longer be in the MS2 file (not sure whether that is a problem or not).

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** [issues:#170] Change MS2 file parsing to read precursor mass from Z line**

Status: open
Milestone: post v2.0
Labels: High priority
Created: Thu Jun 19, 2014 07:50 PM UTC by William S Noble
Last Updated: Thu Jun 19, 2014 07:50 PM UTC
Owner: Kaipo

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[Attila Kertesz-Farkas]

Is there another RAW 2 MS2file converter that we could check and see how it uses the S line?

[Kaipo]

There is MakeMS2 which uses MSToolkit, the relevant source code is here:
https://code.google.com/p/mstoolkit/source/browse/trunk/src/MSToolkit/MSReader.cpp
https://code.google.com/p/mstoolkit/source/browse/trunk/src/MSToolkit/RAWReader.cpp

[William S Noble]

I think we decided last week that Tide should read precursor mass from the Z line, and that Kaipo would look into changing this in Proteowizard. Note that Tide should also report top-match matches for each Z line if a spectrum has more than one, even if those Z lines have the same charge state.

[William S Noble]

The patch that Kaipo sent does not seem to work, at least insofar as the program still parses the S line even when the mstoolkit parser is used. The attached tar file shows an example. Take a look at the tide-search.target.txt file in the mstoolkit and the pwiz subdirectories.

(The attachment is too big, so I will send it by email.)

[Kaipo]

fix committed in r16490