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Re: [proteowizard-support] msconvert: RAW to MS2 format
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From: Matt C. <mat...@gm...> - 2014-01-23 22:52:33
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OK, I think I see what you did Barbara. You are using the isolation m/z in the S line and the
selected ion m/z in the Z line (except it's being converted to a mass by multiplying by charge
state). The problem is that if there is no charge called and no possible charge states called
either, then the selected ion m/z is going to be lost. It's probably better then to switch to using
the most accurate m/z available for both fields, and consider adding an isolation window and/or
target m/z field to the MS2 format ("IW"?) to preserve the isolation information.
Thoughts?
-Matt
On 1/23/2014 3:59 PM, Barbara E Frewen wrote:
> I think there are two things going on here. First, when I wrote the parsers/serializers for .ms2
> files, Thermo instruments did not compute accurate mass and charge for the precursors. Therefore
> the only values in the .raw files were related to the isolation windows. Second, .ms2 files from
> written from different sources got their precursor m/z values in different ways: either the target
> m/z value for isolation OR an accurate m/z computed post acquisition and based on MS1 data.
>
> I was looking for a way to store those two values distinctly when parsing .ms2 files. Looks like
> I used isolation window. It also seems that now that usage conflicts with how things are stored
> in and parsed from the .raw files.
>
> Hope that helps.
>
> Barbara
>
> -------- Original Message --------
> Subject: Re: [proteowizard-support] msconvert: RAW to MS2 format
> Date: Mon, 20 Jan 2014 10:36:10 -0600
> From: Matt Chambers <mat...@gm... <mailto:mat...@gm...>>
> To: Attila Kertesz-Farkas <kfa...@uw... <mailto:kfa...@uw...>>
> CC: su...@pr... <mailto:su...@pr...>, Barbara Frewen
> <frewen@u.washington.edu <mailto:frewen@u.washington.edu>>, Kaipo Tamura
> <ka...@uw... <mailto:ka...@uw...>>
>
> Good point Atilla. I don't know why MS2 is being treated different here. It was UW
> folks that wrote
> this code though, so I'm going to defer to them. Barbara, Kaipo, is there a reason to
> prefer
> isolation m/z over selected ion m/z?
>
> -Matt
>
>
> On 1/18/2014 11:17 PM, Attila Kertesz-Farkas wrote:
>
> Dear Support Team,
>
> I have encountered a problem with MSConvert. It seems MSConvert prints
> out isolation window instead of the precursor mass in the S line when it
> converts Thermo Raw data to .ms2 data format. This happens even though
> the precursor mass does fall inside the isolation window (1.5). However,
> if I convert this RAW file to .mzXML or .mgf format then Msconvert
> writes the correct precursor m/z values.
>
> I have examined the source code a little bit as well however I am not
> familiar with the source code of ProteoWizard expert level. It seems to
> me it prints out the precursor mass for .mgf format,
> Seriaalizer_MGF.cpp(105):
> os << "PEPMASS=" <<si.cvParam(MS_selected_ion_m_z).valueFixedNotation();
>
> while it prints out the isolation window for .ms2 data:
> Serializer_MZn.cpp(166)
> double mz = precur.isolationWindow.cvParam
> (MS_isolation_window_target_m_z).valueAs<double>();
>
> According to definite sources for the definition of MS2 data, S line is
> to contain precursor m/z value:
> http://www.ncbi.nlm.nih.gov/pubmed/15317041
> http://fields.scripps.edu/sequest/unified/MS2Format.html
>
> Finally, I have an example:
> This is a header from the RAW file for the 5866 scan:
>
> Linfeng_080810_HapMap10_1 #3178 RT: 0.0076
> Total Ion Current: 82303.02
> Scan Low Mass: 100.00
> Scan High Mass: 2000.00
> Scan Start Time (min): 61.82
> Scan Number: 5866
> Base Peak Intensity: 11462.79
> Base Peak Mass: 629.34
> Scan Mode: FTMS + p NSI d Full ms2 689.66@hcd45.00 [100.00-2000.00]
> LTQ Orbitrap Velos Data:
> ========================
> AGC: Predicted
> Micro Scan Count: 1
> Ion Injection Time (ms): 300.000
> Reagent Ion AGC: On
> Reagent Ion Injection Time (ms): 0.000
> Scan Segment: 1
> Scan Event: 2
> Master Index: 1
> Elapsed Scan Time (sec): 1.08
> API Source CID Energy: 0.00
> Average Scan by Inst: No
> Charge State: 3
> Monoisotopic M/Z: 689.3286 <--------
> MS2 Isolation Width: 1.5
> MS3 Isolation Width: 0.0
> .
> FT Analyzer Settings: T=5e4 iWf
> FT Analyzer Message: MCal=30d RF=1180V HCD=36eV
> FT Resolution: 7500
> Conversion Parameter I: 0.000
> Conversion Parameter A: 0.000
> Conversion Parameter B: 47472905.475
> Conversion Parameter C: -4283584.272
> Conversion Parameter D: 0.000
> Conversion Parameter E: 0.000
>
>
> while this is the corresponding MS2 header obtained with MSconvert.
> S 5866 5866 689.66
> I RTime 61.82205
> I BPI 11462.79
> I BPM 629.3438
> I TIC 82303.02
> Z 3 2065.971
>
> Here the S line should contain 689.3286
> Both .mgf file and .mzXML files contain 689.3286 as precursor m/z value
> and PEPMASS.
>
> These conversions were tested with both MSconvert version 3.0.5099 64
> bit and version 3.0.5163.
>
> My question:
> 1) Why does MSconvert print out isolation window only in ms2 data?
> 2) If this is indeed a bug, may we expect a release having this issue
> with S line fixed?
>
> Thanks in advance for your support.
>
> Attila Kertesz-Farkas
> University of Washington
>
>
>
>
>
>
>
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