Difference between mxML and mzXML format

[Vijay Kumar]

Hi,

 when i am running my mzML data using comet i got load spectra Number is 694.

when i am running the same data in mzXML format using same comet parameters the load spectra Number is 4508.

Is it possible to get different number of spectra in different format for same data?

can any one tell what may be the reason?

EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/mzXML& c:\Inetpub\tpp-bin\comet -Pc:/Inetpub/wwwroot/ISB/data/parameters/comet.params -Nc:/Inetpub/wwwroot/ISB/data/parameters/17052016_NISHAD_ITRAQ_1 -Dc:/Inetpub/wwwroot/ISB/data/parameters/Chicken_DECOY.fa 17052016_NISHAD_ITRAQ_1.mzXML 

 Comet version "2016.01 rev. 2"

 Search start:  06/18/2016, 02:08:00 AM
 - Input file: 17052016_NISHAD_ITRAQ_1.mzXML
   - Load spectra: 4508

EXECUTING: cd c:/Inetpub/wwwroot/ISB/data& c:\Inetpub\tpp-bin\comet -Pc:/Inetpub/wwwroot/ISB/data/parameters/comet.params -Nc:/Inetpub/wwwroot/ISB/data/parameters/17052016_NISHAD_ITRAQ_1 -Dc:/Inetpub/wwwroot/ISB/data/parameters/Chicken.fa 17052016_NISHAD_ITRAQ_1.mzML 

 Comet version "2016.01 rev. 2"

 Search start:  06/18/2016, 03:22:02 PM
 - Input file: 17052016_NISHAD_ITRAQ_1.mzML
   - Load spectra: 694

[Jimmy Eng]

Vijay,

The likely reason you're seeing differences in spectrum counts loaded by Comet is that you have different data in the converted files.  It's not an issue with the two formats nor Comet but that the converted data is different in your two files.  Fix that and you'll see the two formats give you the same numbers.  To fix, start with the raw file and use a tool like msconvert to convert to mzXML and mzML without changing any other options; if you do this then I'm confident you'll get the same spectrum counts.   I just went through that little conversion exercise to hopefully convince you that the issue is likely that your two files were generated/converted differently:

[engj.engj-PC-64]> comet.exe LTQ_FT.mzML

 Comet version "2016.01 rev. 2"

 Search start:  06/21/2016, 08:30:28 PM

 - Input file: LTQ_FT.mzML

   - Load spectra: 5473

     - Search progress: 100%

     - Post analysis:  done

 Search end:    06/21/2016, 08:30:52 PM

[engj.engj-PC-64]> comet.exe LTQ_FT.mzXML

 Comet version "2016.01 rev. 2"

 Search start:  06/21/2016, 08:30:56 PM

 - Input file: LTQ_FT.mzXML

   - Load spectra: 5473

     - Search progress: 100%

     - Post analysis:  done

 Search end:    06/21/2016, 08:31:18 PM

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[Vijay Kumar]

Hi Jimmy,

My data is from WATERS QTOP, i converted my raw data using proteowizard msconvert tools to convert to mzML and mzXML data  without applying any filter for both data format. Still i will check once again data conversion and then run TPP.

When i am running TPP the search progress not showing complete 100%, instead of less than 100% i.e 64%, 34% but next it showing  post analysis: done; Search end. Is it complete 100% search or not? 

Comet version "2016.01 rev. 2"

 Search start:  06/22/2016, 12:01:13 PM
 - Input file: 17052016_NISHAD_ITRAQ_1.mzML
   - Load spectra: 694
     - Search progress:   0%      0%      0%      0%      0%      0%      0%      0%      0%      0%      0%      0%      0%      0%      0%      0%      1%      1%      1%      1%      1%      1%      1%      1%      1%      1%      1%      1%      1%      1%      2%      2%      2%      2%      2%      2%      2%      2%      2%      2%      2%      2%      2%      2%      3%      3%      3%      3%      3%      3%      3%      3%      3%      3%      3%      3%      3%      3%      4%      4%      4%      4%      4%      4%      4%      4%      4%      4%      4%      4%      4%      4%      4%      5%      5%      5%      5%      5%      5%      5%      5%      5%      5%      5%      5%      5%      5%      5%      5%      6%
     - Post analysis:  done 

 Search end: 06/22/2016, 12:02:00 PM   

[Jimmy Eng]

If it shows "Search end:" then the search is 100% complete.  The percentage bar doesn't necessarily go to 100% depending on the scan number of the last MS/MS scan versus the total number of scan in your file.  When the percentage complete ends before 100%, it's an indication that a large number of the last scans are presumably MS1 scans (last 36% of the scans in your case).  If that shouldn't be the case, you'll have to find some tool to inspect your mzML file, maybe the SeeMS graphical tool from ProteoWizard, to see how many MS/MS scans are really encoded in that file.  You can share it with me (via something like Dropbox) if you'd like me to look at that mzML file for you.