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
On Sat, Jun 18, 2016 at 2:59 AM, Vijay Kumar <nayaganv...@gmail.com> wrote:
> 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
>
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