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
On Wednesday, June 22, 2016 at 2:09:27 AM UTC+5:30, Jimmy Eng wrote:
>
> 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 <[email protected]
> <javascript:>> 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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