Dear Eric
I see now the same thing:
$ /home/hr/openmsall/source/THIRDPARTY/Linux/64bit//spectrast -V
-sLtestLib.splib spectra.mzXML
SpectraST started at Sat Oct 21 02:18:54 2017.
VERBOSE MODE...
Library File loaded: "testLib.splib".
Sorting query spectra in all mzXML files by precursor m/z before
searching...DONE!
Now searching query: spectra.00001.00001.536870927 (PrecursorMZ =
8.98729e-315; PrecursorCharge = 536870927)
Found 0 candidate(s)... Comparing... DONE! Top hit: NO_MATCH
Now searching query: spectra.00002.00002.0 (PrecursorMZ =
8.98729e-315; PrecursorCharge = 2,3,4,5,6)
Found 0 candidate(s)... Comparing... DONE! Top hit: NO_MATCH
Now searching query: spectra.00003.00003.0 (PrecursorMZ = 8.98729e-315)
Found 0 candidate(s)... Comparing... DONE! Top hit: NO_MATCH
Finished searching "spectra.mzXML" (3 spectra searched.)
Output written to "/home/hr/openmsall/builds/openms/spectra.pep.xml".
Total Number of Searches Performed = 3; Run Time per Search = 0.6667 seconds.
Total Run Time = 2 seconds.
SpectraST finished at Sat Oct 21 02:18:56 2017 without error.
so clearly there is a parsing error with the mzXML file. It seems that
precursor charge and precursormz are not initialized properly here,
but they are in the file. Do you see what is going on here? The mzXML
file is based on this file:
https://github.com/OpenMS/OpenMS/blob/develop/src/tests/topp/THIRDPARTY/spectra_comet.mzML
which I converted to mzXML. The file appears to be an LTQ Velos file
that was generated by XCalibur and converted with proteowizard.
Thanks for looking into this
Hannes
On Fri, Oct 20, 2017 at 6:57 PM, Eric Deutsch
<[email protected]> wrote:
> I ran SpectraST on your file with –V and it seems to show that it is not
> reading the precursor mz from you file somehow. All the precursormzs in the
> verbose output are 0. I peeked in the file and I do see precursor mzs in
> there, but I don’t know if they are encoded correctly.
>
>
>
> Where did this mzXML file come from?
>
>
>
>
>
> From: [email protected]
> [mailto:[email protected]] On Behalf Of Hannes Roest
> Sent: Friday, October 20, 2017 3:15 PM
> To: spctools-discuss <[email protected]>
> Subject: Re: [spctools-discuss] spectrast produces empty output file
>
>
>
> Dear Eric
>
>
>
> Thanks for your analysis
>
>
>
> 1. I found that mzXML worked better with SpectraST and the mzML file did not
> work at all:
>
>
>
> $ spectrast -sLtestLib.splib spectra.mzML
>
> SpectraST started at Fri Oct 20 18:06:18 2017.
>
> Library File loaded: "testLib.splib".
>
> Total Number of Searches Performed = 0; Run Time per Search = inf seconds.
>
> Total Run Time = 2 seconds.
>
> SpectraST finished at Fri Oct 20 18:06:20 2017 without error.
>
>
>
> $ spectrast -sLtestLib.splib spectra.mzXML
>
> SpectraST started at Fri Oct 20 18:07:06 2017.
>
> Library File loaded: "testLib.splib".
>
> Sorting query spectra in all mzXML files by precursor m/z before
> searching...DONE!
>
> Searching...10%...20%...30%...DONE!
>
> Finished searching "spectra.mzXML" (3 spectra searched.)
>
> Output written to "/home/hr/openmsall/builds/openms/spectra.pep.xml".
>
> Total Number of Searches Performed = 3; Run Time per Search = 0.6667
> seconds.
>
> Total Run Time = 2 seconds.
>
> SpectraST finished at Fri Oct 20 18:07:08 2017 without error.
>
>
>
> 2. Yes there are only two as comet did only find matches for 2 spectra.
> However, searching a library of 2 spectra against a file of 3 spectra
> should still work?
>
> 3. These are "MaxQuant compatible CR". I have removed those but without any
> change in result. Unfortunately.
>
>
>
> Hannes
>
>
> On Friday, October 20, 2017 at 5:57:45 PM UTC-4, Eric Deutsch wrote:
>
> Hi Hannes, I had a quick peek at your file and while I didn’t do any testing
> a few things come to mind.
>
>
>
> 1) It could be that because you’re using mzXML (you meant to use mzML,
> didn’t you? ;-) SpectraST might not be not detecting that these are HCD
> spectra when building the library? The peptides are labeled (CID) when I
> they should be labeled (HCD) I assume? When creating the library, maybe
> -cIHCD would help? Just guessing
>
>
>
> 2) Unless I mis-count, there are only 2 spectra in the sptxt?
>
>
>
> 3) The mzML has some unusual carriage returns in the third spectrum. It
> could be causing some problem possibly..
>
>
>
> I would investigate those first, but maybe it’s something else..
>
>
>
> Eric
>
>
>
>
>
>
>
>
>
> From: [email protected] [mailto:[email protected]] On
> Behalf Of Hannes Roest
> Sent: Friday, October 20, 2017 1:58 PM
> To: spctools-discuss <[email protected]>
> Subject: [spctools-discuss] spectrast produces empty output file
>
>
>
> Dear Henry
>
> I am trying to set up a minimal example for a spectral library search, but I
> cannot get it to work. I have a spectral library and a corresponding mzXML
> file:
>
> $ spectrast -sLtestLib.splib spectra.mzXML
> SpectraST started at Fri Oct 20 16:43:54 2017.
> Library File loaded: "testLib.splib".
> Sorting query spectra in all mzXML files by precursor m/z before
> searching...DONE!
> Searching...10%...20%...30%...DONE!
> Finished searching "spectra.mzXML" (3 spectra searched.)
> Output written to "/home/hr/openmsall/builds/openms/spectra.pep.xml".
> Total Number of Searches Performed = 3; Run Time per Search = 1 seconds.
> Total Run Time = 3 seconds.
> SpectraST finished at Fri Oct 20 16:43:57 2017 without error.
>
> however, the resulting file spectra.pep.xml appears to be empty. Is there
> any reason for this or any parameter I can change to make this example work?
> Note that I generated the spectral library from that same mzXML file
> (searched with comet) and I expect that the spectra match perfectly, so I
> find an empty result file an unexpected outcome.
>
> Thanks
>
> Hannes
>
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