irt issue

Srinivas Srikanth

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Mar 3, 2020, 7:41:28 PM3/3/20

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Hi,

I have a pepxml from iprophet combining results from Mascot/X!Tandem and MSGF+. When I am trying to create a spectral library using Spectrast with the following command:

spectrast -cNspeclib -cICID-QTOF -cP0.814339 -c_IRTirt.txt -Lspectrastlog_hek.log mascot_xtandem_msgfp_combine.pep.xml

I get and error log which says RT inversion detected at iRT 68.168 for some files and then it creates an empty splib file. Can you tell me what does this error exactly mean?

ERROR PEPXML IMPORT: RT normalization by linear interpolation. Found 21 landmarks in MS run "170825_pc4_hek_2dcon_13". RT inversion detected at iRT = 68.8618. No RT normalization performed.

Also, does spectrast support mzml or we always need mzXML?

Regards,

Srikanth

Eric Deutsch

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Mar 4, 2020, 8:35:33 PM3/4/20

to spctools...@googlegroups.com, Eric Deutsch

Hi Srikanth, I can confirm that SpectraST supports mzML files. In fact we always/only use mzML files.

As far as the iRT error, I am not familiar with this. I could only speculate. Maybe Henry or David have ideas?

Thanks,

Eric

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Srinivas Srikanth

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Mar 9, 2020, 7:37:31 PM3/9/20

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Hi Eric,

I get this error and then it tries to find spectra in an MzXML file, even though I provide mxML in the directory. And the resulting library is empty at the end.

Regards,

Srikanth

On Thursday, March 5, 2020 at 12:35:33 PM UTC+11, Eric Deutsch wrote:

Hi Srikanth, I can confirm that SpectraST supports mzML files. In fact we always/only use mzML files.

As far as the iRT error, I am not familiar with this. I could only speculate. Maybe Henry or David have ideas?

Thanks,
Eric

From: spctools...@googlegroups.com <spctools...@googlegroups.com> On Behalf Of Srinivas Srikanth
Sent: Tuesday, March 3, 2020 4:40 PM
To: spctools-discuss <spctools...@googlegroups.com>
Subject: [spctools-discuss] irt issue

Hi,

I have a pepxml from iprophet combining results from Mascot/X!Tandem and MSGF+. When I am trying to create a spectral library using Spectrast with the following command:

spectrast -cNspeclib -cICID-QTOF -cP0.814339 -c_IRTirt.txt -Lspectrastlog_hek.log mascot_xtandem_msgfp_combine.pep.xml

I get and error log which says RT inversion detected at iRT 68.168 for some files and then it creates an empty splib file. Can you tell me what does this error exactly mean?

ERROR PEPXML IMPORT: RT normalization by linear interpolation. Found 21 landmarks in MS run "170825_pc4_hek_2dcon_13". RT inversion detected at iRT = 68.8618. No RT normalization performed.

Also, does spectrast support mzml or we always need mzXML?

Regards,
Srikanth

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