• Sign In
  1. Requests

SQL Failure Error with Peptide Library

support

View Request

view list print
SQL Failure Error with Peptide Library ed3  2022-01-15 10:16
 

Hello,

I have been having trouble making a peptide library when I import my pep.XML file. Please see the attached picture to see the error message I receive. I am not sure if this is an issue with the pep.XML file, or the mzXML file that I am using, but any help with this error would be greatly appreciated.

Thank You,
Ed
 
 
Nick Shulman responded:  2022-01-15 10:46
Was there a "More Info" button on that message box?
Skyline message boxes usually have a copy button in the lower left corner which copies to the clipboard the text as well as whatever would be revealed by the More Info button. If you could send us the full text of that message it will give a better idea of where the error is happening.

I imagine the error probably does have something to do with the pep.xml file. "NaN" is a symbol that can mean "Not a number". It sounds like BiblioSpec is trying to insert that value into the database (.blib file), and is not using the correct syntax to do that. Probably, BiblioSpec is only trying to do this because of some incorrect data that it found in the pep.xml file, but I'm not sure.

If you send us your pep.xml file and the spectrum file(s) that go with it (i.e. your mzXML file), then we will probably be able to figure out what is going wrong.

If those files are less than 50MB you can attach them to this support request. Otherwise, you can upload them here:
https://skyline.ms/files.url
-- Nick
 
ed3 responded:  2022-01-15 11:43
Hi Nick,

There was a more info button, here is what it said:

"System.IO.IOException: ERROR: SQL failure. no such column: nan [SQL statement 'INSERT INTO Modifications(RefSpectraID, position, mass) VALUES(353,16,-nan)', return code 1]

Command-line: C:\Users\Eduardo De La Toba\AppData\Local\Apps\2.0\9NQC1JQ6.CH6\09DPVGYQ.NMT\skyl..tion_e4141a2a22107248_0015.0002_b6130d78fa8ea9a3\BlibBuild -s -A -H -o -c 0.95 -i QC4 -S "C:\Users\Eduardo De La Toba\AppData\Local\Temp\tmp773.tmp" "C:\Users\Eduardo De La Toba\Documents\Exosome Project\ExerV Project\Skyline\QC4.redundant.blib"
Working directory: C:\Users\Eduardo De La Toba\Documents\Exosome Project\ExerV Project\Skyline
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 149
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_21_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_21_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 157"

I have also uploaded my pep.XML and mzXML file to the link you provided. Thanks for your assistance.

Ed
 
Nick Shulman responded:  2022-01-15 14:47

Thank you for sending those files.

I can get this error to happen on my computer with both the Skyline and Skyline-Daily that I have installed, but I cannot get it to happen under the debugger so I cannot be sure what is going on.

One thing I noticed about that .pep.xml file is that the <search hit peptide=" things have a modified peptide sequence in them, which I am pretty sure they are not supposed to have.
For instance:

        <search_hit hit_rank="1" peptide="M(+15.99)M(+15.99)PHANKVTQTFGENM(+15.99)QK" calc_neutral_pep_mass="2138.9548" massdiff="6.168846973558103" num_tot_proteins="1" protein="P06728|APOA4_MOUSE" protein_descr="Apolipoprotein A-IV OS=Mus musculus OX=10090 GN=Apoa4 PE=1 SV=3" protein_mw="45029.01815908203">
          <modification_info modified_peptide="M(+15.99)M(+15.99)PHANKVTQTFGENM(+15.99)QK">
            <mod_aminoacid_mass position="1" mass="147.03540500854493"></mod_aminoacid_mass>
            <mod_aminoacid_mass position="2" mass="147.03540500854493"></mod_aminoacid_mass>
            <mod_aminoacid_mass position="16" mass="147.03540500854493"></mod_aminoacid_mass>
          </modification_info>
          <search_score name="-10lgP" value="83.62647"/>
          <search_score name="confidence" value="0.9999993"/>
        </search_hit>

That does not appear to be valid, partly because that first peptide=" is supposed to be the unmodified sequence, and partly because the modifications can't seem to agree on whether their mass is 15.99 or 147.035

What ends up getting put into the .blib file ends up looking like this. where the positions of those +147 modifications are incorrect, because there were extra characters which were not amino acids in what was supposed to be the unmodified peptide sequence:
M+16.0M(+15.9[+147.0]9)PHANKVTQTFGENM(+15.99)QK

I will ask around and see whether there is anything that we can do about having BiblioSpec give you a better error message. I think the pep.xml file is probably not valid and you should not be able to build a library from it.
-- Nick
 
ed3 responded:  2022-01-15 17:00

Hi Nick,

I think I actually fixed the problem. I just modified the pepxml file so that the peptide=" does not contain the PTM. Upon doing so, this lets me build the library.

Thanks for your assistance,
Ed