Heeyoun, There's an issue with your sqt files generated by ProLuCID. Peptides have strings that look like
HLK.STLAM(15.9949)SPR.QRK whereas the classical SEQUEST sqt files would be K.STLAM*SPR.Q The extra preceding and trailing amino acid characters are not the problem. It's actually the "(15.9949)" modification encoding that is a problem because it doesn't confirm to the SEQUEST sqt format that the Sqt2XML program expects. You will not be able to use the ProLuCID .sqt files through the TPP as-is. Ideally you should ask the ProLuCID developers to output a proper pep.xml file. Alternately ask them for an option to output results in the classical SQT format. Lastly, you can try and edit your sqt files yourself. If you want to attempt to the last option: For your sqt file, the header includes H DiffMod M*=+15.9949 Do a global substitution of "(15.9949)" with "*". Repeat for any other variable modifications, using the modification character specified in the "H DiffMod" lines. After editing your sqt file this way, I ran sqt2xml 20111216_CON_PE_01.sqt xinteract -dReverse 20111216_CON_PE_01.pep.xml The generated interact.pep.xml file had probability scores and looked generally fine (although there is a weird issue related likely related to ProLuCID -> sqt -> pep.xml conversion that exists but shouldn't affect results). In the sqt2xml conversion, you can ignore the warning "attempting to read mzXML/mzML: Unknown file type. No file loaded." That step just attempts to write instrument info to the resulting pep.xml file if available. It's actually a bug the sqt2xml tool that I just fixed, possibly will be available in the next TPP release, but missing this info should not affect downstream analysis. This means you can also ignore the related warnings in the next step of the processing or do what you did to change the unknown data type to mzML. Good luck. - Jimmy On Tue, Mar 10, 2015 at 6:47 PM, Heeyoun Hwang <[email protected]> wrote: > Hi, Jimmy > > Fist of all, I apollogized that I uploaded the wrong files. I took away > your time against my will. > > In my case, SQT2XML still generate the error. > > >sqt2xml *.sqt > params file here: seqest.params > attempting to read mzXML/mzML: Unknown file type. No file loaded. > Done. File created: 20111216_CON_PE_01.pep.xml > > The pep.xml file was generated, but in the nex step, running peptide > prophet, an error again occured. > > c:\Inetpub\tpp-bin\xinteract (TPP v4.7 POLAR VORTEX rev 1, Build > 201405141849 (MinGW)) > PPM mode in Accurate Mass Model ... > running: "C:/Inetpub/tpp-bin/InteractParser "test.pep.xml" > "20111216_CON_PE_01.pep.xml" -L"7"" > file 1: 20111216_CON_PE_01.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01.unknown in > msms_run_summary tag ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01.unknown in > msms_run_summary tag ... > > So, I chaged the file type regeion in the .pep.xml file. > > <msms_run_summary base_name="20111216_CON_PE_01" raw_data_type="unknown" > raw_data="unknown" > ->>>> <msms_run_summary > base_name="20111216_CON_PE_01" raw_data_type="raw" raw_data=".mzML" > > > Then the program is worked well. BUT! > > In the interact.pep.xml file, there is no probablity score and any other > scores. Surely I checked pipline type "sequest"in the main page, ' home > tab'. > > prob spectrum sscan spscore ions2 peptide protein calc_mass > <http://localhost/tpp-bin/ModelParser.cgi?Xmlfile=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/sqtest.pep.xml&Timestamp=2015-03-11T10:21:45&Spectrum=20111216_CON_PE_01.00996.00996.2&Scores=&Prob=> > *20111216_CON_PE_01.00996.00996.2* > <http://localhost/tpp-bin/sequest-tgz-out.cgi?OutFile=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.00996.00996.2.out>*[image: > SpectraST]* > <http://localhost/ISB/html/post_to_spectrast.html?fasta=neXtProt_human_09-19-2014_reversed.fasta&tppcgi=/tpp-bin/&Dta=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.00996.00996.2.dta> > 996 [unavailable] *[spectrum]* > <http://localhost/tpp-bin/plot-msms-js.cgi?PrecursorMassType=1&FragmentMassType=1&PepMass=1036.26&Isobaric=1&Pep=&Dta=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.00996.00996.2.dta> > . > <http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CDD_SEARCH=on&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=%28none%29&EXPECT=1000&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&SERVICE=plain&SET_DEFAULTS.x=41&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&QUERY=> > .[image: PeptideAtlas] > <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?organism_name=Any;search_key=%25%25;action=GO> > <http://localhost/tpp-bin/comet-fastadb.cgi?Ref=&Db=K:%5CHeeyounH%5CMass_data%5Chuman_brain_CID_files%5CneXtProt_human_09-19-2014_reversed.fasta&Pep=&MassType=1&sample_enzyme=trypsin&min_ntt=2> > [unavailable] > <http://localhost/tpp-bin/ModelParser.cgi?Xmlfile=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/sqtest.pep.xml&Timestamp=2015-03-11T10:21:45&Spectrum=20111216_CON_PE_01.01137.01137.2&Scores=&Prob=> > *20111216_CON_PE_01.01137.01137.2* > <http://localhost/tpp-bin/sequest-tgz-out.cgi?OutFile=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.01137.01137.2.out>*[image: > SpectraST]* > <http://localhost/ISB/html/post_to_spectrast.html?fasta=neXtProt_human_09-19-2014_reversed.fasta&tppcgi=/tpp-bin/&Dta=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.01137.01137.2.dta> > 1137 [unavailable] *[spectrum]* > <http://localhost/tpp-bin/plot-msms-js.cgi?PrecursorMassType=1&FragmentMassType=1&PepMass=1262.19&Isobaric=1&Pep=&Dta=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.01137.01137.2.dta> > . > <http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CDD_SEARCH=on&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=%28none%29&EXPECT=1000&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&SERVICE=plain&SET_DEFAULTS.x=41&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&QUERY=> > .[image: PeptideAtlas] > <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?organism_name=Any;search_key=%25%25;action=GO> > <http://localhost/tpp-bin/comet-fastadb.cgi?Ref=&Db=K:%5CHeeyounH%5CMass_data%5Chuman_brain_CID_files%5CneXtProt_human_09-19-2014_reversed.fasta&Pep=&MassType=1&sample_enzyme=trypsin&min_ntt=2> > [unavailable] > <http://localhost/tpp-bin/ModelParser.cgi?Xmlfile=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/sqtest.pep.xml&Timestamp=2015-03-11T10:21:45&Spectrum=20111216_CON_PE_01.01239.01239.2&Scores=&Prob=> > *20111216_CON_PE_01.01239.01239.2* > <http://localhost/tpp-bin/sequest-tgz-out.cgi?OutFile=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.01239.01239.2.out>*[image: > SpectraST]* > <http://localhost/ISB/html/post_to_spectrast.html?fasta=neXtProt_human_09-19-2014_reversed.fasta&tppcgi=/tpp-bin/&Dta=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.01239.01239.2.dta> > 1239 [unavailable] *[spectrum]* > <http://localhost/tpp-bin/plot-msms-js.cgi?PrecursorMassType=1&FragmentMassType=1&PepMass=2018.65&Isobaric=1&Pep=&Dta=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.01239.01239.2.dta> > . > <http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CDD_SEARCH=on&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=%28none%29&EXPECT=1000&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&SERVICE=plain&SET_DEFAULTS.x=41&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&QUERY=> > .[image: PeptideAtlas] > <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?organism_name=Any;search_key=%25%25;action=GO> > <http://localhost/tpp-bin/comet-fastadb.cgi?Ref=&Db=K:%5CHeeyounH%5CMass_data%5Chuman_brain_CID_files%5CneXtProt_human_09-19-2014_reversed.fasta&Pep=&MassType=1&sample_enzyme=trypsin&min_ntt=2> > [unavailable] > <http://localhost/tpp-bin/ModelParser.cgi?Xmlfile=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/sqtest.pep.xml&Timestamp=2015-03-11T10:21:45&Spectrum=20111216_CON_PE_01.01757.01757.3&Scores=&Prob=> > *20111216_CON_PE_01.01757.01757.3* > <http://localhost/tpp-bin/sequest-tgz-out.cgi?OutFile=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.01757.01757.3.out>*[image: > SpectraST]* > <http://localhost/ISB/html/post_to_spectrast.html?fasta=neXtProt_human_09-19-2014_reversed.fasta&tppcgi=/tpp-bin/&Dta=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.01757.01757.3.dta> > 1757 [unavailable] *[spectrum]* > <http://localhost/tpp-bin/plot-msms-js.cgi?PrecursorMassType=1&FragmentMassType=1&PepMass=2721.92&Isobaric=1&Pep=&Dta=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.01757.01757.3.dta> > . > <http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CDD_SEARCH=on&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=%28none%29&EXPECT=1000&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&SERVICE=plain&SET_DEFAULTS.x=41&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&QUERY=> > .[image: PeptideAtlas] > <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?organism_name=Any;search_key=%25%25;action=GO> > <http://localhost/tpp-bin/comet-fastadb.cgi?Ref=&Db=K:%5CHeeyounH%5CMass_data%5Chuman_brain_CID_files%5CneXtProt_human_09-19-2014_reversed.fasta&Pep=&MassType=1&sample_enzyme=trypsin&min_ntt=2> > [unavailable] > <http://localhost/tpp-bin/ModelParser.cgi?Xmlfile=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/sqtest.pep.xml&Timestamp=2015-03-11T10:21:45&Spectrum=20111216_CON_PE_01.08642.08642.2&Scores=&Prob=> > *20111216_CON_PE_01.08642.08642.2* > <http://localhost/tpp-bin/sequest-tgz-out.cgi?OutFile=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.08642.08642.2.out>*[image: > SpectraST]* > <http://localhost/ISB/html/post_to_spectrast.html?fasta=neXtProt_human_09-19-2014_reversed.fasta&tppcgi=/tpp-bin/&Dta=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.08642.08642.2.dta> > 8642 [unavailable] *[spectrum]* > <http://localhost/tpp-bin/plot-msms-js.cgi?PrecursorMassType=1&FragmentMassType=1&PepMass=1472.23&Isobaric=1&Pep=&Dta=c:/Inetpub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.08642.08642.2.dta> > . > <http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CDD_SEARCH=on&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=%28none%29&EXPECT=1000&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&SERVICE=plain&SET_DEFAULTS.x=41&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&QUERY=> > .[image: PeptideAtlas] > <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?organism_name=Any;search_key=%25%25;action=GO> > <http://localhost/tpp-bin/comet-fastadb.cgi?Ref=&Db=K:%5CHeeyounH%5CMass_data%5Chuman_brain_CID_files%5CneXtProt_human_09-19-2014_reversed.fasta&Pep=&MassType=1&sample_enzyme=trypsin&min_ntt=2> > [unavailable > > > > I will share to you the files including interact.pep.xml file. > > Please check the files once again. > > Regards, > > Heeyoun > > Ps. I hope that was a good trip to S. KOREA in the last year. I attended > to your seminar. :) > > > > > > > > > > > 2015년 3월 11일 수요일 오전 1시 5분 44초 UTC+9, Jimmy Eng 님의 말: > >> Heeyoun, >> >> I was able to run the sqt2xml program on your sqt file fine. The sqt >> file you sent me is a little worrisome (see below) but the conversion to >> pepXML did work. Can you tell me what didn't work for you e.g. did it not >> generate an sqt file? What error message are you getting? Or did the >> conversion work for you too but the resulting pepXML file just seemed bad? >> >> If you're not aware, your sqt file has practically no identifications in >> it; there were around 35 peptide matches out of 12,489 spectral queries. >> And all of the peptide matches had sequences that just contained A, C, T or >> G so it appears that you searched a nucleotide database directly without >> telling ProLuCID to do a codon to amino acid translation. When you >> translate this file to pepXML, the bulk of the pepXML file has no >> identifications because that's what's reflected in the input sqt file. >> >> Anyways, let me know if you need me to follow-up with this any further. >> >> - Jimmy >> >> >> >> On Mon, Mar 9, 2015 at 8:55 PM, Heeyoun Hwang <[email protected]> wrote: >> >>> Ok, I sent the files to you. >>> >>> thx. >>> >>> Heeyoun >>> >>> 2015년 3월 10일 화요일 오전 2시 22분 11초 UTC+9, Jimmy Eng 님의 말: >>>> >>>> Can you make the SQT and sequest.params file available to me? Either >>>> email it to me directly or make it available for download. I'll take a >>>> quick look to see what's happening. The mzXML/mzML file is optional; it >>>> will write instrument info into the resulting pep.xml if present. >>>> >>>> - Jimmy >>>> >>>> On Sun, Mar 1, 2015 at 9:59 AM, Heeyoun Hwang <[email protected]> >>>> wrote: >>>> >>>>> >>>>> Hi, >>>>> >>>>> Because of my project, I have to search with sequest or ProLuCID in >>>>> IP2, and generate pep.XML file from *.sqt file for run the peptide >>>>> prophet. >>>>> >>>>> I know that there is no convert program .sqt to .pep.xml in GUI >>>>> version of TPP. >>>>> >>>>> So, I used sqt2xml program in command line, but it is not working. >>>>> >>>>> the snapshots of .sqt, .sequest.param, and ms2 files were attached in >>>>> here. >>>>> >>>>> I also tried change the path of FASTA file in param file, but sqt2xml >>>>> is still not working. >>>>> >>>>> Surely I converted mzXL from .RAW with msconvert. All files are in the >>>>> same directory including .mxML. I also attach the snapshot of my folder. >>>>> >>>>> >>>>> thanks. >>>>> >>>>> Heeyoun Hwang. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "spctools-discuss" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to [email protected]. >>>>> To post to this group, send email to [email protected]. >>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
