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] > <javascript:>> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
