Jimmy, I appreciate your kindness.
I'll try to fix by myself. *sincerely,Heeyoun* 2015년 3월 12일 목요일 오전 3시 44분 49초 UTC+9, Jimmy Eng 님의 말: > > 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] > <javascript:>> 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] <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.
