dear list, i found my way around...
apparently a solution which works is to copy the sequest.params file into each of the subdirectories which are created for each mzXML file. afterwards, a command like: /usr/local/apps/tpp/bin/Out2XML /IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10105_c 1 -all will work. cheers, andreas On Mon, Oct 5, 2009 at 12:51 PM, Andreas Quandt <[email protected]>wrote: > dear list, > > i executed following command: > > /usr/local/apps/tpp/bin/Out2XML > /IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10105_c -all > -P/IMSB/results/workflow/350/sorcerer/output/13200/original/sequest.params > > where the sequest.params file looks like this: > > > > ------------------------------------------------------------------------------------------------- > > ### PREPARE OPTIONS > database_name = /home/sorcerer/fasta/sp_9606.fasta > mass_type_parent = 1 > max_num_internal_cleavage_sites = 2 > min_peptide_mass = 400 > max_peptide_mass = 6000 > add_C_Cysteine = 57.021465 > ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 > NumEnzymeTermini = 1 > > first_database_name = sp_9606_default > execution_directory = /IMSB/results/workflow/350/sorcerer > #output_directory = > > ## Peptide Search options > peptide_mass_units = 2 # 0=AMU, 1=MMU, 2=PPM > peptide_mass_tolerance = 25.0 # mass window of peptides to search > enable_isotope_mass_shift = 0 # 0=disabled, 1=enabled > isotope_mass_shift = 1.003355 # +/- isotope mass shift (amu) > enable_reversed_peptides = 0 # 0=disabled, 1=enabled > enable_pseudodigest_reversed_peptides = 0 # 0=disabled, 1=enabled > > ## Static Mass Modifications > add_Nterm_peptide = 0.0000 # static peptide N-terminus mod > add_Cterm_peptide = 0.0000 # static peptide C-terminus mod > > ## PTM options > # Diff residues must be specified in UPPER-CASE. Increasing PTM options > may > # exponentially increase search times. > diff_search_options = 15.99492 M 0.98402 N 0.0000 M 0.0000 M 0.0000 M > 0.0000 M > term_diff_search_options = 0.0000 0.0000 # C-term N-term PTM masses > max_num_differential_AA_per_mod = 3 # max instances of each PTM type > max_num_differential_per_peptide = 4 # max PTM instances in a peptide > > ## Peptide Scoring options > mass_type_fragment = 1 # 0=average or 1=monoisotopic > masses > ion_cutoff_percentage = 0.0000 # ion ratio minimum threshold > num_results = 2000 # number of Sp results sent to > XCorr > > ## Output options > num_output_lines = 10 # number of scored peptides to > output > num_description_lines = 0 # number of full proteins to > report > print_duplicate_references = 10 > > ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 # legacy for > TPP? > > > > > enable_tpp_processing = 0 > xinteract_options = -Op > > > enable_scaffoldbatch_processing = 0 > app_description = My Sorcerer search #appears in Scaffold Experiment field > scaffoldbatch_run_tandem = 0 > scaffoldbatch_export_sfd_file = myscaffold.sfd > scaffoldbatch_export_protxml_file = > scaffoldbatch_connect_to_ncbi = 1 > scaffoldbatch_fasta_database_file = > /home/sorcerer/fasta/ipi.HUMAN.v3.52.fasta > scaffoldbatch_input_dir = original/ > > > > > > final_post_processing_command = makePwd777.sh > insert_protein_refs_into_outs = 1 > > > ------------------------------------------------------------------------------------------------- > > problem is that the Out2XML produces a pepXML file which is too small. also > when viewing the file in petunia, it says following > > displaying * 6558 * of 6558 total spectra, page 1 of 132 > * 1 unique peptides, * * 1 unique stripped peptides, 1 unique proteins, 0 > single hits > * > > spectrum xcorr deltacn sprank ions peptide protein calc_mass > O08-10100_c.00002.00002.2<http://imsb-ra-tpp/tpp/cgi-bin/sequest-tgz-out.cgi?OutFile=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00002.00002.2.out>[image: > SpectraST]<http://imsb-ra-tpp/tpp/html/post_to_spectrast.html?fasta=sp_9606_default&tppcgi=/tpp/cgi-bin/&Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00002.00002.2.dta> > [unavailable] [unavailable] [unavailable] > /<http://imsb-ra-tpp/tpp/cgi-bin/plot-msms.cgi?MassType=1&NumAxis=1&ShowB=1&ShowY=1&ShowY2=1&Pep=&Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00002.00002.2.dta&Global_Mod=CS57.021500000000003&Global_Mod=MV15.994899999999999&Global_Mod=NV0.98399999999999999> > ..[image: > PeptideAtlas]<https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?organism_name=Any;search_key=%25%25;action=GO> > [unavailable] > O08-10100_c.00004.00004.2<http://imsb-ra-tpp/tpp/cgi-bin/sequest-tgz-out.cgi?OutFile=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00004.00004.2.out>[image: > SpectraST]<http://imsb-ra-tpp/tpp/html/post_to_spectrast.html?fasta=sp_9606_default&tppcgi=/tpp/cgi-bin/&Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00004.00004.2.dta> > [unavailable] [unavailable] [unavailable] > /<http://imsb-ra-tpp/tpp/cgi-bin/plot-msms.cgi?MassType=1&NumAxis=1&ShowB=1&ShowY=1&ShowY2=1&Pep=&Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00004.00004.2.dta&Global_Mod=CS57.021500000000003&Global_Mod=MV15.994899999999999&Global_Mod=NV0.98399999999999999> > ..[image: > PeptideAtlas]<https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?organism_name=Any;search_key=%25%25;action=GO> > [unavailable] > O08-10100_c.00005.00005.2<http://imsb-ra-tpp/tpp/cgi-bin/sequest-tgz-out.cgi?OutFile=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00005.00005.2.out>[image: > SpectraST]<http://imsb-ra-tpp/tpp/html/post_to_spectrast.html?fasta=sp_9606_default&tppcgi=/tpp/cgi-bin/&Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00005.00005.2.dta> > [unavailable] [unavailable] [unavailable] > /<http://imsb-ra-tpp/tpp/cgi-bin/plot-msms.cgi?MassType=1&NumAxis=1&ShowB=1&ShowY=1&ShowY2=1&Pep=&Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00005.00005.2.dta&Global_Mod=CS57.021500000000003&Global_Mod=MV15.994899999999999&Global_Mod=NV0.98399999999999999> > ..[image: > PeptideAtlas]<https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?organism_name=Any;search_key=%25%25;action=GO> > [unavailable] > O08-10100_c.00009.00009.2<http://imsb-ra-tpp/tpp/cgi-bin/sequest-tgz-out.cgi?OutFile=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00009.00009.2.out>[image: > SpectraST]<http://imsb-ra-tpp/tpp/html/post_to_spectrast.html?fasta=sp_9606_default&tppcgi=/tpp/cgi-bin/&Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00009.00009.2.dta> > [unavailable] [unavailable] [unavailable] > /<http://imsb-ra-tpp/tpp/cgi-bin/plot-msms.cgi?MassType=1&NumAxis=1&ShowB=1&ShowY=1&ShowY2=1&Pep=&Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00009.00009.2.dta&Global_Mod=CS57.021500000000003&Global_Mod=MV15.994899999999999&Global_Mod=NV0.98399999999999999> > ..[image: > PeptideAtlas]<https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?organism_name=Any;search_key=%25%25;action=GO> > [unavailable] > O08-10100_c.00012.00012.2<http://imsb-ra-tpp/tpp/cgi-bin/sequest-tgz-out.cgi?OutFile=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00012.00012.2.out>[image: > SpectraST]<http://imsb-ra-tpp/tpp/html/post_to_spectrast.html?fasta=sp_9606_default&tppcgi=/tpp/cgi-bin/&Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00012.00012.2.dta> > [unavailable] [unavailable] [unavailable] > /<http://imsb-ra-tpp/tpp/cgi-bin/plot-msms.cgi?MassType=1&NumAxis=1&ShowB=1&ShowY=1&ShowY2=1&Pep=&Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00012.00012.2.dta&Global_Mod=CS57.021500000000003&Global_Mod=MV15.994899999999999&Global_Mod=NV0.98399999999999999> > ..[image: > PeptideAtlas]<https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?organism_name=Any;search_key=%25%25;action=GO> > [unavailable] > > but when clicking on one of the spectrum, the scores are visible: > > # Rank/Sp (M+H)+ deltCn XCorr Sp Ions Reference > Peptide > > --- -------- -------- ------ ------ ----- ---- --------- > ------- > 1. 1 / 84 998.50541 0.0000 1.3657 175.4 9/18 > <http://imsb-ra-tpp/tpp/cgi-bin/plot-msms.cgi?Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00002.00002.2.dta&MassType=1&Pep=QPFATGAAVH> > DECOY_Q8IWD4 > <http://imsb-ra-tpp/tpp/cgi-bin/comet-fastadb.cgi?Ref=DECOY_Q8IWD4&Db=sp_9606.fasta&Pep=QPFATGAAVH&MassType=1> > +1 > <http://imsb-ra-tpp/tpp/cgi-bin/comet-fastadb.cgi?Db=sp_9606.fasta&Pep=QPFATGAAVH&MassType=1> > R.QPFATGAAVH > <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=QPFATGAAVH>.K > > DECOY_Q8IWD4_ISOFORM_2 \ID=CC117_HUMAN \MODRES= > \VARIANT=(38|R|S)(163|S|N) \ACOR=Q8IWD4 \NCBITAXID=9606 \DE=Coiled-coil > domain-containing protein 117 [ISOFORM 2] > 2. 2 / 213 998.52654 0.0515 1.2954 146.8 8/16 > <http://imsb-ra-tpp/tpp/cgi-bin/plot-msms.cgi?Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00002.00002.2.dta&MassType=1&Mod6=115.02694747&Pep=EPKVPNSAR> > Q96PV7 > <http://imsb-ra-tpp/tpp/cgi-bin/comet-fastadb.cgi?Ref=Q96PV7&Db=sp_9606.fasta&Pep=EPKVPNSAR&MassType=1> > +1 > <http://imsb-ra-tpp/tpp/cgi-bin/comet-fastadb.cgi?Db=sp_9606.fasta&Pep=EPKVPNSAR&MassType=1> > T.EPKVPN#SAR > <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=EPKVPNSAR>.A > > Q96PV7_ISOFORM_2 \ID=K1931_HUMAN \MODRES= \VARIANT=(362|P|S) > \ACOR=Q96PV7 \NCBITAXID=9606 \DE=Uncharacterized protein KIAA1931 [ISOFORM 2] > 3. 3 / 78 998.49754 0.1079 1.2183 178.0 9/20 > <http://imsb-ra-tpp/tpp/cgi-bin/plot-msms.cgi?Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00002.00002.2.dta&MassType=1&Pep=MAPPGPASALS> > Q9Y663 > <http://imsb-ra-tpp/tpp/cgi-bin/comet-fastadb.cgi?Ref=Q9Y663&Db=sp_9606.fasta&Pep=MAPPGPASALS&MassType=1> > -.MAPPGPASALS > <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=MAPPGPASALS>.T > > 4. 4 / 108 998.52654 0.1695 1.1343 167.5 9/16 > <http://imsb-ra-tpp/tpp/cgi-bin/plot-msms.cgi?Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00002.00002.2.dta&MassType=1&Pep=PEEALLGNR> > Q5SXM2 > <http://imsb-ra-tpp/tpp/cgi-bin/comet-fastadb.cgi?Ref=Q5SXM2&Db=sp_9606.fasta&Pep=PEEALLGNR&MassType=1> > L.PEEALLGNR > <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=PEEALLGNR>.L > > 5. 5 /1819 998.51530 0.2011 1.0911 75.3 6/18 > <http://imsb-ra-tpp/tpp/cgi-bin/plot-msms.cgi?Dta=/IMSB/results/workflow/350/sorcerer/output/13200/original/O08-10100_c/O08-10100_c.00002.00002.2.dta&MassType=1&Pep=IVSQEPAGTP> > P32926 > <http://imsb-ra-tpp/tpp/cgi-bin/comet-fastadb.cgi?Ref=P32926&Db=sp_9606.fasta&Pep=IVSQEPAGTP&MassType=1> > +1 > <http://imsb-ra-tpp/tpp/cgi-bin/comet-fastadb.cgi?Db=sp_9606.fasta&Pep=IVSQEPAGTP&MassType=1> > K.IVSQEPAGTP > <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=IVSQEPAGTP>.M > > does any of you have an idea,what i am doing wrong? > > cheers, > andreas > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
