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. 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