Made a mess of the example as Sequest used chymotrypsin while the TPP pepXML creation process was set to trypsin. The following is a better example:
Sequest output file: 10HNE-1ACO-Trypsin4-Orbit1.8062.8062.2.out SEQUEST v.28 (rev. 13), (c) 1998-2007 Molecular Biotechnology, Univ. of Washington, J.Eng/S.Morgan/J.Yates Licensed to Thermo Fisher Scientific Inc. 02/22/2012, 07:00 PM, 0.3 sec. on VCU-D409FC038FB (M+H)+ mass = 1745.88017 ~ 0.0262 (+2), fragment tol = 0.0100, MONO/ MONO total inten = 8137.7, lowest Sp = 1.8, # matched peptides = 2361 # amino acids = 267050, # proteins = 49378, C:\Xcalibur\database \Aconitase_Pig_RefSeq_20120219_GPM_cRAP_DECOY.fasta ion series nABY ABCDVWXYZ: 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 display top 10/1, ion % = 0.0, CODE = 001050 (M* +15.99492) (C# +101.10922) (H@ +158.13068) (K^ +158.13068) (K~ +140.12012) (nt] -17.02655) C=160.03064 Enzyme:Trypsin(KR/P) (3) # Rank/Sp Id# (M+H)+ deltCn XCorr Sp Sf Ions Reference Peptide --- -------- -------- -------- ------ ------ ----- ---- ---- --------- ------- 1. 1 / 1 1 1745.87448 0.0000 3.4809 610.9 0.93 15/30 gi|47522738|ref|NP_999119.1| K.Q]GLLPLTFADPADYNK.I 2. 2 / 4 24102 1745.87448 0.7340 0.9259 33.8 0.00 4/26 gi|47523048|ref|NP_999285.1| K.K]VVYKQYQDESFTK.R 3. 3 / 37 17482 1745.89245 0.7641 0.8211 12.5 0.00 3/24 gi|335297918|ref|XP_003131644.2| R.FRK^DMM*KNASESK.L 4. 4 / 5 29008 1745.85672 0.7694 0.8028 32.4 0.00 4/26 decoy_4319 +1 R.LFCIYSTLHESFTK.L 5. 5 / 15 42361 1745.89694 0.7725 0.7919 20.0 0.00 3/28 decoy_17672 K.EPVSSGLPNRQWTFK.S 6. 6 / 8 401 1745.90434 0.7808 0.7630 26.2 0.00 3/24 gi|358679347|ref|NP_001240636.1| K.E]HVK~WVHAEM*VNK.N 7. 7 / 62 6413 1745.86661 0.7821 0.7584 8.3 0.00 2/28 gi|311250321|ref|XP_003124098.1| R.YEVC#LAGGSGLDEFK.F 8. 8 / 77 21448 1745.89561 0.7843 0.7507 5.8 0.00 2/28 gi|311259750|ref|XP_003128242.1| R.Y]GSH@DGGSAAPDGK^K.K 9. 9 / 7 6126 1745.86208 0.7875 0.7395 28.1 0.00 4/22 gi|311252102|ref|XP_003124922.1| R.KWPRQYEWFFMK.L 10. 10 / 77 10016 1745.85607 0.7887 0.7356 5.8 0.00 2/26 gi|350592534|ref|XP_001924671.3| R.VGEYKKM*QQM*DTKK.L 1. 1 gi|47522738|ref|NP_999119.1| aconitate hydratase, mitochondrial precursor, minus transit peptide [Sus scrofa] TPP pepXML result: <?xml version="1.0" encoding="UTF-8"?> <?xml-stylesheet type="text/xsl" href="http://regis- web.systemsbiology.net/pepXML_std.xsl"?> <msms_pipeline_analysis date="2012-02-23T16:10:09" xmlns="http://regis- web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/ XMLSchema-instance" xsi:schemaLocation="http://regis- web.systemsbiology.net/pepXML C:\Inetpub\wwwrootpepXML_v117.xsd" summary_xml="c:/Inetpub/wwwroot/ISB/data/extension/N_Term_Example/ 10HNE-1ACO-Trypsin4-Orbit1.pep.xml"> <msms_run_summary base_name="c:/Inetpub/wwwroot/ISB/data/extension/ N_Term_Example/10HNE-1ACO-Trypsin4-Orbit1" raw_data_type="raw" raw_data="(null)"> <sample_enzyme name="trypsin"> <specificity cut="KR" no_cut="P" sense="C"/> </sample_enzyme> <search_summary base_name="c:/Inetpub/wwwroot/ISB/data/extension/ N_Term_Example/10HNE-1ACO-Trypsin4-Orbit1" search_engine="SEQUEST" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" out_data_type="out" out_data=".tgz" search_id="1"> <search_database local_path="C:\Inetpub\wwwroot\ISB\data\dbase \Aconitase_Pig_RefSeq_20120219_GPM_cRAP_DECOY.fasta" type="AA"/> <aminoacid_modification aminoacid="M" massdiff="15.9949" mass="147.0354" variable="Y" symbol="*"/> <aminoacid_modification aminoacid="C" massdiff="101.1092" mass="261.1399" variable="Y" symbol="#"/> <aminoacid_modification aminoacid="H" massdiff="158.1307" mass="295.1896" variable="Y" symbol="@"/> <aminoacid_modification aminoacid="K" massdiff="158.1307" mass="286.2256" variable="Y" symbol="^"/> <aminoacid_modification aminoacid="K" massdiff="140.1201" mass="268.2151" variable="Y" symbol="~"/> <aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.0306" variable="N"/> <terminal_modification terminus="n" massdiff="-17.0265" mass="-16.0187" variable="Y" symbol="]" protein_terminus="N"/> <parameter name="peptide_mass_tol" value="15.000"/> <parameter name="fragment_ion_tol" value="0.010"/> <parameter name="ion_series" value=" 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0"/> <parameter name="max_num_differential_AA_per_mod" value="4"/> <parameter name="nucleotide_reading_frame" value="0"/> <parameter name="num_output_lines" value="10"/> <parameter name="remove_precursor_peak" value="0"/> <parameter name="ion_cutoff_percentage" value="0.0"/> <parameter name="match_peak_count" value="0"/> <parameter name="match_peak_allowed_error" value="1"/> <parameter name="match_peak_tolerance" value="1.0"/> <parameter name="protein_mass_filter" value="0 0"/> <parameter name="sequence_header_filter" value=""/> </search_summary> <spectrum_query spectrum="10HNE-1ACO-Trypsin4-Orbit1.8062.8062.2" start_scan="8062" end_scan="8062" precursor_neutral_mass="1744.8729" assumed_charge="2" index="1"> <search_result> <search_hit hit_rank="1" peptide="QGLLPLTFADPADYNK" peptide_prev_aa="K" peptide_next_aa="I" protein="gi|47522738|ref| NP_999119.1|" num_tot_proteins="1" num_matched_ions="15" tot_num_ions="30" calc_neutral_pep_mass="1744.8672" massdiff="+0.005690" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="xcorr" value="3.481"/> <search_score name="deltacn" value="0.734"/> <search_score name="deltacnstar" value="0.000"/> <search_score name="spscore" value="610.9000"/> <search_score name="sprank" value="1"/> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> David Simpson Virginia Commonwealth University -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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