I have a problem with a variable N-terminal modification that's not being transcribed correctly from Sequest output files to TPP pepXML. I've copied an example below. How do I fix this issue? I'm using TPP 4.5.2 on Windows.
Thanks, David Simpson Virginia Commonwealth University Sequest output: 1HNE-1ACO-Chymo3-LTQ1.10999.10999.2.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. 02/21/2012, 04:22 AM, 14.5 sec. on node1 (M+H)+ mass = 1813.67400 ~ 2.0000 (+2), fragment tol = 1.0000 , AVG/ MONO total inten = 4549.1, lowest Sp = 112.9, # matched peptides = 1207331 # amino acids = 100312932, # proteins = 49378, /usr/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 10/5, ion % = 0.0, CODE = 001050 (M* +15.99492) (C# +101.10922) (H@ +158.13068) (K^ +158.13068) (K~ +140.12011) (K$ +42.01056) (nt] -17.02655) C=160.16519 Enzyme:FWYML_Chymo (4) # Rank/Sp Id# (M+H)+ deltCn XCorr Sp Sf Ions Reference Peptide --- -------- -------- -------- ------ ------ ----- ---- ---- --------- ------- 1. 1 / 1 1 1814.02122 0.0000 3.7584 1016.3 0.92 22/28 gi|47522738|ref|NP_999119.1| -.Q]RAKVAMSHFEPHEY.I 2. 2 / 48 5983 1814.95616 0.4649 2.0110 202.9 0.06 12/28 gi|311253094|ref|XP_003125390.1| F.A]GRYYSSENTRPK$FL.S 3. 3 / 41 1237 1814.02846 0.4919 1.9096 207.1 0.07 12/26 gi|47523006|ref|NP_999263.1| F.LHH@AGKLFNVTK$TF.N 4. 4 / 41 1237 1814.02846 0.4934 1.9041 207.1 0.06 12/26 gi|47523006|ref|NP_999263.1| F.LH@HAGKLFNVTK$TF.N 5. 5 /343 22781 1814.14209 0.5153 1.8218 128.6 0.00 9/24 gi|346644752|ref|NP_001231142.1| W.K]RLFTLK~EEKPK$M.Y 6. 6 / 81 3904 1814.98302 0.5209 1.8006 182.9 0.04 12/26 gi|335288241|ref|XP_001926685.3| L.D]K$IYQEDIFPCLTF.S 7. 7 /343 22781 1814.14209 0.5231 1.7926 128.6 0.00 9/24 gi|346644752|ref|NP_001231142.1| W.K]RLFTLK~EEK$PKM.Y 8. 8 / 96 46183 1815.06456 0.5322 1.7583 179.1 0.02 9/22 decoy_21494 F.K]FK~ELEQNKK^KL.D 9. 9 / 96 46183 1815.06456 0.5348 1.7484 179.1 0.02 9/22 decoy_21494 F.K]FK~ELEQNKKK^L.D 10. 10 /154 969 1814.95939 0.5423 1.7202 161.0 0.02 10/24 gi|254292371|ref|NP_001156878.1| L.N]K$YNRTRYELREF.L 1. 1 gi|47522738|ref|NP_999119.1| aconitate hydratase, mitochondrial precursor, minus transit peptide [Sus scrofa] 2. 5983 gi|311253094|ref|XP_003125390.1| PREDICTED: structural maintenance of chromosomes protein 6 [Sus scrofa 3. 1237 gi|47523006|ref|NP_999263.1| interleukin-18 receptor alpha chain precursor [Sus scrofa 4. 1237 gi|47523006|ref|NP_999263.1| interleukin-18 receptor alpha chain precursor [Sus scrofa 5. 22781 gi|346644752|ref|NP_001231142.1| ADP-ribosylation factor-like protein 6-interacting protein 1 [Sus scrofa pepXML output: <?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="2012-02-23T13:00:14" 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/Example/ Test.pep.xml"> <msms_run_summary base_name="c:/Inetpub/wwwroot/ISB/data/extension/ Example/Test" 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/ Example/Test" search_engine="SEQUEST" precursor_mass_type="average" 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="147.1875" variable="Y" symbol="*"/> <aminoacid_modification aminoacid="C" massdiff="101.1092" mass="261.2695" variable="Y" symbol="#"/> <aminoacid_modification aminoacid="H" massdiff="158.1307" mass="295.2718" variable="Y" symbol="@"/> <aminoacid_modification aminoacid="K" massdiff="158.1307" mass="286.3048" variable="Y" symbol="^"/> <aminoacid_modification aminoacid="K" massdiff="140.1201" mass="268.2942" variable="Y" symbol="~"/> <aminoacid_modification aminoacid="K" massdiff="42.0106" mass="170.1847" variable="Y" symbol="$"/> <aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.1603" variable="N"/> <terminal_modification terminus="n" massdiff="-17.0265" mass="-16.0187" variable="Y" symbol="]" protein_terminus="N"/> <parameter name="peptide_mass_tol" value="2.000"/> <parameter name="fragment_ion_tol" value="1.000"/> <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="1HNE-1ACO-Chymo3-LTQ1.10999.10999.2" start_scan="10999" end_scan="10999" precursor_neutral_mass="1812.6667" assumed_charge="2" index="1"> <search_result> <search_hit hit_rank="1" peptide="QRAKVAMSHFEPHEY" peptide_prev_aa="-" peptide_next_aa="I" protein="gi|47522738|ref| NP_999119.1|" num_tot_proteins="1" num_matched_ions="22" tot_num_ions="28" calc_neutral_pep_mass="1813.0139" massdiff="-0.347220" num_tol_term="1" num_missed_cleavages="2" is_rejected="0"> <search_score name="xcorr" value="3.758"/> <search_score name="deltacn" value="0.465"/> <search_score name="deltacnstar" value="0.000"/> <search_score name="spscore" value="1016.3000"/> <search_score name="sprank" value="1"/> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> -- You 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