There's a search parameter (print_duplicate_references) which defines printing out the additional protein references that a peptide matches. Should be a straightforward fix to Out2XML to handle these files (which I'll look at next week when I get back if no one has updated the program by that time). To avoid the problem in the near term, set that parameter to 0 (which equals false).
On Fri, Sep 4, 2009 at 12:36 PM, nik<[email protected]> wrote: > > Hello, > > Some SEQUEST *.out files have uncommon format. In these files there > are multiple lines representing the first hit. The second hit > information starts after several lines of first hit information. For > such OUT files get following XML output (below SEQUEST output > example). The second hit information in XML output is wrong. > > Did you come across such OUT files (and see mistake in XML output )? > Please help. > > SEQUEST OUT Example: **************** > > 2009_0813_04.11113.11113.1.out > SEQUEST v.28 (rev. 12), (c) 1998-2007 > Molecular Biotechnology, Univ. of Washington, J.Eng/S.Morgan/J.Yates > Licensed to Thermo Fisher Scientific Inc. > 08/28/2009, 08:46 PM, 0.0 sec. on EIDOTHEA > (M+H)+ mass = 605.89500 ~ 1.5000 (+1), fragment tol = 2.0000, MONO/ > MONO > total inten = 2611.6, lowest Sp = 43.9, # matched peptides = 2351 > # amino acids = 28842, # proteins = 75484, F:\Databases > \Human_NCBI_36_3_Rev.fasta, F:\Databases\Human_NCBI_36_3_Rev.fasta.hdr > 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 20/5, ion % = 0.0, CODE = 101040 > C=160.03064 M=147.03540 Enzyme:Trypsin(KR) (2) > > # Rank/Sp Id# (M+H)+ deltCn XCorr Sp Ions > Reference Peptide > --- -------- -------- -------- ------ ------ ----- ---- > --------- ------- > 1. 1 / 6 10663 607.26819 0.0000 0.2996 43.9 5/ 8 gi| > 91206454|ref|NP_001035146.1| +12 -.SSEER.- > 22105 gi|149944548|ref|NP_055990.1| neur > 31637 gi|91206456|ref|NP_690002.2| hypot > 31801 gi|116812577|ref|NP_057103.2| LUC7 > 34015 gi|169167854|ref|XP_001723047.1| P > 34369 gi|169178513|ref|XP_001715551.1| P > 39319 gi|157364943|ref|NP_005232.2| ecot > 49195 gi|157364945|ref|NP_001098548.2| e > 55866 Rev_gi|116008442|ref|NP_055885.3| > 56885 gi|63055053|ref|NP_055575.2| TatD > 60751 gi|113416552|ref|XP_001128002.1| P > 2. 2 / 6 29973 606.32056 0.0226 0.2928 43.9 5/ 8 gi| > 156119625|ref|NP_002206.2| +3 -.SSEKR.- > 45044 Rev_gi|10863967|ref|NP_066993.1| h > 55866 Rev_gi|116008442|ref|NP_055885.3| > 55866 Rev_gi|116008442|ref|NP_055885.3| > 3. 3 / 6 31801 606.32056 0.0501 0.2846 43.9 5/ 8 gi| > 116812577|ref|NP_057103.2| -.SSKER.- > ... > ************************************** > > XML output for above SEQUEST OUT: > ********************** > > <spectrum_query spectrum="2009_0813_04.11113.11113.1" > start_scan="11113" end_scan="11113" precursor_neutral_mass="604.8877" > assumed_charge="1" index="1123"> > <search_result> > <search_hit hit_rank="1" peptide="SSEER" peptide_prev_aa="-" > peptide_next_aa="-" protein="gi|91206454|ref|NP_001035146.1|" > num_tot_proteins="13" num_matched_ions="5" tot_num_ions="8" > calc_neutral_pep_mass="606.2609" massdiff="-1.373190" num_tol_term="2" > num_missed_cleavages="0" is_rejected="0"> > <search_score name="xcorr" value="0.300"/> > <search_score name="deltacn" value="0.050"/> > <search_score name="deltacnstar" value="0.000"/> > <search_score name="spscore" value="43.9"/> > <search_score name="sprank" value="6"/> > </search_hit> > <search_hit hit_rank="2" peptide="SSEER" peptide_prev_aa=" > is_rejected="0"> > <search_score name="xcorr" value="0.000"/> > <search_score name="deltacn" value="0.050"/> > <search_score name="deltacnstar" value="0.000"/> > <search_score name="spscore" value="0.0"/> > <search_score name="sprank" value="0"/> > </search_hit> > </search_result> > </spectrum_query> > > *********************************************** > > Thanks, > ~Nikhil > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
