Hello Mr. Eng, Did you get chance to fix the OUT2XML output for SEQUEST outfiles with "duplicate_references"? Actually the current data I have has few experiments with duplicate refrences options used and hence would be good if an XML file can be created for such experiments.
Please let me know. Thanks and regards, ~Nikhil Garge Biostatistics analyst RTI International Durham NC 27709 Email: [email protected] Phone: 919-541-5902 On Fri, Sep 4, 2009 at 10:18 PM, Jimmy Eng <[email protected]> wrote: > > 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 -~----------~----~----~----~------~----~------~--~---
