I am using OUT2XML.exe for our purpose. So Windows binary would be fine. Thanks, ~Nikhil
On Wed, Sep 9, 2009 at 1:32 PM, Jimmy Eng <[email protected]> wrote: > > Thanks for reminding me. I was on vacation when I sent that email > last week and forgot all about it. But I'm back and will look into > the Out2XML code right now. Assuming (big assumption) I can get it > modified today, would you need a Windows binary or are you using the > TPP tools on a different platform? > > - Jimmy > > On Wed, Sep 9, 2009 at 10:23 AM, Nikhil Garge<[email protected]> > wrote: > > 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. 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