Hello, The new Mascot server version 2.3.01 can output DAT files in pepXML format. But the format of the pepxml is different from the one generated by running Mascot2XML.exe in TPP on the DAT file. As a result, the pepXML directly from the Mascot is not recognized by the xinteract.
Here is an example, thus is the output from Mascot directly <spectrum_query spectrum="controllerType=0 controllerNumber=1 scan=5015" start_scan="0" end_scan="0" precursor_neutral_mass="604.365448" assumed_charge="2" search_specification="intensity(2563.6060)" index="310"> <search_result search_id="1"> <search_hit hit_rank="4" peptide="SIGSGGK" peptide_prev_aa="R" peptide_next_aa="E" protein="IPI00919912" num_tot_proteins="1" num_matched_ions="3" calc_neutral_pep_mass="604.318039" massdiff="+0.0474" num_missed_cleavages="0" is_rejected="0" protein_descr="Tax_Id=7955 Gene_Symbol=si:ch211-219o4.1 hypothetical protein" protein_mw="41847"> <search_score name="ionscore" value="6.62"/> <search_score name="identityscore" value="33"/> <search_score name="homologyscore" value="18"/> <search_score name="expect" value="24"/> </search_hit> </search_result> </spectrum_query> This one is from Mascot2XML.exe. <spectrum_query spectrum="T.2" start_scan="0000" end_scan="0000" precursor_neutral_mass="3346.0733" assumed_charge="2" index="3354"> <search_result> <search_hit hit_rank="1" peptide="TVNSGK" peptide_prev_aa="R" peptide_next_aa="F" protein="IPI00650958" num_tot_proteins="1" num_matched_ions="3" calc_neutral_pep_mass="3346.5465" massdiff="-0.4732" num_tol_term="2" is_rejected="0"> <search_score name="ionscore" value="6.99"/> <search_score name="identityscore" value="33"/> <search_score name="star" value="0"/> <search_score name="homologyscore" value="18"/> <search_score name="expect" value="22"/> </search_hit> </search_result> </spectrum_query> Does anyone has experience on this problem? Thanks, Chen -- 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.
