Hi! During postprocessing of InterProphet results (pepXML), I've seen some irregularities that I don't understand. It would be great if someone could shed some light on them.
1. additional modifications in X! Tandem results: X! Tandem seems to add some modifications to the search parameters that were not explicitly specified. The relevant lines from the pepXML are below (sub-elements of "search_summary"). What's the meaning of those? <aminoacid_modification aminoacid="C" massdiff="-17.0265" mass="143.0041" variable="Y" symbol="^"/> <!--X! Tandem n-terminal AA variable modification--> <aminoacid_modification aminoacid="E" massdiff="-18.0106" mass="111.0320" variable="Y" symbol="^"/> <!--X! Tandem n-terminal AA variable modification--> <aminoacid_modification aminoacid="Q" massdiff="-17.0265" mass="111.0321" variable="Y" symbol="^"/> <!--X! Tandem n-terminal AA variable modification--> 2. alternative proteins in OMSSA results: OMSSA doesn't seem to handle peptides that occur in different proteins in the database consistently. It may not list alternative proteins and give different protein references for the same peptide (A), or it may give different numbers of alternative proteins for the same peptide (B). Examples below. Is there a way to make sense of that or is it a bug? A: (note different "protein" values) <search_hit hit_rank="1" peptide="SVLTVLHQDWLNGK" peptide_prev_aa="V" peptide_next_aa="E" protein="P01860" num_tot_proteins="3" num_matched_ions="20" tot_num_ions="26" calc_neutral_pep_mass="1608.862" massdiff="0.013" is_rejected="0" protein_descr="[snip]" num_tol_term="1" num_missed_cleavages="0"> <search_score name="pvalue" value="0.000000000000005"/> <search_score name="expect" value="0.000000000413624"/> <search_hit hit_rank="1" peptide="SVLTVLHQDWLNGK" peptide_prev_aa="V" peptide_next_aa="E" protein="P01861" num_tot_proteins="3" num_matched_ions="19" tot_num_ions="26" calc_neutral_pep_mass="1608.862" massdiff="0.006999999999915" is_rejected="0" protein_descr="[snip]" num_tol_term="1" num_missed_cleavages="0"> <search_score name="pvalue" value="0.000000000003367"/> <search_score name="expect" value="0.000000279733183"/> B: (note different number of alternative proteins) <search_hit hit_rank="1" peptide="FLEQQNQVLQTK" peptide_prev_aa="R" peptide_next_aa="W" protein="P04264_CHAIN_0" num_tot_proteins="3" num_matched_ions="20" tot_num_ions="22" calc_neutral_pep_mass="1474.78" massdiff="0.007000000000035" is_rejected="0" protein_descr="[snip]" num_tol_term="2" num_missed_cleavages="0"> <alternative_protein protein="P35908" protein_descr="[snip]" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="W"/> <alternative_protein protein="P04264" protein_descr="[snip]" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="W"/> <search_score name="pvalue" value="0.000000000000005"/> <search_score name="expect" value="0.000000000451822"/> <search_hit hit_rank="1" peptide="FLEQQNQVLQTK" peptide_prev_aa="V" peptide_next_aa="W" protein="Q7Z794" num_tot_proteins="4" num_matched_ions="19" tot_num_ions="22" calc_neutral_pep_mass="1474.78" massdiff="0.007000000000035" is_rejected="0" protein_descr=[snip]" num_tol_term="1" num_missed_cleavages="0"> <alternative_protein protein="P35908" protein_descr="[snip]" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="W"/> <alternative_protein protein="P04264" protein_descr="[snip]" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="W"/> <alternative_protein protein="P04264_CHAIN_0" protein_descr="[snip]" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="W"/> <search_score name="pvalue" value="0.000000000000001"/> <search_score name="expect" value="0.000000000071547"/> Thanks in advance Hendrik -- 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.
