{"action":"created","issue":{"url":"https://api.github.com/repos/crux-toolkit/crux-toolkit/issues/375","repository_url":"https://api.github.com/repos/crux-toolkit/crux-toolkit","labels_url":"https://api.github.com/repos/crux-toolkit/crux-toolkit/issues/375/labels{/name}","comments_url":"https://api.github.com/repos/crux-toolkit/crux-toolkit/issues/375/comments","events_url":"https://api.github.com/repos/crux-toolkit/crux-toolkit/issues/375/events","html_url":"https://github.com/crux-toolkit/crux-toolkit/issues/375","id":215043980,"node_id":"MDU6SXNzdWUyMTUwNDM5ODA=","number":375,"title":"crux percolator n-terminal modification","user":{"login":"wsnoble","id":22529318,"node_id":"MDQ6VXNlcjIyNTI5MzE4","avatar_url":"https://avatars2.githubusercontent.com/u/22529318?v=4","gravatar_id":"","url":"https://api.github.com/users/wsnoble","html_url":"https://github.com/wsnoble","followers_url":"https://api.github.com/users/wsnoble/followers","following_url":"https://api.github.com/users/wsnoble/following{/other_user}","gists_url":"https://api.github.com/users/wsnoble/gists{/gist_id}","starred_url":"https://api.github.com/users/wsnoble/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wsnoble/subscriptions","organizations_url":"https://api.github.com/users/wsnoble/orgs","repos_url":"https://api.github.com/users/wsnoble/repos","events_url":"https://api.github.com/users/wsnoble/events{/privacy}","received_events_url":"https://api.github.com/users/wsnoble/received_events","type":"User","site_admin":false},"labels":[{"id":452414441,"node_id":"MDU6TGFiZWw0NTI0MTQ0NDE=","url":"https://api.github.com/repos/crux-toolkit/crux-toolkit/labels/Percolator","name":"Percolator","color":"ededed","default":false},{"id":452386700,"node_id":"MDU6TGFiZWw0NTIzODY3MDA=","url":"https://api.github.com/repos/crux-toolkit/crux-toolkit/labels/bug","name":"bug","color":"ee0701","default":true},{"id":452414836,"node_id":"MDU6TGFiZWw0NTI0MTQ4MzY=","url":"https://api.github.com/repos/crux-toolkit/crux-toolkit/labels/crux-users","name":"crux-users","color":"ededed","default":false}],"state":"open","locked":false,"assignee":{"login":"acheng94","id":11834339,"node_id":"MDQ6VXNlcjExODM0MzM5","avatar_url":"https://avatars2.githubusercontent.com/u/11834339?v=4","gravatar_id":"","url":"https://api.github.com/users/acheng94","html_url":"https://github.com/acheng94","followers_url":"https://api.github.com/users/acheng94/followers","following_url":"https://api.github.com/users/acheng94/following{/other_user}","gists_url":"https://api.github.com/users/acheng94/gists{/gist_id}","starred_url":"https://api.github.com/users/acheng94/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/acheng94/subscriptions","organizations_url":"https://api.github.com/users/acheng94/orgs","repos_url":"https://api.github.com/users/acheng94/repos","events_url":"https://api.github.com/users/acheng94/events{/privacy}","received_events_url":"https://api.github.com/users/acheng94/received_events","type":"User","site_admin":false},"assignees":[{"login":"acheng94","id":11834339,"node_id":"MDQ6VXNlcjExODM0MzM5","avatar_url":"https://avatars2.githubusercontent.com/u/11834339?v=4","gravatar_id":"","url":"https://api.github.com/users/acheng94","html_url":"https://github.com/acheng94","followers_url":"https://api.github.com/users/acheng94/followers","following_url":"https://api.github.com/users/acheng94/following{/other_user}","gists_url":"https://api.github.com/users/acheng94/gists{/gist_id}","starred_url":"https://api.github.com/users/acheng94/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/acheng94/subscriptions","organizations_url":"https://api.github.com/users/acheng94/orgs","repos_url":"https://api.github.com/users/acheng94/repos","events_url":"https://api.github.com/users/acheng94/events{/privacy}","received_events_url":"https://api.github.com/users/acheng94/received_events","type":"User","site_admin":false}],"milestone":null,"comments":0,"created_at":"2017-03-17T15:50:48Z","updated_at":"2018-12-13T16:11:53Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"The following was reported on crux-users by sy.rodrigo.proteomics@gmail.com\r\n\r\n\r\nHi\r\n    I have a question about crux percolator. The input file is pepXML format, and I found that in the output make-pin file and the percolator.target.psms.txt file all the n-terminal modification is missing. Is there anything wrong with my command?\r\n\r\nMy cmd line input is (both windows and linux 64bit binaries, version3.0 and 3.1, were tried ):\r\n> crux percolator --protein T --decoy-prefix REVERSE_ --overwrite T 20151117ecoli_iTRAQ_2_10ul.tandem.pep.xml\r\n\r\nThe pepXML is quoted as:\r\n    ...\r\n     <search_result>\r\n         <search_hit hit_rank=\"1\" peptide=\"LPAKLPITVVRNK\" peptide_prev_aa=\"R\" peptide_next_aa=\"A\" protein=\"EG10997\" protein_descr=\"mnmE\" num_tot_proteins=\"1\" num_matched_ions=\"4\" tot_num_ions=\"48\" calc_neutral_pep_mass=\"2360.5397\" massdiff=\"0.039\" num_tol_term=\"2\" num_missed_cleavages=\"2\" is_rejected=\"0\">\r\n            <modification_info mod_nterm_mass=\"305.2132\">\r\n               <mod_aminoacid_mass position=\"4\" mass=\"432.3003\" />\r\n               <mod_aminoacid_mass position=\"13\" mass=\"432.3003\" />\r\n            </modification_info>\r\n            <search_score name=\"hyperscore\" value=\"107\"/>\r\n            <search_score name=\"nextscore\" value=\"100\"/>\r\n            <search_score name=\"bscore\" value=\"0\"/>\r\n            <search_score name=\"yscore\" value=\"0\"/>\r\n            <search_score name=\"cscore\" value=\"0\"/>\r\n            <search_score name=\"zscore\" value=\"0\"/>\r\n            <search_score name=\"ascore\" value=\"0\"/>\r\n            <search_score name=\"xscore\" value=\"0\"/>\r\n            <search_score name=\"expect\" value=\"870\"/>\r\n         </search_hit>\r\n      </search_result>\r\n    ...\r\n\r\nThe corresponding sequence in output make-pin file is :\r\nR.LPAK[304.21]LPITVVRNK[304.21].A\r\n"},"comment":{"url":"https://api.github.com/repos/crux-toolkit/crux-toolkit/issues/comments/447025707","html_url":"https://github.com/crux-toolkit/crux-toolkit/issues/375#issuecomment-447025707","issue_url":"https://api.github.com/repos/crux-toolkit/crux-toolkit/issues/375","id":447025707,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NzAyNTcwNw==","user":{"login":"jvolkening","id":11667655,"node_id":"MDQ6VXNlcjExNjY3NjU1","avatar_url":"https://avatars2.githubusercontent.com/u/11667655?v=4","gravatar_id":"","url":"https://api.github.com/users/jvolkening","html_url":"https://github.com/jvolkening","followers_url":"https://api.github.com/users/jvolkening/followers","following_url":"https://api.github.com/users/jvolkening/following{/other_user}","gists_url":"https://api.github.com/users/jvolkening/gists{/gist_id}","starred_url":"https://api.github.com/users/jvolkening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jvolkening/subscriptions","organizations_url":"https://api.github.com/users/jvolkening/orgs","repos_url":"https://api.github.com/users/jvolkening/repos","events_url":"https://api.github.com/users/jvolkening/events{/privacy}","received_events_url":"https://api.github.com/users/jvolkening/received_events","type":"User","site_admin":false},"created_at":"2018-12-13T16:11:53Z","updated_at":"2018-12-13T16:11:53Z","author_association":"NONE","body":"Just ran into the same bug with crux 3.2. Fixed N-terminal modifications are present in the comet pepXML but missing in the percolator pepXML. As a result, the `calc_neutral_pep_mass` and `massdiff` values are off by the mass of the modification. As an example, a partial record after comet search:\r\n```\r\n<spectrum_query spectrum=\"comet.44557.44557.3\" spectrumNativeID=\"controllerType=0 controllerNumber=1 scan=44557\" start_scan=\"44557\" end_scan=\"44557\" precursor_neutral_mass=\"2347.342673\" assumed_charge=\"3\" index=\"36970\" retention_time_sec=\"6697.2\">\r\n  <search_result>\r\n    <search_hit hit_rank=\"1\" peptide=\"GYINSLGALTGGQALQQAK\" peptide_prev_aa=\"K\" peptide_next_aa=\"A\" protein=\"P0A9G6\" num_tot_proteins=\"1\" num_matched_ions=\"26\" tot_num_ions=\"72\" calc_neutral_pep_mass=\"2347.326540\" massdiff=\"0.016133\" num_tol_term=\"2\" num_missed_cleavages=\"0\" num_matched_peptides=\"3660\">\r\n      <modification_info modified_peptide=\"GYINSLGALTGGQALQQAK\" mod_nterm_mass=\"230.170757\">\r\n        <mod_aminoacid_mass position=\"19\" mass=\"357.257895\" static=\"229.162932\"/>\r\n      </modification_info>\r\n```\r\nand after percolator run on the above file:\r\n```\r\n<spectrum_query spectrum=\".44557.44557.3\" start_scan=\"44557\" end_scan=\"44557\" precursor_neutral_mass=\"2347.3428\" assumed_charge=\"3\" index=\"4\">\r\n  <search_result>\r\n    <search_hit hit_rank=\"0\" peptide=\"GYINSLGALTGGQALQQAK\" peptide_prev_aa=\"K\" peptide_next_aa=\"A\" protein=\"P0A9G6\" num_tot_proteins=\"1\" calc_neutral_pep_mass=\"2118.1638\" massdiff=\"+229.1790\" num_tol_term=\"2\" num_missed_cleavages=\"0\" num_matched_peptides=\"3660\" is_rejected=\"0\" protein_descr=\"\">\r\n      <modification_info modified_peptide=\"GYINSLGALTGGQALQQAK\">\r\n        <mod_aminoacid_mass position=\"19\" mass=\"357.26\"/>\r\n      </modification_info>\r\n```\r\n\r\n"}}
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