{"action":"created","issue":{"url":"https://api.github.com/repos/lgatto/synapter/issues/127","repository_url":"https://api.github.com/repos/lgatto/synapter","labels_url":"https://api.github.com/repos/lgatto/synapter/issues/127/labels{/name}","comments_url":"https://api.github.com/repos/lgatto/synapter/issues/127/comments","events_url":"https://api.github.com/repos/lgatto/synapter/issues/127/events","html_url":"https://github.com/lgatto/synapter/issues/127","id":189748624,"number":127,"title":"Document the columns in the files generated by `writeMatchedEMRTs`.","user":{"login":"sgibb","id":1828443,"avatar_url":"https://avatars.githubusercontent.com/u/1828443?v=3","gravatar_id":"","url":"https://api.github.com/users/sgibb","html_url":"https://github.com/sgibb","followers_url":"https://api.github.com/users/sgibb/followers","following_url":"https://api.github.com/users/sgibb/following{/other_user}","gists_url":"https://api.github.com/users/sgibb/gists{/gist_id}","starred_url":"https://api.github.com/users/sgibb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sgibb/subscriptions","organizations_url":"https://api.github.com/users/sgibb/orgs","repos_url":"https://api.github.com/users/sgibb/repos","events_url":"https://api.github.com/users/sgibb/events{/privacy}","received_events_url":"https://api.github.com/users/sgibb/received_events","type":"User","site_admin":false},"labels":[{"id":99543782,"url":"https://api.github.com/repos/lgatto/synapter/labels/TODO","name":"TODO","color":"fbca04","default":false}],"state":"open","locked":false,"assignee":{"login":"sgibb","id":1828443,"avatar_url":"https://avatars.githubusercontent.com/u/1828443?v=3","gravatar_id":"","url":"https://api.github.com/users/sgibb","html_url":"https://github.com/sgibb","followers_url":"https://api.github.com/users/sgibb/followers","following_url":"https://api.github.com/users/sgibb/following{/other_user}","gists_url":"https://api.github.com/users/sgibb/gists{/gist_id}","starred_url":"https://api.github.com/users/sgibb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sgibb/subscriptions","organizations_url":"https://api.github.com/users/sgibb/orgs","repos_url":"https://api.github.com/users/sgibb/repos","events_url":"https://api.github.com/users/sgibb/events{/privacy}","received_events_url":"https://api.github.com/users/sgibb/received_events","type":"User","site_admin":false},"assignees":[{"login":"sgibb","id":1828443,"avatar_url":"https://avatars.githubusercontent.com/u/1828443?v=3","gravatar_id":"","url":"https://api.github.com/users/sgibb","html_url":"https://github.com/sgibb","followers_url":"https://api.github.com/users/sgibb/followers","following_url":"https://api.github.com/users/sgibb/following{/other_user}","gists_url":"https://api.github.com/users/sgibb/gists{/gist_id}","starred_url":"https://api.github.com/users/sgibb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sgibb/subscriptions","organizations_url":"https://api.github.com/users/sgibb/orgs","repos_url":"https://api.github.com/users/sgibb/repos","events_url":"https://api.github.com/users/sgibb/events{/privacy}","received_events_url":"https://api.github.com/users/sgibb/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/lgatto/synapter/milestones/1","html_url":"https://github.com/lgatto/synapter/milestones/2.0","labels_url":"https://api.github.com/repos/lgatto/synapter/milestones/1/labels","id":849290,"number":1,"title":"2.0","description":"","creator":{"login":"sgibb","id":1828443,"avatar_url":"https://avatars.githubusercontent.com/u/1828443?v=3","gravatar_id":"","url":"https://api.github.com/users/sgibb","html_url":"https://github.com/sgibb","followers_url":"https://api.github.com/users/sgibb/followers","following_url":"https://api.github.com/users/sgibb/following{/other_user}","gists_url":"https://api.github.com/users/sgibb/gists{/gist_id}","starred_url":"https://api.github.com/users/sgibb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sgibb/subscriptions","organizations_url":"https://api.github.com/users/sgibb/orgs","repos_url":"https://api.github.com/users/sgibb/repos","events_url":"https://api.github.com/users/sgibb/events{/privacy}","received_events_url":"https://api.github.com/users/sgibb/received_events","type":"User","site_admin":false},"open_issues":9,"closed_issues":46,"state":"open","created_at":"2014-11-01T11:05:40Z","updated_at":"2016-12-02T20:10:24Z","due_on":"2016-11-01T00:00:00Z","closed_at":null},"comments":1,"created_at":"2016-11-16T15:58:22Z","updated_at":"2016-12-02T20:47:56Z","closed_at":null,"body":""},"comment":{"url":"https://api.github.com/repos/lgatto/synapter/issues/comments/264558651","html_url":"https://github.com/lgatto/synapter/issues/127#issuecomment-264558651","issue_url":"https://api.github.com/repos/lgatto/synapter/issues/127","id":264558651,"user":{"login":"sgibb","id":1828443,"avatar_url":"https://avatars.githubusercontent.com/u/1828443?v=3","gravatar_id":"","url":"https://api.github.com/users/sgibb","html_url":"https://github.com/sgibb","followers_url":"https://api.github.com/users/sgibb/followers","following_url":"https://api.github.com/users/sgibb/following{/other_user}","gists_url":"https://api.github.com/users/sgibb/gists{/gist_id}","starred_url":"https://api.github.com/users/sgibb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sgibb/subscriptions","organizations_url":"https://api.github.com/users/sgibb/orgs","repos_url":"https://api.github.com/users/sgibb/repos","events_url":"https://api.github.com/users/sgibb/events{/privacy}","received_events_url":"https://api.github.com/users/sgibb/received_events","type":"User","site_admin":false},"created_at":"2016-12-02T20:47:56Z","updated_at":"2016-12-02T20:47:56Z","body":"@pavel-shliaha Could you please add (by clicking `edit`) the missing cells? I will add it as man page than.\r\n\r\n# IdentPeptides.csv\r\n\r\n| Column                    | Description                                              |\r\n|---------------------------|----------------------------------------------------------|\r\n| protein.Accession         | UniProt Accession Number                                 |\r\n| protein.Description       | Description                                              |\r\n| protein.dataBaseType      |                                                          |\r\n| protein.falsePositiveRate |                                                          |\r\n| peptide.matchType         |                                                          |\r\n| peptide.mhp               | peptide mz (charge corrected)                            |\r\n| peptide.seq               | peptide sequence                                         |\r\n| peptide.score             |                                                          |\r\n| precursor.leID            | low energy scan ID                                       |\r\n| precursor.mhp             | precursor mz (charge corrected)                          |\r\n| precursor.retT            | precursor retention time                                 |\r\n| precursor.inten           | precursor intensity                                      |\r\n| precursor.z               | precursor charge                                         |\r\n| precursor.mz              | precursor mz                                             |\r\n| precursor.Mobility        | precursor ion mobility                                   |\r\n| errorppm                  |                                                          |\r\n| pval                      |                                                          |\r\n| qval                      |                                                          |\r\n| BH                        |                                                          |\r\n| Bonferroni                |                                                          |\r\n| predictedRt               | predicted retention time after retention time correction |\r\n| sdRt                      | standard deviation of the retention time prediction      |\r\n\r\n# MatchedPeptides.csv\r\n\r\n| Column                                    | Description                                                         |\r\n|-------------------------------------------|---------------------------------------------------------------------|\r\n| protein.Accession                         | UniProt Accession Number                                            |\r\n| protein.Description                       | Description                                                         |\r\n| protein.dataBaseType                      |                                                                     |\r\n| protein.falsePositiveRate                 |                                                                     |\r\n| peptide.matchType                         |                                                                     |\r\n| peptide.mhp                               | peptide mz (charge corrected)                                       |\r\n| peptide.seq                               | peptide sequence                                                    |\r\n| peptide.score                             |                                                                     |\r\n| precursor.leID                            | low energy scan ID                                                  |\r\n| precursor.mhp                             | precursor mz (charge corrected)                                     |\r\n| precursor.retT                            | precursor retention time                                            |\r\n| precursor.inten                           | precursor intensity                                                 |\r\n| precursor.z                               | precursor charge                                                    |\r\n| precursor.mz                              | precursor mz                                                        |\r\n| precursor.Mobility                        | precursor ion mobility                                              |\r\n| errorppm                                  |                                                                     |\r\n| pval                                      |                                                                     |\r\n| qval                                      |                                                                     |\r\n| BH                                        |                                                                     |\r\n| Bonferroni                                |                                                                     |\r\n| predictedRt                               | predicted retention time after retention time correction            |\r\n| sdRt                                      | standard deviation of the retention time prediction                 |\r\n| matchedEMRTs                              | comma-separated list of matched EMRTs                               |\r\n| spectrumID                                | high energy scan Id (quantitation)                                  |\r\n| rt_min                                    | retention time in minutes (quantitation)                            |\r\n| mwHPlus                                   | mz (quantitation)                                                   |\r\n| charge                                    | charge (quantitation)                                               |\r\n| Intensity                                 | intensity (quantitation)                                            |\r\n| Counts                                    | counts (quantitation)                                               |\r\n| clust_drift                               | ion mobility (quantitation)                                         |\r\n| isFid                                     |                                                                     |\r\n| ion_ID                                    | single ion/fragment ID (quantitation)                               |\r\n| ion_z                                     | single ion/fragment charge (quantitation)                           |\r\n| ion_iso                                   | single ion/fragment isotop (quantitation)                           |\r\n| ion_area                                  |                                                                     |\r\n| ion_counts                                | single ion/fragment counts (quantitation)                           |\r\n| Model                                     |                                                                     |\r\n| isotopicDistr                             | list of isotopic distribution (format: charge_isotope:intensity;)   |\r\n| matched.quant.spectrumIDs                 | comma-separated list of matched quantitation spectra IDs            |\r\n| precursor.leID.quant                      | precursor low energy scan ID (quantitation)                         |\r\n| idSource                                  |                                                                     |\r\n| synapterPlgsAgreement                     | agree/disagree between PLGS and synapter                            |\r\n| FragmentMatching                          | fragment matching result                                            |\r\n| matchedEMRTs.beforeFilterUniqueMatches    | comma-separated list of matched EMRTs before filterUniqueMatches    |\r\n| matchedEMRTs.beforeFilterNonUniqueMatches | comma-separated list of matched EMRTs before filterNonUniqueMatches |\r\n| matchedMultipleIdentEMRTs                 | matches multiple identification EMRTs TRUE/FALSE                    |\r\n| intensityCorrectionFactor                 | applied intensity correction factor (generated by intensityModel)   |\r\n\r\n# MergedPeptides.csv\r\n\r\n| Column                          | Description                                                                   |\r\n|---------------------------------|-------------------------------------------------------------------------------|\r\n| peptide.seq                     | peptide sequence                                                              |\r\n| protein.Accession.ident         | UniProt Accession Number (identification)                                     |\r\n| protein.Description.ident       | Description                                                                   |\r\n| protein.dataBaseType.ident      |                                                                               |\r\n| protein.falsePositiveRate.ident |                                                                               |\r\n| peptide.matchType.ident         |                                                                               |\r\n| peptide.mhp.ident               | peptide mz (charge corrected) (identification)                                |\r\n| peptide.score.ident             |                                                                               |\r\n| precursor.leID.ident            | low energy scan ID (identification)                                           |\r\n| precursor.mhp.ident             | precursor mz (charge corrected) (identification)                              |\r\n| precursor.retT.ident            | precursor retention time (identification)                                     |\r\n| precursor.inten.ident           | precursor intensity (identification)                                          |\r\n| precursor.z.ident               | precursor charge (identification)                                             |\r\n| precursor.mz.ident              | precursor mz (identification)                                                 |\r\n| precursor.Mobility.ident        | precursor ion mobility (identification)                                       |\r\n| errorppm.ident                  |                                                                               |\r\n| pval.ident                      |                                                                               |\r\n| qval.ident                      |                                                                               |\r\n| BH.ident                        |                                                                               |\r\n| Bonferroni.ident                |                                                                               |\r\n| protein.Accession.quant         | UniProt Accession Number (quantitation)                                       |\r\n| protein.Description.quant       | Description                                                                   |\r\n| protein.dataBaseType.quant      |                                                                               |\r\n| protein.falsePositiveRate.quant |                                                                               |\r\n| peptide.matchType.quant         |                                                                               |\r\n| peptide.mhp.quant               | peptide mz (charge corrected) (quantitation)                                  |\r\n| peptide.score.quant             |                                                                               |\r\n| precursor.leID.quant            | low energy scan ID (quantitation)                                             |\r\n| precursor.mhp.quant             | precursor mz (charge corrected) (quantitation)                                |\r\n| precursor.retT.quant            | precursor retention time (quantitation)                                       |\r\n| precursor.inten.quant           | precursor intensity (quantitation)                                            |\r\n| precursor.z.quant               | precursor charge (quantitation)                                               |\r\n| precursor.mz.quant              | precursor mz (quantitation)                                                   |\r\n| precursor.Mobility.quant        | precursor ion mobility (quantitation)                                         |\r\n| errorppm.quant                  |                                                                               |\r\n| pval.quant                      |                                                                               |\r\n| qval.quant                      |                                                                               |\r\n| BH.quant                        |                                                                               |\r\n| Bonferroni.quant                |                                                                               |\r\n| deltaRt                         | difference between identification and quantitation run in retention time      |\r\n| intenRatio                      | intensity ratio between identification and quantitation run in retention time |\r\n\r\n# QuantPeptides.csv\r\n\r\n| Column                    | Description                                              |\r\n|---------------------------|----------------------------------------------------------|\r\n| protein.Accession         | UniProt Accession Number                                 |\r\n| protein.Description       | Description                                              |\r\n| protein.dataBaseType      |                                                          |\r\n| protein.falsePositiveRate |                                                          |\r\n| peptide.matchType         |                                                          |\r\n| peptide.mhp               | peptide mz (charge corrected)                            |\r\n| peptide.seq               | peptide sequence                                         |\r\n| peptide.score             |                                                          |\r\n| precursor.leID            | low energy scan ID                                       |\r\n| precursor.mhp             | precursor mz (charge corrected)                          |\r\n| precursor.retT            | precursor retention time                                 |\r\n| precursor.inten           | precursor intensity                                      |\r\n| precursor.z               | precursor charge                                         |\r\n| precursor.mz              | precursor mz                                             |\r\n| precursor.Mobility        | precursor ion mobility                                   |\r\n| errorppm                  |                                                          |\r\n| pval                      |                                                          |\r\n| qval                      |                                                          |\r\n| BH                        |                                                          |\r\n| Bonferroni                |                                                          |\r\n"}}
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