(Sample: PPvsDR_concise_0714, Replicate: 0)įri Jul 14 11:00: Importing sequences from > Reply to this email directly, view it on GitHubįri Jul 14 11:00: Import process for PPvsDR_concise > You are receiving this because you authored the thread. > automatic backup that could interfere with the files during the analysis? > example, are the data stored on a network drive or at a location with > BTW, is there anything special with regards to your computer setup? For > Perhaps you could try simply reloading the data and see if that solves the > FDR, quality control of matches' step though and it all seems to work fine. I'm already passed the 'Validating identifications at 1% I have now started to process your data in On Fri, at 4:08 AM, Harald Barsnes Hi Joe, Wed Jul 12 10:03: An error occurred: null Wed Jul 12 09:52: Validating identifications at 1% FDR, quality control of matches. Wed Jul 12 09:49: Saving protein probabilities. Wed Jul 12 09:49: Correcting protein probabilities. 7 protein groups remaining (1 suspicious). Wed Jul 12 09:34: Resolving protein inference issues, inferring peptide and protein PI status. Wed Jul 12 09:33: Generating protein map. Wed Jul 12 09:30: Saving peptide probabilities. Wed Jul 12 09:30: Computing peptide probabilities. Wed Jul 12 09:28: Generating peptide map. Wed Jul 12 09:28: Note: a group can present combinations of these criteria. Wed Jul 12 09:28: - 14 groups explained by a simpler group. Wed Jul 12 09:28: - 19 protein groups supported by non-enzymatic shared peptides. Wed Jul 12 09:28: 27 unlikely protein mappings found:

Wed Jul 12 09:28: Simplifying protein groups. Wed Jul 12 09:24: Saving probabilities, building peptides and proteins. Wed Jul 12 09:24: Resolving peptide inference issues. Wed Jul 12 09:22: Scoring PTMs in PSMs (D-score and PhosphoRS) Wed Jul 12 09:22: Computing PSM probabilities. Wed Jul 12 09:22: Selecting best peptide per spectrum. Wed Jul 12 09:22: Saving assumptions probabilities. Wed Jul 12 09:22: Computing assumptions probabilities. 82855 first hits imported (423505 secondary) from 52232 spectra. Wed Jul 12 09:22: - 4.5% unrecognized modifications. Wed Jul 12 09:22: - 64.1% peptide presenting high mass or isotopic deviation. Wed Jul 12 09:22: - 31.3% peptide length less than 8 or greater than 30. Wed Jul 12 09:22: 14137 of the best scoring peptides were excluded by the import filters: Wed Jul 12 09:22: 9715 identified spectra (24.4%) did not present a valid peptide. Wed Jul 12 09:22: Mapping peptides to proteins. Wed Jul 12 09:22: Collecting peptides to map. Wed Jul 12 09:21: Mapping peptides to proteins. Wed Jul 12 09:21: Collecting peptides to map. Wed Jul 12 09:21: Reading identification files.

Wed Jul 12 09:21: Establishing local database connection. Gene and GO annotation for this species will not be available. Wed Jul 12 09:21: Importing gene mappings. Wed Jul 12 09:21: FASTA file import completed.

Wed Jul 12 09:21: Importing sequences from uniprot-proteome%253AUP000002524_DR_concatenated_target_decoy.fasta. Wed Jul 12 09:21: Import process for PPvsDR_concise (Sample: PPvsDR_concise_0711, Replicate: 0) Recently, I have encountered an issue that Peptideshaker got stuck at 'Validating identifications at 1% FDR' step when trying to process the files from SearchGUI.

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