search

compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
48 stars 18 forks source link

Peptideshaker found spectrum match null #539

Open giovanni-cro opened 2 months ago

giovanni-cro commented 2 months ago

Dear developers,

I am encountering an issue with peptide-shaker, which I paste here:

------------------------------------------------------------------

PeptideShaker 2.2.25 Report File

#

Originally saved by: Giovanni @ DESKTOP-G6PFOB1

on: 13 Sep 2024, 11:29

as: report_error

------------------------------------------------------------------

Fri Sep 13 11:24:27 CEST 2024 Import process for Au_Pt_Tutorial

Fri Sep 13 11:24:28 CEST 2024 Importing sequences from uniprotkb_human_reviewed_plusTrypsin_2024_09_11_concatenated_target_decoy.fasta. Fri Sep 13 11:24:28 CEST 2024 Importing gene mappings. Fri Sep 13 11:24:29 CEST 2024 Neanderthal (Homo sapiens neanderthalensis) not available in Ensembl. Fri Sep 13 11:24:32 CEST 2024 Establishing local database connection. Fri Sep 13 11:24:32 CEST 2024 Reading identification files. Fri Sep 13 11:24:32 CEST 2024 Parsing Au_1H_051_a_dda.omx.gz. Fri Sep 13 11:24:54 CEST 2024 Checking spectra for Au_1H_051_a_dda.omx.gz. Fri Sep 13 11:24:54 CEST 2024 Importing PSMs from Au_1H_051_a_dda.omx.gz Fri Sep 13 11:25:00 CEST 2024 118 identified spectra (0.4%) did not present a valid peptide. Fri Sep 13 11:25:00 CEST 2024 30453 of the best scoring peptides were excluded by the import filters: Fri Sep 13 11:25:00 CEST 2024 - 97.4% peptide length less than 8 or greater than 30. Fri Sep 13 11:25:00 CEST 2024 - 2.5% peptide presenting high mass or isotopic deviation. Fri Sep 13 11:25:00 CEST 2024 Parsing Au_1H_051_a_dda.t.xml.gz. Fri Sep 13 11:25:02 CEST 2024 Checking spectra for Au_1H_051_a_dda.t.xml.gz. Fri Sep 13 11:25:02 CEST 2024 Importing PSMs from Au_1H_051_a_dda.t.xml.gz Fri Sep 13 11:25:03 CEST 2024 779 identified spectra (2.9%) did not present a valid peptide. Fri Sep 13 11:25:03 CEST 2024 3766 of the best scoring peptides were excluded by the import filters: Fri Sep 13 11:25:03 CEST 2024 - 78.7% peptide length less than 8 or greater than 30. Fri Sep 13 11:25:03 CEST 2024 - 20.4% peptide presenting high mass or isotopic deviation. Fri Sep 13 11:25:03 CEST 2024 Parsing CLT_1H_066_a_dda.omx.gz. Fri Sep 13 11:25:30 CEST 2024 Checking spectra for CLT_1H_066_a_dda.omx.gz. Fri Sep 13 11:25:30 CEST 2024 Importing PSMs from CLT_1H_066_a_dda.omx.gz Fri Sep 13 11:25:34 CEST 2024 116 identified spectra (0.4%) did not present a valid peptide. Fri Sep 13 11:25:34 CEST 2024 33232 of the best scoring peptides were excluded by the import filters: Fri Sep 13 11:25:34 CEST 2024 - 97.6% peptide length less than 8 or greater than 30. Fri Sep 13 11:25:34 CEST 2024 - 2.3% peptide presenting high mass or isotopic deviation. Fri Sep 13 11:25:34 CEST 2024 Parsing CLT_1H_066_a_dda.t.xml.gz. Fri Sep 13 11:25:35 CEST 2024 Checking spectra for CLT_1H_066_a_dda.t.xml.gz. Fri Sep 13 11:25:35 CEST 2024 Importing PSMs from CLT_1H_066_a_dda.t.xml.gz Fri Sep 13 11:25:36 CEST 2024 774 identified spectra (2.8%) did not present a valid peptide. Fri Sep 13 11:25:36 CEST 2024 3885 of the best scoring peptides were excluded by the import filters: Fri Sep 13 11:25:36 CEST 2024 - 79.5% peptide length less than 8 or greater than 30. Fri Sep 13 11:25:36 CEST 2024 - 19.8% peptide presenting high mass or isotopic deviation. Fri Sep 13 11:25:36 CEST 2024 Parsing Pt_1H_076_a_dda.omx.gz. Fri Sep 13 11:26:03 CEST 2024 Checking spectra for Pt_1H_076_a_dda.omx.gz. Fri Sep 13 11:26:03 CEST 2024 Importing PSMs from Pt_1H_076_a_dda.omx.gz Fri Sep 13 11:26:06 CEST 2024 126 identified spectra (0.5%) did not present a valid peptide. Fri Sep 13 11:26:06 CEST 2024 30757 of the best scoring peptides were excluded by the import filters: Fri Sep 13 11:26:06 CEST 2024 - 97.4% peptide length less than 8 or greater than 30. Fri Sep 13 11:26:06 CEST 2024 - 2.6% peptide presenting high mass or isotopic deviation. Fri Sep 13 11:26:06 CEST 2024 Parsing Pt_1H_076_a_dda.t.xml.gz. Fri Sep 13 11:26:07 CEST 2024 Checking spectra for Pt_1H_076_a_dda.t.xml.gz. Fri Sep 13 11:26:07 CEST 2024 Importing PSMs from Pt_1H_076_a_dda.t.xml.gz Fri Sep 13 11:26:08 CEST 2024 783 identified spectra (2.9%) did not present a valid peptide. Fri Sep 13 11:26:08 CEST 2024 3761 of the best scoring peptides were excluded by the import filters: Fri Sep 13 11:26:08 CEST 2024 - 78.7% peptide length less than 8 or greater than 30. Fri Sep 13 11:26:08 CEST 2024 - 20.4% peptide presenting high mass or isotopic deviation. Fri Sep 13 11:26:08 CEST 2024 File import completed. 163554 first hits imported (771634 total) from 91746 spectra. Fri Sep 13 11:26:08 CEST 2024 [148704 first hits passed the initial filtering] Fri Sep 13 11:26:08 CEST 2024 Computing assumptions probabilities. Fri Sep 13 11:26:09 CEST 2024 Saving assumptions probabilities, selecting best match, scoring modification localization. Fri Sep 13 11:26:16 CEST 2024 Computing PSM probabilities. Fri Sep 13 11:26:17 CEST 2024 Resolving peptide inference issues. Fri Sep 13 11:26:18 CEST 2024 Saving probabilities, building peptides and proteins. Fri Sep 13 11:26:21 CEST 2024 Generating peptide map. Fri Sep 13 11:26:22 CEST 2024 Computing peptide probabilities. Fri Sep 13 11:26:22 CEST 2024 Saving peptide probabilities. Fri Sep 13 11:26:23 CEST 2024 Simplifying protein groups. Fri Sep 13 11:26:23 CEST 2024 507 unlikely protein mappings found: Fri Sep 13 11:26:23 CEST 2024 - 42 protein groups supported by predicted or uncertain proteins. Fri Sep 13 11:26:23 CEST 2024 - 28 protein groups supported by low confidence peptides. Fri Sep 13 11:26:23 CEST 2024 - 417 protein groups explained by simpler groups. Fri Sep 13 11:26:24 CEST 2024 Mapping shared peptides. Fri Sep 13 11:26:24 CEST 2024 Generating protein map. Fri Sep 13 11:26:25 CEST 2024 Selecting leading proteins, inferring peptide and protein inference status. Fri Sep 13 11:26:25 CEST 2024 Computing protein probabilities. Fri Sep 13 11:26:26 CEST 2024 Saving protein probabilities. Fri Sep 13 11:26:31 CEST 2024 Validating identifications at 1% FDR, quality control of matches. Fri Sep 13 11:27:00 CEST 2024 An error occurred: Cannot invoke "com.compomics.util.experiment.identification.matches.SpectrumMatch.getBestPeptideAssumption()" because "spectrumMatch" is null Fri Sep 13 11:27:00 CEST 2024 Please contact the developers (https://github.com/compomics/peptide-shaker/issues).

Fri Sep 13 11:27:00 CEST 2024 Importing Data Canceled! Fri Sep 13 11:27:00 CEST 2024 An error occurred: Cannot invoke "com.compomics.util.experiment.identification.matches.SpectrumMatch.getUrParam(com.compomics.util.experiment.personalization.UrParameter)" because "spectrumMatch" is null Fri Sep 13 11:27:00 CEST 2024 Please contact the developers (https://github.com/compomics/peptide-shaker/issues). Fri Sep 13 11:27:00 CEST 2024 An error occurred: Cannot invoke "com.compomics.util.experiment.identification.matches.SpectrumMatch.getKey()" because "spectrumMatch" is null Fri Sep 13 11:27:00 CEST 2024 Please contact the developers (https://github.com/compomics/peptide-shaker/issues).

I was able to produce an output for searchGUI butcould not open it with peptide-shaker. Could you please help me with this issue?

Meanwhile, I thank you for developing such useful tools, Giovanni

hbarsnes commented 2 months ago

Hi Giovanni,

It seems like you are using a very old version of PeptideShaker (v2.2.25). Please update to the most recent version (v3.0.11) to see if that solves the problem. You probably also want to update to the latest version of SearchGUI at the same time. Note that you may have to research your data in SearchGUI in order to guarantee compatible output.

Best regards, Harald

lutfia95 commented 1 month ago

Hi,

I got same problem with 3.0.11, in the start page increase the memory usage from Java, in my case using 10 GB (was 5) solved the problem.

Best, Ahmad