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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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An error occurred: Cannot invoke "com.compomics.util.experiment.identification.matches.SpectrumMatch.getPeptideAssumptionsMap()" because "spectrumMatch" is null #450

Closed Jacky11 closed 3 years ago

Jacky11 commented 3 years ago

Hello,

I tried to use peptideshaker from 3 replicates in 2 biological conditions to identify proteins of helicobacter pylori

I tried before with MaxQuant, but had very little protein identified, so I wanted to see with SearchGUI and PeptideShaker if I can find more protein using non-specific enzyme search.

SearchGUI seems to have worked, but PeptideShaker did not automatically launch following SearchGUI. As I was able to get a number of results so I used PeptideShaker from those results. Unfortunately, it doesn't work out and so I don't have any results. But it seems SearchGUI provided many results... Could you help me find the solution? I am a little lost.

Please find here the reports: peptideshaker_report.txt searchgui_report.txt

Many thanks in advance !

hbarsnes commented 3 years ago

Could you please also share the PeptideShaker log file? You'll find it via the PeptideShaker Welcome dialog > Settings & Help > Help > Bug Report. It will hopefully make it easier to locate the root of the problem.

Jacky11 commented 3 years ago

Hello,

Here is the log file: PeptideShaker 2.0.18 log.txt

Thanks !

Jacky11 commented 3 years ago

Interestingly, when I used only the novor results (i.e. files .novor.csv.gz), PeptideShaker works.

hbarsnes commented 3 years ago

I'm afraid you've come across a known (but yet unsolved) issue with the PeptideShaker backend. The only known fix at the moment is to increase the amount of memory given to PeptideShaker. This you can do via the Welcome dialog > Settings & Help > Settings > Java Settings.

The reason why it works if only loading the Novor results is that this requires less memory, thus avoiding the issue.

Jacky11 commented 3 years ago

Thank you so much Harald ! It works for Comet outputs after I change 4GB to 16GB and it is pretty nice ! I am testing to merge all outputs (finger cross).