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compomics / fragmentation-analyzer

A standalone java tool for analyzing ms/ms fragmentation data.
http://compomics.github.io/projects/fragmentation-analyzer.html
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Being able to load data exported from PeptideShaker #5

Open bhanu2008 opened 7 years ago

bhanu2008 commented 7 years ago

Hi, I am loading .omx file after search gui analysis. Analyser asks me to select the folder with mod and usermod .xml files of the omssa installation folder, i did that. I was able to load the file. However, after loading i am unable to see specific chemical labels which i used for omssa analysis. i see that labels of <119>,<120>,<121>..so on randomly placed in the peptide sequence I cross checked if the error was at search gui level by analysing the same .omx file with peptide shaker where i could see the labelling of target residues. Need help. Regards Bhanu

hbarsnes commented 7 years ago

Hi Bhanu,

I've now released FragmentationAnalyzer v1.5.17 which replaces the OMSSA modification indexes with the OMSSA modification names when importing data from omx files.

Let me know if it does not work as expected on your side and I'll reopen the issue.

Note however that the OMSSA search engine has been retired for several years now. I would recommend looking into some of the newer search engines available in SearchGUI as an upgrade. The same can also be said for FragmentationAnalzyer, where it is strongly recommend switching to PeptideShaker, which is where we focus our development efforts going forward.

Best regards, Harald

bhanu2008 commented 7 years ago

Hello Harald, Thanks For your efforts. I am already using peptide shaker and completely understand the thrust of your work. However, thanks to your group fragmentation analyzer gives me unique opportunity to check changes in fragmentation patterns with different chemical labels.. You have rightly suggested that I omssa is not active but unfortunately we didn't have a choice as our mascot server was down... Is it possible to broaden the scope of analysis by allowing .msf files as inputs as most labs these days have Thermo instruments. I once again thank you for your efforts..Will check new version and come back to you Regards Bhanu

hbarsnes commented 7 years ago

Hi Bahnu,

Is it possible to broaden the scope of analysis by allowing .msf files as inputs as most labs these days have Thermo instruments.

Most likely not. I think it would be more likely that we might add the fragmentation patterns analysis to PeptideShaker, but I cannot guarantee anything there either for the near future.

One thing you could perhaps try is to export the data from PeptideShaker in the format required by FragmentationAnalyzer and see if you're able to open the data in FragmentationAnalyzer? Look into the DataSets folder of FragmentationAnalyzer for examples of the files and the formatting required, it's basically two tab separated text files and the spectra as individual pkl files. If you manage to get this to work, you can basically load any data processed in PeptideShaker, independent of the search engine, or from any other source that can generate this format.

I will try to look into this myself as well, but I cannot give any promises. But I will reopen the issue so that I don't forget. :)

Best regards, Harald