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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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unable to do fragment ion selection #2

Open bhanu2008 opened 8 years ago

bhanu2008 commented 8 years ago

hi I am using fragmentation analyzer ver 1.5.13. earlier version of the same (1.5.11)had an option to select the fragment ion type (right click on the top tab) when we do a fragment ion probability map. however i am unable to find this option in the latest version. I wanted to specifically look at b,y and neutral loss ions. Regards, Bhanu

hbarsnes commented 8 years ago

Hi Bhanu,

Thanks for letting us know. The right click pop up menu indeed seems to have disappeared. I will look into it and get back to you.

Best regards, Harald

bhanu2008 commented 8 years ago

hi Herald, Thanks for prompt response, hope bug will be fixed. I also would like to know if there is a means by which the data or stasical significance values can be incorporated in the out put for intensity, ion occurence studies. Best Regards Bhanu

hbarsnes commented 8 years ago

Hi Bhanu,

The issue with the popup menu has now been corrected and a new version will be released as soon as possible. I will let you know when it is available. Note that you may have to select the internal frame header first via a left click before you can use the right click option to make the menu appear.

I also would like to know if there is a means by which the data or stasical significance values can be incorporated in the out put for intensity, ion occurence studies.

I'm afraid this information is not directly available right now. It ought to be possible to add such an export though. However, as FragmentationAnalyzer is not actively maintained at the moment (we've moved on to PeptideShaker which includes some of the same functionality, see http://compomics.github.io/projects/peptide-shaker.html), I cannot tell you when I might get the time to look into this. But if you tell me exactly what you need I will let you know if I get the time to implement it.

Best regards, Harald

bhanu2008 commented 8 years ago

Hi Herald, Thank you, Eagerly waiting for new release. \ But if you tell me exactly what you need I will let you know if I get the time to implement it.** I chemically labelled my peptides and was looking at its influence on fragment ion distribution, I used FTICR orbitrap, Although the average fragment ion occurence shows distinct changes in terms of b/y ion occurence. I am unable to deduce actual data (b/y) at each amino acid position from the plot, same is the case for individual intensity plots at each position. will it be possible to have separate output folder for processed data (individual PSM or normalized ion occurence)?. I am actually using peptide shaker too, can you tell me how can i compare effectiveness of modification on peptide fragmentation/ protein identification using peptide shaker. Thanks and Regards Bhanu

hbarsnes commented 8 years ago

Hi Bhanu,

Maybe you already noticed, but the updated FragmentationAnlyzer is now available: http://genesis.ugent.be/maven2/no/uib/FragmentationAnalyzer/1.5.14/FragmentationAnalyzer-1.5.14.zip

Please let me know if you still have issues with the pop up menu. (As mentioned above, note that you may have to select the internal frame header first via a left click before you can use the right click option to make the menu appear.)

I chemically labelled my peptides and was looking at its influence on fragment ion distribution, I used FTICR orbitrap, Although the average fragment ion occurence shows distinct changes in terms of b/y ion occurence. I am unable to deduce actual data (b/y) at each amino acid position from the plot, same is the case for individual intensity plots at each position. will it be possible to have separate output folder for processed data (individual PSM or normalized ion occurence)?

I will try to look into it, but I'm afraid it most likely won't happen for the next couple of weeks, as we're swamped with other work already...

I am actually using peptide shaker too, can you tell me how can i compare effectiveness of modification on peptide fragmentation/ protein identification using peptide shaker.

Could you not simply do two searches, one with the modification and one without, and compare the results? We don't have a way of comparing PeptideShaker projects yet, but I guess you could compare the exports? Not perfect, but should give you an indication?

Best regards, Harald

bhanu2008 commented 8 years ago

Hi Herald, Thank you.. Regards Bhanu