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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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export algorithm score #508

Closed danyunghsu closed 1 year ago

danyunghsu commented 1 year ago

Hi all, I want to export each phosphorylated site and the respective algorithm score. I didn't find any instructions for the term algorithm score and algorithm raw score both on the website and in the paper. I did notice that Harold mentioned algorithm raw score is the unchanged score by the search engine. How does peptideshaker process the algorithm raw score into algorithm score actually? Besides, i find one phospho site corresponding to more than one score in the output txt file. Why does this happen? Can you help me? issuepeptideshaker

mvaudel commented 1 year ago

Hi and thank you for your question. For search engine results, the raw score is indeed the unprocessed score of the search engine, and the score is the combination of scores from all search engines. If only one search engine was used the raw score equals the score unless the score increases with the quality of matches, then we transform it (typically using -10log(raw_score) but this can vary depending on the algorithm). For peptides and proteins, the score is the combination of PSMs and peptide posterior error probabilities, respectively. If you are looking at phosphosites we recommend exporting results at the PSM or peptide level, then you will find site-level scoring. My understanding is that you are currently looking at the protein level. Then, if a peptide can be found on multiple proteins, or on multiple sites of the same protein, it will be reported multiple times. This is most likely the reason why you find the same peptides multiple times. Hope it helps, Marc

danyunghsu commented 1 year ago

Hi Marc, Thank you for your answer. What I want is the original score of each phosphorylated peptide given by amanda, not PEP. I found amanda score in the searchgui_output.zip, but i'm not sure which score it relates to when i export my results from peptide shaker. What score should i choose? Thanks Danyung amandascore

hbarsnes commented 1 year ago

Hi Danyung,

To get the original search engine scores you can make your own custom export which includes the "Identification Algorithm Results":

image

You'll find this option via the Export > Identification Features menu option, and then choose "Add new report type" at the bottom left.

hbarsnes commented 1 year ago

Issue assumed resolved. If this is not the case, please let us know and we'll reopen the issue.