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I have mass-spectrometry data (Human cellsanalyzed and annotated by MaxQuant). I want to find which peptides are covering positions of former splice junctions (on the mRNA sequence), based on protein id and peptide positions.

Where could I find an appropriate data? I want to know, based on peptide-sequence, annotaion and position on protein, whether this peptide is a single exon, or if it contained areas of former splice junctions.

Itai

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    $\begingroup$ Hello Itai, what do you mean by "appropriate data'? Do you mean where you can find annotations of splice junctions? What species? Please, edit your question and be clear and verbose. The second thing that could be improved is that your question shows very little research effort. What have you tried? Have you found any clue how the problem could be resolved? Yes? Write it here. $\endgroup$
    – Kamil S Jaron ♦
    May 19 '19 at 11:38
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    $\begingroup$ I edited the question $\endgroup$
    – Itai Roth
    May 19 '19 at 12:29
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    $\begingroup$ Well done, It's way clearer now. Maybe just add the species you are looking at and the results of your own research on the topic... $\endgroup$
    – Kamil S Jaron ♦
    May 19 '19 at 15:01
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If you are considering the human genome as "data" (not mRNA), I would run your single peptide via tblastn which will take your protein(s) translate them to nucleotides and run a blast against Genbank. The splice sites will be immediately apparent because they force indels in your query. If there are no indels there are no introns (splice sites). If you want to process several proteins, one solution is to use eblast, a command line version of tblastn (Anaconda package). You can confirm this against a full genome annotation (note, I don't work on humans).

Alot of work has been done on splice sites, a friend worked on this, but I think you just want to focus on a restricted number of target peptides in your mass spec. output.

mRNA should be avoided IMO if you are looking for splice sites, i.e. intron boundaries.

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    $\begingroup$ eblast sounds like a great idea, thanks! $\endgroup$
    – Itai Roth
    May 20 '19 at 8:42

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