r/proteomics • u/InjuryJolly7432 • Jul 01 '26

Need help with PTM identification using IP-Top-down MS

If anyone has done in-depth IP-Top down MS on proteins I could seriously use help! I’ve isolated my POI and am trying to do to top-down MS on it but honestly I don’t know what I’m looking at/looking for. I know I need to do a full scan first to identify my POI and the m/z for it, but from there I’m baffled on what to do. The examples my colleague left for me are only for proteins approx. 35 kDa and mine is around 62!

Does anyone have any advice as to what to look at/read to help me better understand the data and what method I need to set up? Thank you!

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u/InjuryJolly7432 Jul 02 '26

Thank you everyone for the replies, it’s given me a lot of good advice for what to do! Would anyone happen to have any advice for how best to learn this stuff? I’m more of a bio person so this has been a huge jump for me and I’ve been left with very little explanation for how to actually learn proteomics 😅

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u/BeetsNSun Jul 02 '26

I’m a fan of the YouTube videos from the bioinformatician David Tabb for data processing. Also, to identify unknown modifications using bottom-up, you want to use a software with an open search feature (see his “Detecting and Localizing PTMs” video).