AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAHHHH!!!
One of the biggest challenges in adopting a new piece of hardware is that you might lose access to software that you've used for years and are very comfortable using. Losing MetaMorpheus by adopting TIMSTOFs hurt. For real. And this isn't a dig on other great software out there - I just know how to use MM and how to read the data and how to make MM do what I want it to do. I have whole downstream pipelines for HLA peptide analysis that uses MM scoring output as the input.
This week when I thought I was seeing artifacts in a collaborators Orbitrap Eclipse data - boom - broke out MM - and found some weird peptide mods I've never even heard of before.
If you need my pitch for MM this is it - it can look through your data for dozens or hundreds of PTMs and technical artifacts - and it can provide relative quantification data for them. If there is something out there that can point out ....ummm....that's a lot of iron adducts on your peptides...what's up in this batch?? This is the software.
And now I can use it again!?!?!?
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