I'm not going to say I know everything that is going on in this rapidly expanding field. But...I feel like I read kindof a lot of papers. So...when someone in a building that I walk by ALL THE TIME writes a piece of software that converts Proteome Discoverer output into the very useful mzIdentML format, I feel pretty dumb for not catching it for a couple of years.
And...that is exactly what this awesome paper from Paul Aiyetan et al., does.
Since it was published in 2014, and presumably work started on it earlier than that, it was originally designed for PD 1.3. Fortunately, however, if you go to Dr. Aiyetan's BitBucket account here, you'll see that he's updated it with new versions as recently as around this time last summer. You'll also see some stuff that sounds really cool that I'll need to investigate!
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