Oh yeah! Can't wait to try this out!
Most interesting, maybe is that in the application of isobaric match between runs and new stats with/without reference normalization - it looks like pooled reference channels between plexes may not be necessary. The link above is my kluged together solution for matching between TMT plexes without reference/pools using high abundance "boring" proteins and I largely put that post there so I could find those same data and quickly compare the two.
Something I hoped to get a good answer to from the paper is whether the TMT MBR was working well for non-Orbitrap data. I used it for a relatively small TIMSTOF TMT set from early 2021 and it did appear to decrease missing values, but n=1 and I could have just got one of my settings off between runs 1 and 2, but it could be a gamechanger for some of the stuff we're working on. You want to hear that it is working before you ask MaxQuant to load up 600 Bruker .d files, though, but sometimes you just have to YOLO and apologize to the other users of that PC later.
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