Friday, January 2, 2026

Multi-instrument comparison of a proteomics process control pipelines!

 


How would your favorite mass spec do in a head to head in a process control pipeline? What's that? Something practical in manufacturing things, probably! Ask an AI, it will make some dumb shit up about it. Google's moron of an AI I can't seem to turn off just lied to me extensively about how many points different field goals in basketball count for. Unless I started the New Year with a stroke, I'm pretty sure I can't trust Doogle for anything now and I'm happy about this surprisingly inexpensive IOS migration in progress. 

What, was I typing about a paper? Yes! A preprint. This one! 


These authors prepared multiple combinations of two bacterium mixtures and used everyone's instruments. There's an Orbi, a TIMSTOF HT, a ZenoTOF, and even two Waters instruments. One of which I don't think I've ever even heard of. Either it's old or they called it something different in the UK, or I did have that stroke. Further evidence for the latter thing is that they somehow got Waters data into DIA-NN and MSStats! Except the Waters I don't know about, which was processed with Skyline. Sure, there are raw numbers here, but the cool part is that the authors focus on the pathways that they actually care about, and basically every instrument does really well in that regard, with the Vion being the clear outlier (on the bad side, but that might be Skyline 😜). 

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