Fixed it! Wrong butterfly, but I don't care and neither do you! This is the whole genomics vs proteomics argument -
same genome - different proteome! Where are the wing proteins in the early life cycle stages, Mr.Genome person? Checkmate.
Let's go!
The data was acquired on a Q Exactive Classic using nanoLC and DDA. Data was searched in Proteome Discoverer 1.4 (I guess they could have cited something for the software. I wonder where they'd find a reference for that?) and a RefSeq genome with 19k protein sequences (whoa!) was used for analysis. Okay, peptide mass tolerance is too high by about 20x for this instrument, but maybe they did that to increase the number of bad hits for the FDR. The method for estimating FDR isn't disclosed, so it might be anyone's guess.
Oh. Weird. I think they spectral counted. In 2025 2026 on a Q Exactive which has onboard electronics to limit repetitive peptide sampling...? Interesting.... And they used a microarray normalization R package for differential quan....which...is.... whatever.
They did pull data from a previous paper where they did transcriptomics on another pile of these butterflies, which is cool, and demonstrates that basically transcript abundance is a pretty uselessthing to do with your time.
The data is up on ProteomeXchange if you wanted to do a reanalysis with a less eccentric data analysis pipeline as well!
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