It is a frustrating situation. To give context to others
I track plant proteomics. When I read Mesnage 2016 something felt off. In the suppl data, protein masses were way too small, and there were protein IDs listed multiple times w/ both increasing & decreasing fold changes 1/5
I track plant proteomics. When I read Mesnage 2016 something felt off. In the suppl data, protein masses were way too small, and there were protein IDs listed multiple times w/ both increasing & decreasing fold changes 1/5
I found that while the papers claimed to find protein-level changes, they actually quantified peptides. If any peptide measured differently between samples the entire protein was called perturbed - Even if all other peptides mapping to that protein had no/conflicting changes 2/5
Peptide-level quantification just isn't equivalent to a protein-level quantification. Using a single peptide species to make conclusions about a protein's level while ignoring measurements of all its other peptides will definitely lead to high numbers of false-positives. 3/5
My proteomics colleague at UT and I sent a Letter to the Editor of Scientific Reports.
I've described the quantification methods in Mesnage 2016 & 2017 to every TMT expert I've met, and they encourage me that: No, it's not OK, keep going, keep following up w/ the journal. 4/5
I've described the quantification methods in Mesnage 2016 & 2017 to every TMT expert I've met, and they encourage me that: No, it's not OK, keep going, keep following up w/ the journal. 4/5
I wouldn't publicly call out something like this frivolously. It's not as Antoniou says just 'isoforms and PTMs' or me needing to read an Intro to Mass Spec textbook. The papers' statistics are wrong. What's the course to take? 5/5
