Inspired by “Computation and statistics for mass spectrometry and proteomics” meeting,

”ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of
Differentially Abundant Proteins in Label-Free Quantitative LC−MS/MS
Experiments”, Choi et al., Journal of Proteome Research, 2017.
https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.6b00881?src=recsys

Tandem mass spec -- ioniziation, spearation, fragmentation, separation

Comparison of validation results from multiple core facilities. Provide samples
with no biological variation. Many have terrible outputs, full of false
positives and inconsistent results between experiments. Many used the same
tools, but parameters matter a lot: recommend markdown or executable notebooks.

Statistical analysis of counts with DEseq2, lots of zeros so need negative
binomial distribution. Use peak intensities with real data.

Also looked at software used to call peaks: Skyline.
