Monday, January 26, 2015

Do you think your label free mass spec quan algorithm is the best? Want to prove it??!?!

Every few months I tell myself I need to pay better attention to what those smart people in ABRF are doing.  Unfortunately, it tends to slip down my impossibly large list and I don't get around to it.

Point in case:  This awesome analysis ABRF is doing right now!   The study is called "Differential Abundance Analysis in Label Free Quantitative Proteomics".  I should probably stop to read  the whole thing but I won't have time until much later tonight.  I had to get this out there because the deadline is really soon.  Like 5 days soon.  The files, requirements and everything are available.  The challenge?  Download these files and run them through your label free quantification pipeline.  Then lets all compare our results.

If you are interested you'll probably want to download these now, cause we know how long an analysis of this type tends to take!

Shout out to Brett Phinney for sending me an email tipping me off to this pending deadline!


  1. "Therefore, peptide identifications that can be assigned to multiple proteins should be ignored. Such identifications have already been removed from the provided files."

    These proteins can sometimes be estimated quite accurately, if they're shared with another protein that has unique peptides. It's a shame they've assumed that they are too difficult to use.

  2. Hello Ben,
    They included only technical replicates (3) for the analysis and no biological ones. This unfortunately prevents you from doing proper t-test or anova based statistics and limits you to rather simple FC vs intensity statistics.
    I would say that is a poorly designed study for the purposes of evaluation of LFQ algorithms and downstream differential analysis statistics.