Current triple quadrupole mass spectrometers allow measurement of more than 1000 precursor to fragment ion transitions in a single LC-MS run [1]. This corresponds to hundreds of peptides/proteins in a single multiple reaction monitoring run and a multiple of that in a full day. Combined with the increased throughput in assay generation [2, 3], this increase in throughput enables the design of high information content experiments. Manual processing of such experiments is tedious. But even more important manual curation is inconsistent as illustrated by the following example: Assume there are two samples, one with a synthetic peptide in solution, and another with the protein extract of a human cell culture. A very low intense signal derived from the pure peptide solution is likely to be the correct one. However, in the human cell culture sample, such signals as observed in the first sample can be observed just randomly given the sheer complexity of this type of sample.

In order to circumvent such biases and to speed up the process we use our mQuest software to automate scoring, and mProphet to have a statistically sound confidence assignment [4].

1. Stahl-Zeng J, Lange V, Ossola R, Eckhardt K, Krek W, Aebersold R, Domon B: High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics 2007, 6(10):1809-1817.
2. Picotti P, Rinner O, Stallmach R, Dautel F, Farrah T, Domon B, Wenschuh H, Aebersold R: High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nature methods 2010, 7(1):43-46.
3. MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ: Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics (Oxford, England) 2010, 26(7):966-968.
4. Reiter L, Rinner O, Picotti P, Huttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R: mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nature methods 2011, 8(5):430-435