Proteomics in mixtures: Study results of ABRF-PRG02

The trend in proteomics is to work with increasingly complex protein mixtures, limiting the protein separation steps prior to analysis. This is due in part to the difficulties encountered with detecting low abundance proteins, protein losses during SDS PAGE, and the limited separation capability of even 2D PAGE where a single protein spot may still contain multiple proteins. Hence, the ABRF-PRG02 sample was designed to study a simple protein mixture of five proteins at the approximately 2 pmol and approximately 200 fmol levels. The sample, after a tryptic digestion, was sent out by the Proteomics Research Group of the ABRF to interested member labs. A total of 41 labs participated in this study, with each participant using some type of mass spectrometric analysis. Laboratories that used microLC-NSI (microLC with nanospray ionization) with MS/MS analysis had a higher percent accuracy than labs using MALDI-MS (matrix assisted laser desorption ionization mass spectrometry).