The 2012 PRG Study: Assessing Longitudinal Variability in Routine Peptide LC-MS/MS Analysis

The PRG study for 2012 is intended to catalog critical parameters of variability influencing LC-MS/MS data quality within labs over a nine month period between March and November, 2012. This study is intended to inform participant labs of key areas of variability in their routine qualitative and quantitative analyses. A dried digested protein mix is sent to labs in aliquots with the expectation that once per month a new vial will be reconstituted and analyzed using routine LC-MS and data-dependent MS/MS acquisition settings. Participants will return the raw data to a centralized server for analysis. The analysis consists of 42 MS and MS/MS metrics that have been determined through the efforts of the CPTC consortium and implemented in open source software from NIST (“MSQC”) and Vanderbilt University (“QuaMeter”). Of key importance in the design of this study is the lack of a standard operating protocol. The concept is to determine variability within a lab when that lab uses their own routine settings and QC measures. A survey is conducted with each sample submission to catalog changes in operators, acquisition settings, as well as routine and non-routine maintenance procedures. As of date, there were 95 labs in 23 countries requesting sample. Within these labs are 25 different models of mass spectrometers from 6 commercial vendors.