iPRG 2011: A Study on the Identification of Electron Transfer Dissociation (ETD) Mass Spectra

The field of mass spectrometry based proteomics has seen several key innovations over the last several years, including novel experimental methods, new instruments, and unique fragmentation strategies. The latter, in the form of electron capture dissociation (ECD) and electron transfer dissociation (ETD) have captured the imaginations of many researchers, expanding their ability to identify and analyze peptides and proteins. However, since ECD/ETD spectra differ substantial from more traditional collision induced dissociation (CID) spectra in both their prominent ion series as well as their preferred bond-breaking characteristics, the (automatic) interpretation of ECD/ETD spectra requires novel algorithm optimizations. Efficient identification of ECD/ETD spectra thus remains an active and exciting field of proteomics informatics research. In this work, the ABRF Proteome Informatics Research Group (iPRG) presents the results of a collaborative study focusing on the analysis of an LC-MS/MS dataset from a yeast lysate digested with Lys-C and enriched for highly charged peptides using strong cation exchange fractionation. The data derived from one fraction analyzed exclusively by ETD was distributed to participants for analysis in several equivalent formats, along with a standardized sequence database derived from the UniProtKB/Swiss-Prot yeast complement, a decoy version of this database, and an applicable spectral library. Participants were free to use any and all methods available to them to identify this fraction, and results were to be submitted using an Excel template. All participant identities were subsequently anonymized, and a survey was used to collect information about participant experience and software tools used to produce the submitted analysis. This uniform collection of data has allowed a thorough comparison of participant results. A summary, including a comparison of results submitted by members of the iPRG, will be presented.