Researchers at the Institute for Systems Biology and the Swiss Federal Institute of Technology have developed a new repository for collecting experimental selected-reaction monitoring mass spec data.
Named Passel, the database is intended to provide experimental SRM assay data to complement the synthetic peptide-derived assays that currently compose the bulk of the ISB- and ETH Zurich-developed SRMAtlas. The researchers detailed their work in a paper currently in press in the journal Proteomics.
"There are four components to SRMAtlas," Terry Farrah, an ISB researcher and first author on the paper, told ProteoMonitor. "The synthetic peptide measurements; The measurements from shotgun proteomics experiments that we incorporate for peptides for which we don't have synthetic peptide data; [theoretical predictions] for those peptides for which we have neither synthetic peptides nor shotgun experiments; and now we are going to incorporate the data from Passel [so that] people can see which peptides worked best in real experiments."
Led by ISB director of proteomics Robert Moritz and ETH Zurich researcher Ruedi Aebersold, the SRMAtlas project has compiled more than 170,000 single reaction-monitoring assays – one each for at least five proteotypic peptides for each of the 20,300 human genes currently annotated as protein-encoding.
The aim of the work is to build a set of standardized SRM assays that proteomics researchers can use to more easily investigate proteins of interest. Building SRM assays from scratch is a time-consuming process in which researchers must identify the peptides on which to base assays for a given protein; determine the best transition to explore using mass spec; and develop and optimize methods for performing the separation and the assay.
The SRMAtlas essentially takes care of these steps for proteomics researchers, allowing them to detect and quantify proteins important to their research without going through the process of developing mass spec assays for each protein.
However, as Aebersold noted at the Human Proteome Organization's 10th annual meeting last September, the assays in the SRMAtlas won't necessarily be best suited to all biological sources and situations. "Even though [these assays] generate very good fragment ion spectra, they may not be detectable in a biology source for many reasons," he said.
Because "most of the data in the SRMAtlas are … not derived from measurements in biological samples," Farrah and her co-authors wrote, "[they] do not account for sample-specific issues such as interfering signals, ion suppression, or other chemical components that can confound an assay."
Indeed, in previous interviews, several researchers doing independent SRM-MS work have told ProteoMonitor that the assays contained in the SRMAtlas have not turned out to be the best ones for their projects. For instance, in a discussion of his research using SRM-MS for drug-metabolism studies, Tohoku University scientist Tetsuya Terasaki said, "frankly, we are not too satisfied with those databases. We've compared results [using peptides] selected by our algorithm and [peptides] from the [SRMAtlas] and our experience is that we prefer to use our own selection criteria."
ISB researcher Eric Deutsch, who is leading the Passel effort, introduced the database at last year's HUPO meeting in September, and aims to round out the SRMAtlas resource by adding other researchers' experimentally derived SRM-MS assays and datasets.
"As you dial in a protein or proteins in SRMAtlas, you'll be able to see successful experiments that have been used [for that protein] before," Deutsch noted at the HUPO meeting.
The database, Moritz added at the time, would enable researchers to compile "multiple views of the same peptide by different groups … and we can start analyzing how well … a particular peptide performs in the different biological experiments that people are doing."
As mass spec-based proteomics moves towards the clinic, SRM-MS has become one of the field's more prominent and most clinically promising technologies.
"Now that a substantial number of datasets are being published, an SRM experimental data repository would be of great benefit to the community by providing a centralized location where well-annotated SRM data and results, with all their sample and experimental-specific issues and raw data files, can be permanently stored, explored, cross-compared, assessed by reviewers, and reused by other resources," the authors of the Proteomics paper wrote.
According to Farrah, Passel currently holds publicly available SRM data from seven experiments, along with data from ten experiments that the researchers will make public once the studies have been published. All of the experiments submitted thus far have come from academic and non-profit labs, she said.
Farrah added that Passel could prove a valuable tool for journals that ask researchers to provide the raw mass spec data from their SRM experiments – much as the ISB's PeptideAtlas and University of Michigan's Tranche databases have done for shotgun proteomics data.
"A couple of people have approached me and said, 'I'm submitting a manuscript to this journal and they want me to make my data available to the reviewers, can I do that by way of Passel?'" she said. "We've done that, and we do hope that Passel will serve [as a way for researchers] to fulfill journal requirements that data be shared in order for an experiment to be published."
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