In a development that is expected to further the use of MS for proteomics research and biomarker analysis, the Institute for Systems Biology and the Swiss Federal Institute of Technology have announced that they have generated gold-standard reference mass spectra for each of the human genome’s 20,300 protein-encoding genes. This completes the first phase of a two-year Human Proteome MRM Atlas project. According to the project’s National Institutes of Health grant proposal, the MRM Atlas “will contain all the relevant peptide biophysical information, fragmentation information, instrumentation conditions, as well as links to some validated assays.” Such information will allow for the improved detection and quantification of human proteins in biological samples.

For the project’s first phase, AB SCIEX and Agilent Technologies provided instrument support, JPT Peptide Technologies and Thermo Fisher Scientific supplied synthetic peptides, and OriGene provided purified human proteins. Thermo announced that it expects to supply more than 100,000 synthetic peptides for the entire project.

In the first phase, the researchers created more than 150,000 multiple reaction monitoring (MRM) assays. MRM MS, a targeted proteomics approach, monitors a set of selected fragment ions for precise peptide quantification using triple quadrupole MS. To create the assays, proteotypic peptides were derived using algorithms for peptide prediction and the Institute for Systems Biology’s Peptide Atlas. The information will be available through the MRM Atlas website, from which it can be downloaded and used in any MRM method for triple quadrupole MS.