Introduction:
Selected reaction monitoring (SRM) using triplequadrupole mass spectrometers has been the foundationfor smallmolecule quantitation for several decades. It isalso emerging as a powerful technique for targetedquantitativeproteomics due to its high sensitivity,selectivity, and throughput1,2. However, developing anSRM assay for targeted proteins remains challenging. One of the main obstacles is finding the best peptides that aresequence specific or unique and give sufficient signal intensity without using specific protein/peptide standards.

Peptide selection generally relies on using either prior proteomics discovery data or computational prediction3. A candidate peptide list can be rather long to cover multiple proteins of interest and the required transition list can easily exceed one thousand. To quickly find the best prototypic peptides and the best SRM transitions for each peptide from the large number of candidates, a triple quadrupole system must be able to survey hundreds of
peptides, with proof of their identities, in a single HPLC-MS run.

To address this challenge, we’ve incorporated a new intelligent SRM (iSRM) technology into the current Thermo Scientific TSQ family of triple quadrupole mass spectrometers for quantitative proteomics. This technology enables processing of over 15,000 SRM transitions for simultaneous quantification and identity confirmation of up to 1000 peptides in a single HPLC-MS run4, which dramatically reduces the labor and cost of developing multiplexed SRM assays. It is fully supported by our Pinpoint software5 (www.thermo.com/pinpoint) from iSRM instrument method generation to data processing.

To read/download the complete application note, please use the link on this page.