Two new proteomics technology papers published by Olsen Group

The Group of Prof. Jesper V. Olsen published two technical notes in Journal of Proteome Research describing new Q Exactive HF mass spectrometric instrumentation and proteomics sample fractionation strategy.

1. High pH reversed-phase peptide fractionation for ultra-deep phosphoproteomics

The first paper (Batth et al) describes a practical offline peptide fractionation strategy based on high pH reversed-phase chromatography that in combination with phosphopeptide enrichment and optimized parameters for orbitrap mass spectrometry analysis allows us to identify close to 40,000 phosphopeptides from single samples in less than one day of MS instrument time. This is more than twice the number compared to current state of the art technologies. The result is better quantitation, much deeper coverage of signaling pathways, and in particular of low abundant tyrosine phosphorylation sites that are especially interesting since tyrosine kinases are key initiators of signaling cascades and prominent drug targets.

2. Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Q Exactive HF Mass Spectrometer

The second paper (Kelstrup et al) describes the latest generation of orbitrap mass spectrometer, the Q Exactive HF, for ultra-deep analysis of proteomes and post-translational modifications from human samples. This new ultra-high-field Orbitrap mass analyzer is capable of sequencing speeds above 20 Hz and it routinely exceeds 10 peptide spectrum matches per second or up to 600 new peptides sequenced per gradient minute. We demonstrate how we can now identify 4400 human proteins in one hour and achieve very deep proteome coverage by identifying more than 140,000 unique peptides from 14 high pH reversed-phase fractionated peptide samples each analyzed by one hour LC-MS gradients.