Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation

Mass spectrometry (MS) based proteomics now enables the analysis of thousands of phosphorylation sites in single projects Among a wide range of analytical approaches, the combination of high resolution MS scans in an Orbitrap analyzer with low resolution MS/MS scans in a linear ion trap has proven to be particularly successful ( high-low strategy) Here we investigate if the improved sensitivity of higher energy collisional dissociation (HCD) on an LTQ-Orbitrap Velos instrument allows a high-high strategy A high resolution MS scan was followed by up to 10 HCD MS/MS scans and we achieved cycle times of about 3 s making the method compatible with chromatographic time scales Fragment mass accuracy increased about 50 fold compared to the high low strategy Unexpectedly, the HCD approach mapped up to 16 000 total phosphorylation sites in one day s measuring time the same or better than the standard high low strategy Reducing the target values from a standard of 30 000 to 5000 ions did not severely affect identification rates but did decrease identification and localization scores for phosphorylation sites We conclude that HCD in the new configuration is now a viable method for large scale phosphoproteome analysis alongside collisional induced dissociation (CID) and electron capture/transfer dissociation (ECD/ETD)