The choice of a specific mass spectrometer for a specific proteomic application is critical. Furthermore, the combination of optimized settings with efficient data analysis pipelines or parameters can heavily influence results. The aim of this study was to maximize protein identification on instruments available in the Mass Spectrometry Core Facility at the Sydney University. A single tryptic digest of mouse liver was analysed using highly similar chromatography conditions on a variety of instruments including the TripleTOF 6600, Q-Exactive and LTQ-Oribtrap Velos Pro. Initially, optimization of settings was performed on the TripleTOF 6600 to maximize protein identification with nanoUHPLC and long gradients. A “Fast” and “Sensitive” acquisition strategy was devised similar to (Kelstrup et. al., J. Proteome Res., (2012), 11(6); 3467) and used to compare triplicate high load injections for single-shot proteome analysis. Next, data-analysis pipelines were directly compared including Proteome Discoverer, MaxQuant and Protein Pilot. These data will provide valuable insights into efficient protein identification with various platforms.
To access your personal details, event notifications, favourite abstracts, recorded notes and other features please provide your Currinda login details below.
PROTEOMICS 2015*