MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments.

Authors: Matthew J. Rardin, Birgit Schilling, Lin-Yang Cheng, Brendan X. MacLean, Dylan J. Sorensen, Alexandria K. Sahu, Michael J. MacCoss, Olga Vitek, and Bradford W. Gibson.

Data sets acquired on a TripleTOF 5600 mass spectrometer and uploaded to Panorama:

• MS1 and SWATH-MS – Kinase Inhibitor Study for quantifying changes in endogenous phosphopeptide isomers YHGHpS²⁹³MSDPGVSYR and YHGHSMSDPGVpS³⁰⁰YR from PDHE1a (3 injection replicates), go to Kinase Inhibitor Study in Panorama, download Kinase Inhibitor Study.
• MS1 and SWATH-MS – dilution curve of heavy labeled phosphopeptide isomers YHGHpS²⁹³MSDPGVSYR and YHGHSMSDPGVpS³⁰⁰YR from PDHE1a (3 injection replicates), download various isomer ratio sub files: 16:1/1:16, 8:1/1:8, 4:1/1:4, 1:2, 1:1.

• MS1 and SWATH-MS – Optimization of SWATH window size (25 and 10 m/z, respectively) to reduce interferences in a mitochondrial lysate (5 injection replicates), go to SWATH Optimization Study in Panorama, download SWATH Optimization Study.

• MS1 and SWATH-MS – MS1 and MS2 Data Processing Study for removal of interferences using mitochondrial lysates at a concentration of 100 ng or 33 ng (2 process replicates, 3 injection replicates), go to Data Processing Study in Panorama, download Data Processing Study (sample legend).