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

摘要

As quantitation in DIA is carried out using ion intensities of MS2 fragments, the role of MS1 precursors ions in these workflows have largely been ignored, despite the fact that their respective ion abundances are higher. In our case a high resolution MS1 scan of good quality requires <8% of the total DIA duty cycle, making its acquisition time minimally disruptive for the majority of experiments. We have described a new approach developed as part of the Skyline software platform for extraction of ion intensity measurements from MS1 and MS2 scans, called Integrated Dual Scan Analysis (IDSA) that has several distinct advantages. Importantly, both MS1 and MS2 data sets can be readily extracted and analyzed from a single acquisition in combination or individually using the Skyline software platform. Moreover, we show that this data can be used to better detect MS2 ion interferences, combined for downstream statistical analysis, help assign peptide isomers, and be used independently for validation of MS2-based quantitation.