A novel algorithm for protein profiling based on cross-run correlations in SWATH-MS data implemented in Spectronaut

Abstract

References [1] Gillet, L.C., et al., “Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.” Molecular & cellular proteomics MCP, 2012. 11(6): p. O111 016717. [2] Bernhardt O. M. et al. “Spectronaut A fast and efficient algorithm for MRM-like processing of data independent acquisition (SWATH-MS) data.” ASMS 2012. [3] Escher C, Reiter L et al. “Using iRT, a normalized retention time for more targeted measurement of peptides.” Proteomics. 2012 Apr;12(8):1111-21. Figure 2. Schematic illustration of an analyte profile (green shade) spanning three different LC-MS runs. The retention time scale is normalized to iRT, remaining RT shifts are residual fluctuations. The analyte signal is above the limit of detection (LOD) in only a single run (*). In the two remaining runs the signals are below the detection limit and would typically result in missing values. In the illustration there is also an interference signal on the left side of the true signal (grey shade). Such signals, although nonspecific, are typically reproducible in similar sample matrices. Our algorithm uses the significantly identified signal from the first run as a template to rescue the correct signals in the remaining runs by means of cross-run correlations of the ion traces. The surrounding region including interferences is used as well.