Fig. 1

Schematic Overview. (a) Sample preparation for the H. salinarum NRC-1 library. H. salinarum NRC-1 grown to mid-exponential and stationary phase was subjected to data-dependent acquisition as unfractionated and fractionated digest. Endogenous samples were supplemented with synthetic peptide measurements for increased proteome coverage; (b) Library generation scheme. Data were searched with Comet, X!Tandem and OMSSA. Data were analyzed with the Trans-Proteomic Pipeline including PeptideProphet and iProphet followed by the generation of a raw, consensus, and spectral ion library; (c) DIALib-QC. The quality of the full spectral assay library and the 100 variable windows applied library was assessed with DIALib-QC, a software tool to evaluate libraries for defects and weaknesses; (d) Application of the H. salinarum NRC-1 spectral assay library. Analysis of H. salinarum NRC-1 collected at four time points of growth and in three biological replicates employing DIA/SWATH-MS and targeted data extraction using the developed H. salinarum NRC-1 100 variable window spectral assay library.