There are amendments to 10.1038/nbt. 2841

220 volume 32 NumBeR 3 mARCH 2014 NATURE BIoTECHNoloGy as Skyline23 and PeakView (AB SCIEX), can visualize the XIC data, making manual analysis possible. Automation of this process is critical, however, because in a single typical SWATH-MS data set tens of thousands of peptides are identified. Here we present OpenSWATH, an opensource (Modified BSD License) software that allows targeted analysis of DIA data in an automated, high-throughput fashion. OpenSWATH is cross-platform software, written in C++, that relies only on open data formats, allowing it to analyze DIA data from multiple instrument vendors (Supplementary Note 1) 24. The algorithm can be summarized in the following five steps (Fig. 1 and