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. Author manuscript; available in PMC: 2021 Mar 14.
Published in final edited form as: Nat Methods. 2020 Sep 14;17(10):981–984. doi: 10.1038/s41592-020-0955-0

Figure 1 : Outline of MassIVE.quant repository structure, and reanalysis of three DDA-based experiments.

Figure 1 :

Each step can be performed with multiple algorithms and software tools, generating tool-specific files in diverse formats. For the experiments in the figure, MassIVE.quant stores the intermediate outputs from combinations of algorithms and tools for peptide ion identification and quantification. For example, DDA:Choi2017 was processed with eight combinations of parameter settings in Skyline. Each reanalysis is saved with a unique reanalysis ID, prefixed by RMSV, under the experiment repository prefixed by MSV in MassIVE.quant.