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MS/MS Data

MS/MS Data. Protein Database. Sipros configurations: Peptide/Protein identification Post-translational modification Amino acid mutation Stable isotope probing. Database searching MPI/OpenMP. Sipros. Filtering/Assembly. ProRata configurations: Label-free quantification

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MS/MS Data

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  1. MS/MS Data Protein Database • Sipros configurations: • Peptide/Protein identification • Post-translational modification • Amino acid mutation • Stable isotope probing Database searching MPI/OpenMP Sipros Filtering/Assembly • ProRata configurations: • Label-free quantification • PTM quantification • Isobaric chemical labeling • Metabolic labeling Spectral counting Statistical analysis ProRata TMT/iTRAQ SIC analysis Supplementary Figure 1: Sipros/ProRata software framework. Programs can be executed with flexible user-defined configurations. Workflows for different types of measurements are shown on the right. Modules were developed in C++ (red), Python (blue), or R (green). SIC – selected ion chromatography.

  2. Supplementary Figure 2: Scalability test of Sipros on Titan. The speed-up was normalized based on the speed of 4000 CPU cores (250 nodes). The actual speed-up of Sipros on 8000, 16000, and 24000 CPU cores (red dotted line) was close to the ideal linear speed-up (green solid line).

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