Fig. 1
From: Scientific workflow optimization for improved peptide and protein identification
The complete peptide matching and retention time workflow within the optimization perspective. We optimized the workflow in two stages. The figure above shows the optimization of the X!Tandem peptide identification with following major steps: 1. decomposing the input files, 2. database search by X!Tandem, 3. recomposing the output files 4. statistical analysis of the result by PeptideProphet and 5. modeling of chromatographic retention times using an optimum choice of training set and prediction algorithm. The parts of the workflow, here the retention time prediction, are made partially transparent as they were not part of the optimization within this stage. The bottom left window also shows the dependency settings for the two input parameter MME+ and MME