Enhanced Match Between Runs Output Explained

If you have followed the protocol for enhanced match between runs, which used spectral similarity as an added measure of confidence for peak assignment then new output is generated and some additional information is added to existing quantitative output files. MbrAnalysis.psmtsvMbrAnalysis.psmtsv

The first output is a new folder, MbrAnalysis. This folder contains a single, tab-delimited output file, MbrAnalysis.psmtsv. This file contains peptide quantification data for all data files searched. If a peptide was observed in a raw file during the search prior to quantification, then its results are included. There is no filter for score. Only one copy of a peptide is included for each file. This is not a PSM list. The first round q-value, PEP value and PEP q-value are provided. If an MS2 spectrum for the peptide is found during the round of enhanced MBR, a spectrum similarity calculation is performed against a library spectrum generated from the top scoring version of the peptide from the entire data set. Once all spectral similarity calculations are performed, a second round of FDR analysis is performed and a new set of FDR values is computed (q-value, PEP value and PEP q-value). These columns are added as the last columns of the MbrAnalysis.psmtsv output file. In this way, it is easy to see the confidence for the MBR peak.

The second output generated is simply an update to an existing output file, AllQuantifiedPeptides.tsv. Each quantified peptide will be given one of the following designations: NotDetected, MSMSIdentifiedButNotQuantified, MSMS, MBR, MSMSAmbiguousPeakfinding. In addition, four more designations are possible with respect to the spectral angles: NA, Spectrum Not Found, a numerical value for the spectrum similarity between 0 and 1, or -1.