Peptide-Spectrum Matches (PSMs)

Introduction

The Spectrum ID tab details how the peptides were matched to the spectra for the various search engines.


Go to top of page


Spectrum Selection

This table shows all the spectra per MGF file. Selecting a given row/spectrum will show the spectrum to the right and the peptides mapped to that spectrum by each search engine, and the PSM retained by PeptideShaker.

The search engine agreement is color coded in the second column in the table. Hold the mouse over a given color to learn what the colors mean. The same colors are also used in the PSM table in the Overview tab.


Go to top of page


Peptide-Spectrum Matches

For each spectrum it is possible to see all peptide assumptions made by the various search engines with the corresponding confidence. Above is the PSM retained by PeptideShaker. Note that selecting the PSM of choice updates the spectrum annotation.


Go to top of page


Spectrum

The currently selected spectrum is shown here with the annotations corresponding to the currently selected PSM in the Peptide-Spectrum Matches table to the left.

For more details on how to interact with the spectrum see the menu bar below the spectrum.


Go to top of page


Spectrum Identification Overview

The Spectrum Identification Overview plots shows the individual search engines performance and the combined PeptideShaker result.


Go to top of page