Quality Control Analysis

Introduction

In shotgun experiments, it is vital to verify key quality control metrics in order to be sure that nothing went wrong in the identification process. PeptideShaker allows you to screen metrics at the protein, peptide and peptide to spectrum match level. If a metric of interest is missing, please contact the developers and we will try to add it.

PeptideShaker sorts the selected population according to the selected metric. Matches are separated into three classes:

These plots will also help you defining thresholds for downstream analysis like inclusion/exclusion lists generation, quantification analysis or PTM investigations.


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Proteins

For all proteins, it is possible to inspect:
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Peptides

For all peptides, it is possible to inspect:
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PSMs

For all Peptide to Spectrum Matches (PSMs), it is possible to inspect:
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