Mass spectrometry (MS) data usually comprises spectra that must be bioinformatically processed to identify candidate peptides. These peptides include assignments, and counts can then be analyzed using a wide range of techniques and packages. The wide range of graphical user interface-driven tools for proteomics means that there is a proliferation of file formats that can be tough to deal with initially. These recipes will explore how to take advantage of the excellent parsers and reformatters available in the new RforProteomics project and associated tools for analysis and verification of spectra, and even show you how to view your peptides in genome browsers alongside other genomic information such as gene models.

In this chapter, we will cover the following recipes:

• Representing raw MS data visually
• Viewing proteomics data in a genome browser
• Visualizing distributions of peptide hit counts to find thresholds
• Converting MS formats to move data between tools
• Matching spectra to peptides for verification with protViz
• Applying quality control filters to spectra
• Identifying genomic loci that match peptides