Home › Biochemistry › A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Biochemistry JoVE (Open Access) Citable · DOI

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

DOI: 10.3791/57633-v
What you'll learn
  • ✓ Map mass spectrometry-identified peptides to reference genomes using PoGo software
  • ✓ Visualize proteogenomic data with post-translational modifications and variants
  • ✓ Integrate peptide mappings with genomics browsers (IGV, UCSC Genome Browser)
Protocol

Here we present the proteogenomic tool PoGo and protocols for fast, quantitative, post-translational modification and variant enabled mapping of peptides identified through mass spectrometry onto reference genomes. This tool is of use to integrate and visualize proteogenomic and personal proteomic studies interfacing with orthogonal genomics data.

Difficulty
intermediate
Total time
~2–4 hours per dataset (depending on file size and number of samples)

Steps

1
Map peptides using PoGoGUI interface

Load mass spectrometry-identified peptides and reference genome into PoGoGUI to perform fast, quantitative peptide-to-genome mapping with PTM and variant support.

▶ 00:51
2
Visualize mapped peptides in IGV

Import mapped peptide results into Integrative Genomics Viewer (IGV) to inspect alignment quality and genomic context.

▶ 02:36
3
Map peptides from custom variant database

Apply PoGoGUI to peptides identified through variant-aware databases to map genetic variants onto the reference genome.

▶ 03:57
4
Process multiple peptide files batch

Use PoGoGUI batch processing to map peptides from multiple mass spectrometry runs simultaneously.

▶ 04:44
5
Generate and visualize track hub

Convert mapped peptide results into a UCSC Genome Browser track hub for web-based collaborative visualization.

▶ 05:48
6
Review PTM and variant mapping results

Examine output showing post-translational modifications and genetic variants mapped to genomic coordinates for quality control.

▶ 06:50
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