Bioinformatics for Proteomics
The classic Bioinformatics for Proteomics course: a hands-on walk through a full mass spectrometry data-analysis pipeline, from a raw spectrum file to a shared, quantified result. Work through the four modules in order, or jump to the step you need.
Archived materials. This page preserves the original course. Some tools, formats, and versions reflect the field as it was when the course was written and are now partly outdated (for example, PRIDE XML has been superseded by mzIdentML and mzTab). A modernised version is in preparation.
Identification
The full path from a raw file to validated peptides and proteins: format conversion, spectrum processing, database preparation, peptide-spectrum matching, inference, validation, PTM analysis, and de novo sequencing.
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1.1
Database generation
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1.2
Peak list generation
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1.3
Peptide to spectrum matching
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1.4
Browsing identification results
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1.5
Peptide and protein validation
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1.6
PTM analysis
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1.7
De novo peptide identification
Functional analysis
Turning an identification list into biology: retrieving protein information, pathway analysis, 3D structure visualisation, and Gene Ontology annotation.
Data sharing
Submitting and reusing data through community repositories: converting results to standard formats, submitting to PRIDE and ProteomeXchange, browsing published datasets, and reprocessing.
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3.0
Introduction
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3.1
Submit
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3.2
Browse
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3.3
Reprocess
Quantification
Estimating protein abundance across several orders of magnitude, covering the main quantification strategies and their trade-offs.
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4.0
Introduction
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4.1
Spectrum counting
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4.2
Reporter ions
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4.5
Statistical analysis