Shotgun Proteomics and Biomarker Discovery

Abstract

Coupling large‐scale sequencing projects with the amino acid sequence information that can be gleaned from tandem mass spectrometry (MS/MS) has made it much easier to analyze complex mixtures of proteins. The limits of this “shotgun” approach, in which the protein mixture is proteolytically digested before separation, can be further expanded by separating the resulting mixture of peptides prior to MS/MS analysis. Both single dimensional high pressure liquid chromatography (LC) and multidimensional LC (LC/LC) can be directly interfaced with the mass spectrometer to allow for automated collection of tremendous quantities of data. While there is no single technique that addresses all proteomic challenges, the shotgun approaches, especially LC/LC‐MS/MS‐based techniques such as MudPIT (multidimensional protein identification technology), show advantages over gel‐based techniques in speed, sensitivity, scope of analysis, and dynamic range. Advances in the ability to quantitate differences between samples and to detect for an array of post‐translational modifications allow for the discovery of classes of protein biomarkers that were previously unassailable.

Cited by papers we hold 4

• Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition · 2020
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• The lethal cargo of Myxococcus xanthus outer membrane vesicles · 2014
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• Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease · 2012
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• Small Changes Huge Impact: The Role of Protein Posttranslational Modifications in Cellular Homeostasis and Disease · 2011
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