Proteomics and Protein Mass Spectrometry Workflows

Elucidating protein identity and function

Protein digestion and labeling technologies, when coupled to liquid chromatography and mass spectrometry (LC-MS), offer powerful methods for identifying and quantifying peptides, proteins, and posttranslational modifications (PTMs) such as phosphorylation and glycosylation. Some of the most commonly used proteomics workflows include sample digestion, SILAC, and TMT, after which the protein fragments and peptides are separated by LC and undergo MS analysis.

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Qualititative or bottom-up proteomics is still the mainstay for most proteomics experiments, with the objective being to identify as many protein components in a biological sample as possible. Understand more about bottom-up protein digestion, LC separation, MS, and data interpretation here.   

Posttranslational modifications (PTMs) play crucial roles in regulating protein structure, activity, and expression. MS analysis, when coupled to multiple fragmentation techniques, yields the most comprehensive structural characterization of PTMs such as glycosylation and phosphorylation. 

Finding out the roles that individual proteins play in biological systems requires measurement of protein abundance changes relative to those of the systems. Discovery-based relative quantification via MS uncovers protein level changes across different sample sets without having to know protein identity.

Mass spectrometry (MS) technologies have provided a versatile platform to protein structure and dynamics that can lead to the understanding of protein function and mechanism of action. Several approaches have been developed, each capable of revealing specific structural information for proteins.

Top-down analysis involves examination of the protein at the intact protein level instead of the peptide level, as is the case with bottom-up proteomics. The main advantages of the top-down approach include detection of protein degradation products, sequence variants, and combinations of PTMs.

The latest advances in mass spectrometry have skyrocketed the capabilities in translational proteomics, impacting our understanding of health and disease. Translational proteomics complements other omics disciplines (genomics, transcriptomics, and metabolomics/lipidomics), delivering new workflows that produce clinically relevant results that are quantitative, reproducible, standardized and scalable.