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Protocols for Mass Spec proteomics

The challenges that Fixing Proteomics helps you overcome become bigger when you're using mass-spectrometry. This is because analysis workflows and data interpretation are complex and vary depending on your study so many proteomics studies involving mass-spectrometry have proved difficult to reproduce.

Analysis of protein complexes by 1D-PAGE and LC-MS-MS

Analysis of protein complexes by 1D-PAGE and LC-MS-MS
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The protocol described here is applicable to any protein complex that can be isolated to sufficient purity and quantity, its components separated by gel electrophoresis and sequence databases for the source organism are available.

Using this protocol, repeated LC-MS-MS analysis of an SDS-PAGE gel band identifies 90% of proteins in all three replicate and 94% in two out of three replicate LC-MS/MS experiments.

This level of reproducibility is essential for comprehensive characterization of the components of protein complexes, especially when quantitative differences in the composition of complexes are being investigated.

See also: 4-steps to Fixing Proteomics

Protocol provided by Dr. Mark. Collins from The Wellcome Trust Sanger Institute.