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Benchmarking SILAC Proteomics Workflows and Data Analysis Platforms

ABSTRACT: SILAC proteomics is a powerful metabolic labeling technique that limits experimental variation, while enabling accurate protein quantification. However, multiple isotopic versions (e.g. heavy and light) of the same proteins are generated, increasing spectral complexity and requiring sample deconvolution. Despite the widespread application of SILAC proteomics, various acquisition modes and software have not been comparatively evaluated. Here, we designed a comprehensive benchmarking workflow to systematically compare the performance of several software (e.g. FragPipe, MaxQuant, Proteome Discoverer, DIA-NN and Spectronaut) compatible with SILAC proteomics.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Ling Hao

PROVIDER: MSV000095236 | MassIVE | Wed Jul 03 12:08:00 BST 2024

SECONDARY ACCESSION(S): PXD053612

REPOSITORIES: MassIVE

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