Benchmarking and Best Practices for Quantitative Proteomics

ABSTRACT: We use an integrated benchmarking approach to empirically establish guidelines for data acquisition, statistical approach, and replicate numbers for accurate quantification. We evaluated three workflows for protein- and peptide-level quantitative accuracy: data dependent acquisition (DDA), data independent acquisition (DIA), and chemical labeling via tandem mass tags (TMT). The former two datasets were generated in our lab, so we have published them here.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606)

SUBMITTER: John Denu  

PROVIDER: MSV000085239 | MassIVE | Mon Apr 06 13:50:00 BST 2020

SECONDARY ACCESSION(S): PXD018408

REPOSITORIES: MassIVE