MS Protocols - Global Proteome Analysis
There are many strategies to obtain near comprehensive coverage and quantification of a cellular proteome. If your goal is to detect subtle proteome changes upon a perturbation, you may consider to use either SILAC or TMT labeling for accurate quantification. Compared to label-free quantification (LFQ) this methods will negatively impact on the depth of coverage. Therefore we recommend to include peptide fractionation (SCX or High pH) in the workflow.
In solution digest
TMT labeling - Thermo protocol
TMT labeling - SP3 protocol
In-gel digest, FASP, Stage-Tipping, SCX Fractionation, High pH Fractionation, BCA Assay, LFQ, SILAC.