Protocol for Data Dependent Acquisition
Davies V, Wandy J, Weidt S, et al. Rapid Development of Improved Data-Dependent Acquisition Strategies. Anal Chem. 2021;93(14):5676-5683. doi:10.1021/acs.analchem.0c03895
https://pubs.acs.org/doi/10.1021/acs.analchem.0c03895

Protocol for Data Independent Acquisition
Gillet LC, Navarro P, Tate S, et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics. 2012;11(6):O111.016717. doi:10.1074/mcp.O111.016717
https://www.sciencedirect.com/science/article/pii/S1535947620304424

Protocol for TMT
Zecha J, Satpathy S, Kanashova T, et al. TMT Labeling for the Masses: A Robust and Cost-efficient, In-solution Labeling Approach. Mol Cell Proteomics. 2019;18(7):1468-1478. doi:10.1074/mcp.TIR119.001385
https://www.mcponline.org/article/S1535-9476(20)31552-8/fulltext

Protocol for SILAC
Wang X, He Y, Ye Y, et al. SILAC-based quantitative MS approach for real-time recording protein-mediated cell-cell interactions. Sci Rep. 2018;8(1):8441. Published 2018 May 31. doi:10.1038/s41598-018-26262-2
https://www.nature.com/articles/s41598-018-26262-2

Protocol for iTRAQ
Wiese S, Reidegeld KA, Meyer HE, Warscheid B. Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics. 2007;7(3):340-350. doi:10.1002/pmic.200600422
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.200600422

Protocol for Phosphoproteomics
He M, Wang J, Herold S, Xi L, Schulze WX. A Rapid and Universal Workflow for Label-Free-Quantitation-Based Proteomic and Phosphoproteomic Studies in Cereals. Curr Protoc. 2022;2(6):e425. doi:10.1002/cpz1.425
https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.425