Whole-cell proteomics and Analysis with or without nutrient stress by Tandem Mass Tagging-based proteomics V2 v1

• DOI: 10.17504/protocols.io.yxmvm32nbl3p/v1
• Publication Date: 2023-10-02T15:21:31Z
• Authors: Sharan Swarup; J. Wade Harper wa...; Kelsey Hickey
• Keywords: Tandem mass tag; Isobaric labeling; Proteome; Label-free Quantification

The analysis of relative protein abundance has emerged as an important tool in cell biology. Typically, it is possible to quantify >8000 proteins under standard conditions. Tandem Mass Tags (TMT) are isobaric reagents that contain a set isotopically distinct reporter ions, which can be used individual peptides samples through multiplexing(McAlister et al., 2014). Because the TMT performed multiplexed format (up 18 plex), examine effect different perturbations (treatments, time courses, etc) on total proteome and include replicate desired. This protocol applicable many types, although number quantified may differ, depending complexity proteomes types. small amount needed (50-100 μg) makes application this approach simple for types cells. explicitly effects nutrient stress lines with or without autophagy.