Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling

Koenig, CMartinez-Val, ANaicker, PrevinStoychev, SJordaan, JOlsen, JV2023-12-112023-12-112023-09Koenig, C., Martinez-Val, A., Naicker, P., Stoychev, S., Jordaan, J. & Olsen, J. 2023. Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling. Star Protocols, 4(3). http://hdl.handle.net/10204/133842666-1667https://doi.org/10.1016/j.xpro.2023.102536http://hdl.handle.net/10204/13384Tandem mass tags data-dependent acquisition (TMT-DDA) as well as data-independent acquisition-based label-free quantification (LFQ-DIA) have become the leading workflows to achieve deep proteome and phosphoproteome profiles. We present a modular pipeline for TMT-DDA and LFQ-DIA that integrates steps to perform scalable phosphoproteome profiling, including protein lysate extraction, clean-up, digestion, phosphopeptide enrichment, and TMT-labeling. We also detail peptide and/or phosphopeptide fractionation and pre-mass spectrometry desalting and provide researchers guidance on choosing the best workflow based on sample number and input.FulltextenProtein BiochemistryProteomicsMass spectrometryProtocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profilingArticleKoenig, C., Martinez-Val, A., Naicker, P., Stoychev, S., Jordaan, J., & Olsen, J. (2023). Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling. Star Protocols, 4(3), http://hdl.handle.net/10204/13384Koenig, C, A Martinez-Val, Previn Naicker, S Stoychev, J Jordaan, and JV Olsen "Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling." Star Protocols, 4(3) (2023) http://hdl.handle.net/10204/13384Koenig C, Martinez-Val A, Naicker P, Stoychev S, Jordaan J, Olsen J. Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling. Star Protocols, 4(3). 2023; http://hdl.handle.net/10204/13384.TY - Article AU - Koenig, C AU - Martinez-Val, A AU - Naicker, Previn AU - Stoychev, S AU - Jordaan, J AU - Olsen, JV AB - Tandem mass tags data-dependent acquisition (TMT-DDA) as well as data-independent acquisition-based label-free quantification (LFQ-DIA) have become the leading workflows to achieve deep proteome and phosphoproteome profiles. We present a modular pipeline for TMT-DDA and LFQ-DIA that integrates steps to perform scalable phosphoproteome profiling, including protein lysate extraction, clean-up, digestion, phosphopeptide enrichment, and TMT-labeling. We also detail peptide and/or phosphopeptide fractionation and pre-mass spectrometry desalting and provide researchers guidance on choosing the best workflow based on sample number and input. DA - 2023-09 DB - ResearchSpace DP - CSIR J1 - Star Protocols, 4(3) KW - Protein Biochemistry KW - Proteomics KW - Mass spectrometry LK - https://researchspace.csir.co.za PY - 2023 SM - 2666-1667 T1 - Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling TI - Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling UR - http://hdl.handle.net/10204/13384 ER -27093