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.
Reference:
Koenig, 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/10204/13384
Koenig, 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/10204/13384
Koenig, 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/10204/13384
Koenig 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.
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