biostudies-literatureUnknown13(24)Almeida NPlasma analysis by mass spectrometry-based proteomics remains a challenge due to its large dynamic range of 10 orders in magnitude. We created a methodology for protein identification known as Wise MS Transfer (WiMT). Melanoma plasma samples from biobank archives were directly analyzed using simple sample preparation. WiMT is based on MS1 features between several MS runs together with custom protein databases for ID generation. This entails a multi-level dynamic protein database with different immunodepletion strategies by applying single-shot proteomics. The highest number of melanoma plasma proteins from undepleted and unfractionated plasma was reported, mapping >1200 proteins from >10,000 protein sequences with confirmed significance scoring. Of these, more than 660 proteins were annotaCancers6224https://www.ebi.ac.uk/biostudies/studies/S-EPMC8699267biostudies-literatureMapping the Melanoma Plasma Proteome (MPP) Using Single-Shot Proteomics Interfaced with the WiMT Database.PMC8699267C S Nogueira FKarpati SMarko-Varga GPerez-Riverol YPizzatti LAlmeida NRodriguez JSzasz AMPla Parada IB Domont GWoldmar NAppelqvist RBetancourt LSahlin KBMalm JSanchez AValdes JGOskolas HKim YfalseMapping the Melanoma Plasma Proteome (MPP) Using Single-Shot Proteomics Interfaced with the WiMT Database.Plasma analysis by mass spectrometry-based proteomics remains a challenge due to its large dynamic range of 10 orders in magnitude. We created a methodology for protein identification known as Wise MS Transfer (WiMT). Melanoma plasma samples from biobank archives were directly analyzed using simple sample preparation. WiMT is based on MS1 features between several MS runs together with custom protein databases for ID generation. This entails a multi-level dynamic protein database with different immunodepletion strategies by applying single-shot proteomics. The highest number of melanoma plasma proteins from undepleted and unfractionated plasma was reported, mapping >1200 proteins from >10,000 protein sequences with confirmed significance scoring. Of these, more than 660 proteins were annota2021-01-01T00:00:00Z2021 Dec2026-07-09T11:57:11.736Z2022-02-11T14:27:54.757ZS-EPMC86992673494484210.3390/cancers13246224