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Evaluation of drift time specific collision energies

ABSTRACT: Comparison among the following data independent acquisition modes provided on the Waters Synapt G2-S instrument: MSE, MSE with Ion Mobility (HDMSE), and MSE with Ion Mobility and drift time specific collision energies (UDMSE). The following on-column loads and LC gradient lengths have been used for the DDA data (1-20130710-63647): * 200 ng, 90 minutes gradient * 300 ng, 180 minutes gradient * 1000 ng, 180 minutes gradient. DDA data has been processed by using MaxQuant (v.1.3.0.5) software, searching against a organism specific (Homo Sapiens) Uniprot/Swissprot database. FDR has been controlled by using a pseudo-reverse (KR positions kept) database at both protein and peptide levels to 1%. Proteins with less than two peptides (minimum of 6 amino acids length, up to 2 missed cleavages and 3 variable modifications allowed. Variable identifications were : methionine oxidation, fixed modifications were : cysteine carbamidomethylation ) identified have been discarded. A match between runs of a 2 minutes windows among the three technical replicates has been performed.

INSTRUMENT(S): Synapt MS, Q Exactive

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Ute Distler

PROVIDER: PXD000303 | Pride | 2013-12-05

REPOSITORIES: Pride

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