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Towards defining the urinary proteome using liquid chromatography‐tandem mass spectrometry II.Limitations of complex mixture analyses
Author(s) -
Davis Michael T.,
Spahr Chris S.,
McGinley Michael D.,
Robinson John H.,
Bures Edward J.,
Beierle Jill,
Mort Jessica,
Yu Wen,
Luethy Roland,
Patterson Scott D.
Publication year - 2001
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/1615-9861(200101)1:1<108::aid-prot108>3.0.co;2-5
Subject(s) - mass spectrometry , tandem mass spectrometry , chemistry , chromatography , proteome , top down proteomics , liquid chromatography–mass spectrometry , analytical chemistry (journal) , selected reaction monitoring , biochemistry
With an emphasis on obtaining a multitude of high quality tandem mass spectrometry spectra for protein identification, instrumental parameters are described for the liquid chromatography‐tandem mass spectrometry analysis of trypsin digested unfractionated urine using a hybrid quadrupole‐time‐of‐flight (Q‐TOF) mass spectrometer. Precursor acquisition rates of up to 20 distinct precursors/minute in a single analysis were obtained through the use of parallel precursor selection (four precursors/survey period) and variable collision induced dissociation integration time (1 to 6 periods summed). Maximal exploitation of the gas phase fractionated ions was obtained through the use of narrow survey scans and iterative data‐dependent analyses incorporating dynamic exclusion. The impact on data fidelity as a product of data‐dependent selection of precursor ions from a dynamically excluded field is discussed with regards to sample complexity, precursor selection rates, survey scan range and facile chemical modifications. Operational and post‐analysis strategies are presented to restore data confidence and reconcile the greatest number of matched spectra.