NDLI: Factors that affect ion trap data-dependent MS/MS in proteomics

Content Provider	Springer Nature Link
Author	Wenner, Brett R. Lynn, Bert C.
Copyright Year	2004
Abstract	Quadrupole ion trap scanning parameters for performing bottom-up proteomics in a data-dependent fashion were evaluated on a Finnigan LCQ Deca mass spectrometer. Evaluation of parameters such as the number of averaged full scans, the number of averaged MS/MS scans, and ion injection times were necessary for acquiring high quality MS/MS spectra that yield favorable b and y ion coverage and high correlation to proteins using database searching algorithms. In this study, we demonstrated how the duty cycle of the mass spectrometer affects the number of peptides that can be successfully identified by SEQUEST using a model system of tryptic BSA peptides to mimic a typical complex mixture associated with bottom-up proteomics. The number of averaged scans and the duration of ion accumulation in the trap had a significant effect on the quality of acquired MS/MS spectra. For example, by increasing the ion injection time from 500 ms to 600 ms, peptide HLVDEPQNLIK improved from being improperly identified to being correctly identified with a SEQUEST cross-correlation score of 3.60. As a result of these experiments, we have devised the following set of ion trap parameters for performing bottom-up proteomics analysis in our laboratory: Three averaged full scans, five averaged MS/MS scans, and a maximum ion injection time of 600 ms.
Starting Page	150
Ending Page	157
Page Count	8
File Format	PDF
ISSN	10440305
Journal	Journal of The American Society for Mass Spectrometry
Volume Number	15
Issue Number	2
e-ISSN	18791123
Language	English
Publisher	Springer-Verlag
Publisher Date	2004-01-01
Publisher Institution	The American Society for Mass Spectrometry
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Analytical Chemistry Biotechnology Organic Chemistry Proteomics Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Spectroscopy Structural Biology

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Factors that affect ion trap data-dependent MS/MS in proteomics

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Multiplexed MS/MS in a Miniature Rectilinear Ion Trap

MS/MS of ions in a low pressure linear ion trap using a pulsed gas

Origin of product ions in the MS/MS spectra of peptides in a quadrupole ion trap

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Factors that affect ion trap data-dependent MS/MS in proteomics

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