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

被引:25
作者
Wenner, BR [1 ]
Lynn, BC [1 ]
机构
[1] Univ Kentucky, Dept Chem, Lexington, KY 40506 USA
关键词
D O I
10.1016/j.jasms.2003.10.006
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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. (C) 2004 American Society for Mass Spectrometry.
引用
收藏
页码:150 / 157
页数:8
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