Hybrid Data Acquisition and Processing Strategies with Increased Throughput and Selectivity: pSMART Analysis for Global Qualitative and Quantitative Analysis

被引：42

作者：

Prakash, Amol ^{[1
]}

Peterman, Scott ^{[1
]}

Ahmad, Shadab ^{[1
]}

Sarracino, David ^{[1
]}

Frewen, Barbara ^{[1
]}

Vogelsang, Maryann ^{[1
]}

Byram, Gregory ^{[1
]}

Krastins, Bryan ^{[1
]}

Vadali, Gouri ^{[1
]}

Lopez, Mary ^{[1
]}

机构：

[1] Thermo Fisher Sci, Cambridge, MA 02139 USA

来源：

JOURNAL OF PROTEOME RESEARCH | 2014年 / 13卷 / 12期

关键词：

peptide; mass spectrometry; Fourier transform; data-independent analysis; decoy searching; qualitative; quantitative; PEPTIDE IDENTIFICATION; ACCURATE MASS; MS/MS; QUANTIFICATION; TAGS;

D O I：

10.1021/pr5003017

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Data-dependent acquisition (DDA) and data-independent acquisition strategies (DIA) have both resulted in improved understanding of proteomics samples. Both strategies have advantages and disadvantages that are well-published, where DDA is typically applied for deep discovery and DIA may be used to create sample records. In this paper, we present a hybrid data acquisition and processing strategy (pSMART) that combines the strengths of both techniques and provides significant benefits for qualitative and quantitative peptide analysis. The performance of pSMART is compared to published DIA strategies in an experiment that allows the objective assessment of DIA performance with respect to interrogation of previously acquired MS data. The results of this experiment demonstrate that pSMART creates fewer decoy hits than a standard DIA strategy. Moreover, we show that pSMART is more selective, sensitive, and reproducible than either standard DIA or DDA strategies alone.

引用

页码：5415 / 5430

页数：16

共 37 条

[1] Intelligent Data Acquisition Blends Targeted and Discovery Methods [J].