Definitive screening design enables optimization of LC–ESI–MS/MS parameters in proteomics. Issue 12 (2nd December 2017)

• Record Type: Journal Article
• Authors: Aburaya, Shunsuke; Aoki, Wataru; Minakuchi, Hiroyoshi; Ueda, Mitsuyoshi
• Is Part Of: Bioscience, biotechnology, and biochemistry. Volume 81:Issue 12(2017)
• Page Start: 2237
• Page End: 2243
• Publication Date: 2017-12-02
• Subjects: proteomics -- mass spectrometry -- HPLC; Biotechnology -- Periodicals; Biochemistry -- Periodicals; 660.6
• DOI: 10.1080/09168451.2017.1391685
• Languages: English
• ISSNs: 0916-8451

Abstract

Abstract: In proteomics, more than 100, 000 peptides are generated from the digestion of human cell lysates. Proteome samples have a broad dynamic range in protein abundance; therefore, it is critical to optimize various parameters of LC–ESI–MS/MS to comprehensively identify these peptides. However, there are many parameters for LC–ESI–MS/MS analysis. In this study, we applied definitive screening design to simultaneously optimize 14 parameters in the operation of monolithic capillary LC–ESI–MS/MS to increase the number of identified proteins and/or the average peak area of MS1. The simultaneous optimization enabled the determination of two-factor interactions between LC and MS. Finally, we found two parameter sets of monolithic capillary LC–ESI–MS/MS that increased the number of identified proteins by 8.1% or the average peak area of MS1 by 67%. The definitive screening design would be highly useful for high-throughput analysis of the best parameter set in LC–ESI–MS/MS systems. Abstract: : Definitive screening design enables simultaneous optimization of LC-ESI-MS/MS parameters in proteomics.