Optimization of Data-Independent Acquisition Mass Spectrometry for Deep and Highly Sensitive Proteomic Analysis
Abstract
:1. Introduction
2. Results and Discussion
2.1. Evaluation of the Flow Rate of nanoLC-MS/MS
2.2. Comparison of MS/MS Acquisition Methods by Single-Shot Proteomics
2.3. Proteomic Analyses of GF and SPF Mouse Cerebrums
3. Materials and Methods
3.1. Cell Culture
3.2. Animal Study
3.3. Sample Preparation for Proteomic Analysis
3.4. LC-MS/MS
3.5. Protein Identification by Searching a Protein Sequence Database
3.6. Protein Identification by Searching a Chromatogram Library
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
MS | Mass spectrometry |
DIA | Liquid chromatography |
HEK293F | Floating human embryonic kidney cells 293 |
DIA | Data-independent acquisition |
DDA | Data-dependent acquisition |
CV | Coefficients of variation |
MudPIT | Multi-dimensional protein identification technology |
TIC | Total ion current |
nDIA | Normal-window data-independent acquisition |
vDIA | Variable-window data-independent acquisition |
oDIA | Overlapping-window data-independent acquisition |
GF | Germ-free |
SPF | Specific-pathogen-free |
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Kawashima, Y.; Watanabe, E.; Umeyama, T.; Nakajima, D.; Hattori, M.; Honda, K.; Ohara, O. Optimization of Data-Independent Acquisition Mass Spectrometry for Deep and Highly Sensitive Proteomic Analysis. Int. J. Mol. Sci. 2019, 20, 5932. https://doi.org/10.3390/ijms20235932
Kawashima Y, Watanabe E, Umeyama T, Nakajima D, Hattori M, Honda K, Ohara O. Optimization of Data-Independent Acquisition Mass Spectrometry for Deep and Highly Sensitive Proteomic Analysis. International Journal of Molecular Sciences. 2019; 20(23):5932. https://doi.org/10.3390/ijms20235932
Chicago/Turabian StyleKawashima, Yusuke, Eiichiro Watanabe, Taichi Umeyama, Daisuke Nakajima, Masahira Hattori, Kenya Honda, and Osamu Ohara. 2019. "Optimization of Data-Independent Acquisition Mass Spectrometry for Deep and Highly Sensitive Proteomic Analysis" International Journal of Molecular Sciences 20, no. 23: 5932. https://doi.org/10.3390/ijms20235932