BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples.
BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples.
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DOI：
10.1021/acs.analchem.0c04293
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发表时间：
2021-02-16
影响因子：
7.4
通讯作者：
Liu Y
中科院分区：
文献类型：
--
作者：
Salovska B;Li W;Di Y;Liu Y
在最新的高分辨率、高速质谱仪中进行的数据独立采集（DIA）为生物研究提供了强大的分析工具。DIA质谱（DIA-MS）结合同位素标记方法对于增加DIA-MS分析的多重性具有特别的希望，这可以辅助相对蛋白质定量和蛋白质组范围的周转谱。然而，在常规DIA方法中采用的宽MS 1分离窗口导致通过肽片段离子鉴定和定量同位素标记的肽对的效率有限。在这里，我们优化了一种名为BoxCarmax的高选择性DIA-MS，它支持复杂样品的分析，例如细胞培养物（SILAC）和脉冲SILAC（pSILAC）实验中氨基酸稳定同位素标记产生的样品。BoxCarmax通过集成BoxCar和MSX功能以及气相分离策略，实现了MS 1和MS 2级别的多路采集。我们发现BoxCarmax通过减轻同位素-肽对的比率抑制显著提高了SILAC和pSILAC样品的定量准确度。我们进一步应用BoxCarmax测量培养细胞在血清饥饿应激期间的蛋白质降解调节，揭示了有价值的生物学见解。我们的研究为蛋白质周转和复杂样品的MS分析提供了一种替代和准确的方法。
The data-independent acquisition (DIA) performed in the latest high-resolution, high-speed mass spectrometers offers a powerful analytical tool for biological investigations. The DIA mass spectrometry (DIA-MS) combined with the isotopic labeling approach holds a particular promise for increasing the multiplexity of DIA-MS analysis, which could assist the relative protein quantification and the proteome-wide turnover profiling. However, the wide MS1 isolation windows employed in conventional DIA methods lead to a limited efficiency in identifying and quantifying isotope-labelled peptide pairs through peptide fragment ions. Here, we optimized a high-selectivity DIA-MS named BoxCarmax that supports the analysis of complex samples, such as those generated from Stable isotope labeling by amino acids in cell culture (SILAC) and pulse SILAC (pSILAC) experiments. BoxCarmax enables multiplexed acquisition at both MS1- and MS2- levels, through the integration of BoxCar and MSX features, as well as a gas-phase separation strategy. We found BoxCarmax significantly improved the quantitative accuracy in SILAC and pSILAC samples by mitigating the ratio suppression of isotope-peptide pairs. We further applied BoxCarmax to measure protein degradation regulation during serum starvation stress in cultured cells, revealing valuable biological insights. Our study offered an alternative and accurate approach for the MS analysis of protein turnover and complex samples.
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影响因子：
16.6
作者：
Liu Y;Borel C;Li L;Müller T;Williams EG;Germain PL;Buljan M;Sajic T;Boersema PJ;Shao W;Faini M;Testa G;Beyer A;Antonarakis SE;Aebersold R
通讯作者：
Aebersold R
影响因子：
7.4
作者：
Haynes, Sarah E.;Majmudar, Jaimeen D.;Martin, Brent R.
通讯作者：
Martin, Brent R.
DOI：
10.1007/s13361-019-02243-1
发表时间：
2019-08-01
影响因子：
3.2
作者：
Li, Wenxue;Chi, Hao;Liu, Yansheng
通讯作者：
Liu, Yansheng
影响因子：
7
作者：
Bruderer, Roland;Muntel, Jan;Reiter, Lukas
通讯作者：
Reiter, Lukas
影响因子：
7
作者：
Huang, Ting;Bruderer, Roland;Reiter, Lukas
通讯作者：
Reiter, Lukas