BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples

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...

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Bibliographic Details
Published in:Analytical chemistry (Washington) 2021-02, Vol.93 (6), p.3103-3111
Main Authors: Salovska, Barbora, Li, Wenxue, Di, Yi, Liu, Yansheng
Format: Article
Language:English
Subjects:
Amino acids
Cell culture
Chemistry
Freight cars
Isotope Labeling
Isotopic labeling
Mass spectrometers
Mass Spectrometry
Mass spectroscopy
Multiplexing
Peptides
Phase separation
Protein turnover
Proteins
Proteolysis
Proteome
Proteomes
Proteomics
Radioactive labeling
Scientific imaging
Selectivity
Spectrometers
Spectroscopy
Stable isotopes
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Summary: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-labeled 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.
ISSN:0003-2700
1520-6882
1520-6882
DOI:10.1021/acs.analchem.0c04293