Dataset Information

BoxCarmax: a novel high-selectivity data-independent acquisition mass spectrometry method for the analysis of protein turnover and complex samples

ABSTRACT: The data-independent acquisition (DIA) mode performed in the latest high-resolution, high-speed mass spectrometers offers a powerful analytical tool for biological investigations. The DIA mass spectrometry (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 isolation windows employed in conventional DIA methods lead to a limited efficiency in identifying and quantifying isotope-labelled peptide pairs. 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 modestly increased the identification rate for label-free and labeled samples but significantly improved the quantitative accuracy in SILAC and pSILAC samples. We further applied BoxCarmax in studying the protein degradation regulation during serum starvation stress in cultured cells, revealing valuable biological insights. Our study offered a new and accurate approach for the MS analysis of protein turnover and complex samples.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Rattus Norvegicus (rat) Homo Sapiens (human)

TISSUE(S): Blood Plasma, Cell Culture

SUBMITTER: Yansheng Liu

LAB HEAD: Yansheng Liu

PROVIDER: PXD021922 | Pride | 2021-02-02

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20200404_pro_1h_2Da_1st_256ms.raw	Raw
	20200404_pro_1h_2Da_2nd_256ms.raw	Raw
	20200404_pro_1h_2Da_3rd_256ms.raw	Raw
	20200404_pro_1h_2Da_4th_256ms.raw	Raw
	20200404_pro_4h_varDIA_asControl.raw	Raw

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Publications

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

Salovska Barbora B Li Wenxue W Di Yi Y Liu Yansheng Y

Analytical chemistry 20210203 6

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 ...[more]

PMID: 33533601

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