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Group-DIA: analyzing multiple data-independent acquisition mass spectrometry data files

Nature Methods volume 12, pages 1105–1106 (2015)Cite this article

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Discovery proteomics has limited quantification capabilities because of stochastic precursor-ion selection. Several data-independent acquisition (DIA) methods have been proposed to overcome this limitation1,2,3,4, including the sequential-window acquisition of all theoretical mass spectra (SWATH-MS)4.

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Figure 1: The principle of Group-DIA and evaluation of its performance in analyzing DIA-MS data files.

References

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Acknowledgements

We thank Z. Xu and Y. Yu for help with the high-performance computer. This work was supported by the National Science Foundation (NSF) of China (grants 91429301 and 31221065), 973 Program 2015CB553800, National Major Project 2013ZX10002-002, 111 Project B12001, funding from Xiamen City (grant 3502Z20130027) and the NSF of China for Fostering Talents in Basic Research (grant J1310027).

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Author notes

  1. Yuanyue Li and Chuan-Qi Zhong: These authors contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China

    Yuanyue Li, Chuan-Qi Zhong, Xiaozheng Xu, Shaowei Cai, Xiurong Wu, Yingying Zhang, Jinan Chen, Shengcai Lin & Jiahuai Han

  2. School of Information Science and Engineering, Xiamen University, Xiamen, Fujian, China

    Jianghong Shi

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  1. Yuanyue Li
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Correspondence to Chuan-Qi Zhong or Jiahuai Han.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–21, Supplementary Notes 1–3 and Supplementary Methods (PDF 2618 kb)

Supplementary Table 1

The peptide ions identified in the yeast SGS data set by Group-DIA and DIA-Umpire software (XLSX 595 kb)

Supplementary Table 2

The peptide ions identified in the human SGS data set by Group-DIA and DIA-Umpire software (XLSX 793 kb)

Supplementary Table 3

The peptide ions identified in the TNFR1 data set by Group-DIA and DIA-Umpire software (XLSX 269 kb)

Supplementary Table 4

The peptides and proteins identified in the TNFR1 data set by shotgun MS (XLSX 750 kb)

Supplementary Table 5

The proteins quantified by Group-DIA, DIA-Umpire and OpenSWATH in the TNFR1 data set (XLSX 484 kb)

Supplementary Table 6

Fractionation techniques used in L929 cell proteome library building (XLSX 8 kb)

Supplementary Table 7

Peptides and proteins identified by shotgun MS in the whole L929 cell data set (XLSX 6467 kb)

Supplementary Table 8

The proteins quantified by Group-DIA and OpenSWATH in the whole L929 cell data set (XLSX 3690 kb)

Supplementary Table 9

The regulated proteins that were manually checked in the whole L929 cell data set (XLSX 29 kb)

Supplementary Data

The XICs of all SIS peptides identified by Group-DIA but not by DIA-Umpire, and the assay libraries of the TNF IP data set and whole L929 cell data set for OpenSWATH analysis (ZIP 29325 kb)

Supplementary Software

Group-DIA software (ZIP 1226 kb)

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Li, Y., Zhong, CQ., Xu, X. et al. Group-DIA: analyzing multiple data-independent acquisition mass spectrometry data files. Nat Methods 12, 1105–1106 (2015). https://doi.org/10.1038/nmeth.3593

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