北京生物醫(yī)學(xué)工程

基于數(shù)據(jù)非依賴采集的無色譜數(shù)據(jù)處理軟件系統(tǒng)

A software system for mass spectrometry data processing based on data-independent acquisition without chromatogram

作者：張振航李青潤陳沖曾嶸鄭浩然

單位：1 中國科學(xué)技術(shù)大學(xué)計算機(jī)科學(xué)與技術(shù)學(xué)院(合肥230027) 2 中國科學(xué)院上海生命科學(xué)研究院（上海200031）

關(guān)鍵詞：數(shù)據(jù)非依賴采集；質(zhì)譜分析法；蛋白質(zhì)定量；保留時間；色譜

分類號：R318.04

出版年·卷·期（頁碼）：2020·39·1（42-47）

摘要：

目的如何高效準(zhǔn)確地定量蛋白質(zhì)一直是蛋白質(zhì)組學(xué)的主要關(guān)注點(diǎn)，基于液相色譜-數(shù)據(jù)依賴模式進(jìn)行譜圖采集的質(zhì)譜方法是目前主流的蛋白質(zhì)測定方式。但是，當(dāng)面對復(fù)雜樣本中蛋白質(zhì)定量的對比實(shí)驗(yàn)，為了使肽段得到有效分離，使用較長時間色譜洗脫的方法占據(jù)了譜圖生成的大量時間。為了解決此問題，并且能夠高效、準(zhǔn)確地定性定量肽段，提出一個基于數(shù)據(jù)非依賴采集（data-independent acquisition, DIA）的無色普數(shù)據(jù)處理軟件系統(tǒng)。方法基于以肽段為中心的蛋白質(zhì)定量理念，利用現(xiàn)有解決混合圖譜的方法對無色譜DIA質(zhì)譜數(shù)據(jù)進(jìn)行定性，隨后仿照DIA方法下色譜面積的計算方法完成定量；最后基于分類模型，對最終結(jié)果給出統(tǒng)計分析控制。結(jié)果本系統(tǒng)能夠處理生成無色譜的DIA質(zhì)譜數(shù)據(jù)，并且在12 min內(nèi)從海拉（Henrietta Lacks，Hela）蛋白質(zhì)樣本中定性定量出1954個肽段。結(jié)論使用本系統(tǒng)處理無色譜質(zhì)譜數(shù)據(jù)，相比于DIA質(zhì)譜數(shù)據(jù)，能夠在更短的時間內(nèi)準(zhǔn)確定量出足夠的肽段，對于在有限時間內(nèi)測定大規(guī)模蛋白質(zhì)樣本有重要的意義。

Objective How to quantify protein efficiently and accurately has always been the focus of proteomics.Liquid chromatography-tandem mass spectrometry is currently the most popular method for identification and quantification of proteins. However, when comparing large-scale samples in protein identification and quantification, multiple mass spectra need be generated, and chromatographic elution would occupy a large amount of time to generate spectra. In order to efficiently and accurately solve this problem, we therefore propose a software system to resolve data-independent acquisition (DIA) mass spectrometry data without chromatographic elution. Methods The method is based on the peptide-centric protein quantification concept. The mass spectrometry data without chromatography is identified by the existing method of solving the mixed spectrum, and then the quantification calculation is performed according to the calculation method of the chromatographic area accomplished by the DIA model. Finally, according to the classification method, we controll the final results by using statistical analysis. Results The system is able to process DIA mass spectrometry data without chromatography and And 1954 peptides is identifiably and quantitatively extracted from the protein samples of Henrietta Lakes (Hela) in 12 minutes. Conclusions Using our system to process non-chromatographic mass spectrometry data is comparable to DIA mass spectrometry data. The system can accurately quantify enough peptides in a short period, which is important for quantify large-scale proteomic samples within an acceptable time spending.

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