Exploring skyline for both MSE-based label-free proteomics and HRMS quantitation of small molecules

CORC > 天津工业生物技术研究所 > 生物质谱与定量生物学研究水雯箐 > 期刊论文

	Exploring skyline for both MSE-based label-free proteomics and HRMS quantitation of small molecules
	Liu, Shanshan 1,2; Chen, Xin 1,2; Yan, Zhihui 1,2; Qin, Shanshan 1,2; Xu, Jinhua 1,2; Lin, Jianping 2,3,4; Yang, Cheng 2,3,4; Shui, Wenqing 1,5
刊名	PROTEOMICS
	2014-02-01
卷号	14 期号:2-3 页码:169-180
关键词	Bioinformatics MSE MS1 filtering Proteomic quantitation Skyline Small molecule quantitation
英文摘要	The MSE (where MSE is low energy (MS) and elevated energy (E) mode of acquisition) acquisition method commercialized by Waters on its Q-TOF instruments is regarded as a unique data-independent fragmentation approach that improves the accuracy and dynamic range of label-free proteomic quantitation. Due to its special format, MSE acquisition files cannot be independently analyzed with most widely used open-source proteomic software specialized for processing data-dependent acquisition files. In this study, we established a workflow integrating Skyline, a popular and versatile peptide-centric quantitation program, and a statistical tool DiffProt to fulfill MSE-based proteomic quantitation. Comparison with the vendor software package for analyzing targeted phosphopeptides and global proteomic datasets reveals distinct advantages of Skyline in MSE data mining, including sensitive peak detection, flexible peptide filtering, and transparent step-by-step workflow. Moreover, we developed a new procedure such that Skyline MS1 filtering was extended to small molecule quantitation for the first time. This new utility of Skyline was examined in a protein-ligand interaction experiment to identify multiple chemical compounds specifically bound to NDM-1 (where NDM is New Delhi metallo--lactamase 1), an antibiotics-resistance target. Further improvement of the current weaknesses in Skyline MS1 filtering is expected to enhance the reliability of this powerful program in full scan-based quantitation of both peptides and small molecules.
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Biochemical Research Methods ; Biochemistry & Molecular Biology
研究领域[WOS]	Biochemistry & Molecular Biology
关键词[WOS]	DATA-INDEPENDENT ANALYSIS ; IONIZATION-MASS-SPECTROMETRY ; LC-MS ; LIQUID-CHROMATOGRAPHY ; PROTEIN IDENTIFICATION ; PEPTIDE IDENTIFICATION ; BIOMARKER DISCOVERY ; COMPLEX SAMPLES ; QUANTIFICATION ; PRECURSOR
收录类别	SCI
语种	英语
WOS记录号	WOS:000331945800006
公开日期	2014-11-25
内容类型	期刊论文
源URL	[http://124.16.173.210/handle/311007/498]
专题	天津工业生物技术研究所_生物质谱与定量生物学研究水雯箐_期刊论文
作者单位	1.Nankai Univ, Coll Life Sci, Tianjin 300071, Peoples R China 2.Tianjin Joint Acad Biotechnol & Med, High Throughput Mol Drug Discovery Ctr, Tianjin, Peoples R China 3.Nankai Univ, State Key Lab Med Chem Biol, Tianjin 300071, Peoples R China 4.Nankai Univ, Coll Pharm, Tianjin 300071, Peoples R China 5.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Tianjin 300308, Peoples R China
推荐引用方式 GB/T 7714	Liu, Shanshan,Chen, Xin,Yan, Zhihui,et al. Exploring skyline for both MSE-based label-free proteomics and HRMS quantitation of small molecules[J]. PROTEOMICS,2014,14(2-3):169-180.
APA	Liu, Shanshan.,Chen, Xin.,Yan, Zhihui.,Qin, Shanshan.,Xu, Jinhua.,...&Shui, Wenqing.(2014).Exploring skyline for both MSE-based label-free proteomics and HRMS quantitation of small molecules.PROTEOMICS,14(2-3),169-180.
MLA	Liu, Shanshan,et al."Exploring skyline for both MSE-based label-free proteomics and HRMS quantitation of small molecules".PROTEOMICS 14.2-3(2014):169-180.