Peak selection matters in principal component analysis: A case study of syntrophic microbes

doi:10.1116/1.5118237

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	Peak selection matters in principal component analysis: A case study of syntrophic microbes
	Yang, CY; Wei, WC; Liu, FH; Yu, XY
发表期刊	BIOINTERPHASES
ISSN	1934-8630
	2019-09
卷号	14 期号:5 页码:51004
关键词	ION MASS-SPECTROMETRY INTERSPECIES ELECTRON-TRANSFER GEOBACTER-SULFURREDUCENS SP-NOV TIME REDUCTION BIOFILMS SIMS SURFACES ADHESION
研究领域	Biophysics ; Materials Science, Biomaterials
DOI	10.1116/1.5118237
产权排序	[Yang, Cuiyun; Wei, Wenchao; Liu, Fanghua] Chinese Acad Sci, Yantai Inst Coastal Zone Res, Key Lab Coastal Biol & Utilizat, Yantai 264003, Shandong, Peoples R China; [Yang, Cuiyun; Yu, Xiao-Ying] Pacific Northwest Natl Lab, Energy & Environm Directorate, Richland, WA 99354 USA
通讯作者	Liu, Fanghua(fhliu@yic.ac.cn)
作者部门	海岸带生物学与生物资源保护实验室
英文摘要	In situ liquid time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful technique to study surface characterization of living biofilms in hydrated conditions. However, ToF-SIMS data analysis is still a great challenge in complicated bacterial biofilms, because many interference peaks from the medium may result in inaccurate interpretation. In this study, two syntrophic Geobacter populations are investigated using in situ liquid ToF-SIMS to reveal the biofilm surface changes between them due to direct interspecies electron transfer. By comparing spectral principal component analysis (PCA) results of all peaks and selected peaks, the authors find that spectral peak overlay is an effective strategy to reduce the matrix effect in handling complex ToF-SIMS data. Additionally, the spectral PCA results of high intensity and high resolution data obtained from liquid ToF-SIMS are compared. Selected peaks, amino acid peaks, and water cluster peaks spectral PCA produce nice separation among samples in both high intensity and high resolution data sets. However, the high resolution data show better separation between coculture planktonic and coculture aggregates, confirming that the higher mass accuracy is useful in the analysis of microbial samples. In conclusion, the results show that peak selection is critical for acquiring effective microbial information and interpretation of syntrophic Geobacter using spectral data from in situ liquid ToF-SIMS.
文章类型	Article
资助机构	Pacific Northwest National Laboratory (PNNL) ; Earth and Biological Sciences Directorate (EBSD) mission seed Laboratory Directed Research and Development (LDRD) ; China National Scholarship ; Office of Biological and Environmental Research [49694, 50569] ; PNNL Alternate Sponsored Fellowship
收录类别	SCI
语种	英语
关键词[WOS]	ION MASS-SPECTROMETRY ; INTERSPECIES ELECTRON-TRANSFER ; GEOBACTER-SULFURREDUCENS ; SP-NOV ; TIME ; REDUCTION ; BIOFILMS ; SIMS ; SURFACES ; ADHESION
研究领域[WOS]	Biophysics ; Materials Science, Biomaterials
WOS记录号	WOS:000487798900001
引用统计	被引频次：7[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.yic.ac.cn/handle/133337/24865
专题	海岸带生物学与生物资源利用重点实验室_海岸带生物学与生物资源保护实验室
作者单位	1.Chinese Acad Sci, Yantai Inst Coastal Zone Res, Key Lab Coastal Biol & Utilizat, Yantai 264003, Shandong, Peoples R China; 2.Pacific Northwest Natl Lab, Energy & Environm Directorate, Richland, WA 99354 USA
推荐引用方式 GB/T 7714	Yang, CY,Wei, WC,Liu, FH,et al. Peak selection matters in principal component analysis: A case study of syntrophic microbes[J]. BIOINTERPHASES,2019,14(5):51004.
APA	Yang, CY,Wei, WC,Liu, FH,&Yu, XY.(2019).Peak selection matters in principal component analysis: A case study of syntrophic microbes.BIOINTERPHASES,14(5),51004.
MLA	Yang, CY,et al."Peak selection matters in principal component analysis: A case study of syntrophic microbes".BIOINTERPHASES 14.5(2019):51004.

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