Peak selection matters in principal component analysis: A case study of syntrophic microbes
Yang, CY; Wei, WC; Liu, FH; Yu, XY
Source PublicationBIOINTERPHASES
ISSN1934-8630
2019-09
Volume14Issue:5Pages:51004
KeywordION MASS-SPECTROMETRY INTERSPECIES ELECTRON-TRANSFER GEOBACTER-SULFURREDUCENS SP-NOV TIME REDUCTION BIOFILMS SIMS SURFACES ADHESION
MOST Discipline CatalogueBiophysics ; Materials Science, Biomaterials
DOI10.1116/1.5118237
Contribution Rank[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
Corresponding AuthorLiu, Fanghua(fhliu@yic.ac.cn)
Department海岸带生物学与生物资源保护实验室
AbstractIn 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.
SubtypeArticle
Indexed BySCI
Language英语
WOS KeywordION MASS-SPECTROMETRY ; INTERSPECIES ELECTRON-TRANSFER ; GEOBACTER-SULFURREDUCENS ; SP-NOV ; TIME ; REDUCTION ; BIOFILMS ; SIMS ; SURFACES ; ADHESION
WOS Research AreaBiophysics ; Materials Science, Biomaterials
Funding ProjectPacific 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] ; Office of Biological and Environmental Research[50569] ; PNNL Alternate Sponsored Fellowship
WOS IDWOS:000487798900001
Funding OrganizationPacific 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
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Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.yic.ac.cn/handle/133337/24865
Collection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
Affiliation1.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
Recommended Citation
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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