Peak selection matters in principal component analysis: A case study of syntrophic microbes
文献类型：期刊论文
| 作者 | Yang, CY ; Wei, WC; Liu, FH; Yu, XY
|
| 刊名 | BIOINTERPHASES
 |
| 出版日期 | 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 |
| ISSN号 | 1934-8630 |
| 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 |
| 文献子类 | Article |
| 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. |
| WOS关键词 | ION MASS-SPECTROMETRY ; INTERSPECIES ELECTRON-TRANSFER ; GEOBACTER-SULFURREDUCENS ; SP-NOV ; TIME ; REDUCTION ; BIOFILMS ; SIMS ; SURFACES ; ADHESION |
| WOS研究方向 | Biophysics ; Materials Science, Biomaterials |
| 语种 | 英语 |
| WOS记录号 | WOS:000487798900001 |
| 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 |
| 源URL | [http://ir.yic.ac.cn/handle/133337/24865]  |
| 专题 | 烟台海岸带研究所_海岸带生物学与生物资源利用所重点实验室 |
| 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. |
入库方式： OAI收割
来源：烟台海岸带研究所
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