Research output: Contribution to Journal/Magazine › Journal article › peer-review
Research output: Contribution to Journal/Magazine › Journal article › peer-review
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TY - JOUR
T1 - Distinguishing cell types or populations based on the computational analysis of their infrared spectra
AU - Martin, Frank
AU - Kerns, Jemma
AU - Llabjani, Valon
AU - Martin-Hirsch, Pierre L.
AU - Patel, Imran I.
AU - Trevisan, Julio
AU - Fullwood, Nigel J.
AU - Walsh, Michael J.
PY - 2010/11
Y1 - 2010/11
N2 - Infrared (IR) spectroscopy of intact cells results in a fingerprint of their biochemistry in the form of an IR spectrum; this has given rise to the new field of biospectroscopy. This protocol describes sample preparation (a tissue section or cytology specimen), the application of IR spectroscopy tools, and computational analysis. Experimental considerations include optimization of specimen preparation, objective acquisition of a sufficient number of spectra, linking of the derived spectra with tissue architecture or cell type, and computational analysis. The preparation of multiple specimens (up to 50) takes 8 h; the interrogation of a tissue section can take up to 6 h (similar to 100 spectra); and cytology analysis (n = 50, 10 spectra per specimen) takes 14 h. IR spectroscopy generates complex data sets and analyses are best when initially based on a multivariate approach (principal component analysis with or without linear discriminant analysis). This results in the identification of class clustering as well as class-specific chemical entities.
AB - Infrared (IR) spectroscopy of intact cells results in a fingerprint of their biochemistry in the form of an IR spectrum; this has given rise to the new field of biospectroscopy. This protocol describes sample preparation (a tissue section or cytology specimen), the application of IR spectroscopy tools, and computational analysis. Experimental considerations include optimization of specimen preparation, objective acquisition of a sufficient number of spectra, linking of the derived spectra with tissue architecture or cell type, and computational analysis. The preparation of multiple specimens (up to 50) takes 8 h; the interrogation of a tissue section can take up to 6 h (similar to 100 spectra); and cytology analysis (n = 50, 10 spectra per specimen) takes 14 h. IR spectroscopy generates complex data sets and analyses are best when initially based on a multivariate approach (principal component analysis with or without linear discriminant analysis). This results in the identification of class clustering as well as class-specific chemical entities.
KW - MICRO-SPECTROSCOPY
KW - MULTIVARIATE-ANALYSIS
KW - MICROSPECTROSCOPY
KW - TISSUE
KW - SYNCHROTRON
KW - CANCER
KW - RAMAN
KW - DISCRIMINATION
KW - IDENTIFICATION
KW - SCATTERING
UR - http://www.scopus.com/inward/record.url?scp=78049323886&partnerID=8YFLogxK
U2 - 10.1038/nprot.2010.133
DO - 10.1038/nprot.2010.133
M3 - Journal article
C2 - 21030951
VL - 5
SP - 1748
EP - 1760
JO - Nature Protocols
JF - Nature Protocols
SN - 1754-2189
IS - 11
ER -