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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 - Using Fourier transform IR spectroscopy to analyze biological materials
AU - Baker, Matthew J.
AU - Trevisan, Júlio
AU - Bassan, Paul
AU - Bhargava, Rohit
AU - Butler, Holly J.
AU - Dorling, Konrad M.
AU - Fielden, Peter R.
AU - Fogarty, Simon W.
AU - Fullwood, Nigel J.
AU - Heys, Kelly A.
AU - Hughes, Caryn
AU - Lasch, Peter
AU - Martin-Hirsch, Pierre L.
AU - Obinaju, Blessing
AU - Sockalingum, Ganesh D.
AU - Sulé-Suso, Josep
AU - Strong, Rebecca
AU - Walsh, Michael J.
AU - Wood, Bayden R.
AU - Gardner, Peter
AU - Martin, Francis L.
PY - 2014/8
Y1 - 2014/8
N2 - IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing.
AB - IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing.
U2 - 10.1038/nprot.2014.110
DO - 10.1038/nprot.2014.110
M3 - Journal article
C2 - 24992094
VL - 9
SP - 1771
EP - 1791
JO - Nature Protocols
JF - Nature Protocols
SN - 1750-2799
IS - 8
ER -