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Using Fourier transform IR spectroscopy to analyze biological materials

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Using Fourier transform IR spectroscopy to analyze biological materials. / Baker, Matthew J.; Trevisan, Júlio; Bassan, Paul; Bhargava, Rohit; Butler, Holly J.; Dorling, Konrad M.; Fielden, Peter R.; Fogarty, Simon W.; Fullwood, Nigel J.; Heys, Kelly A.; Hughes, Caryn; Lasch, Peter; Martin-Hirsch, Pierre L.; Obinaju, Blessing; Sockalingum, Ganesh D.; Sulé-Suso, Josep; Strong, Rebecca ; Walsh, Michael J.; Wood, Bayden R.; Gardner, Peter; Martin, Francis L.

In: Nature Protocols, Vol. 9, No. 8, 08.2014, p. 1771-1791.

Research output: Contribution to journalJournal article

Harvard

Baker, MJ, Trevisan, J, Bassan, P, Bhargava, R, Butler, HJ, Dorling, KM, Fielden, PR, Fogarty, SW, Fullwood, NJ, Heys, KA, Hughes, C, Lasch, P, Martin-Hirsch, PL, Obinaju, B, Sockalingum, GD, Sulé-Suso, J, Strong, R, Walsh, MJ, Wood, BR, Gardner, P & Martin, FL 2014, 'Using Fourier transform IR spectroscopy to analyze biological materials', Nature Protocols, vol. 9, no. 8, pp. 1771-1791. https://doi.org/10.1038/nprot.2014.110

APA

Baker, M. J., Trevisan, J., Bassan, P., Bhargava, R., Butler, H. J., Dorling, K. M., Fielden, P. R., Fogarty, S. W., Fullwood, N. J., Heys, K. A., Hughes, C., Lasch, P., Martin-Hirsch, P. L., Obinaju, B., Sockalingum, G. D., Sulé-Suso, J., Strong, R., Walsh, M. J., Wood, B. R., ... Martin, F. L. (2014). Using Fourier transform IR spectroscopy to analyze biological materials. Nature Protocols, 9(8), 1771-1791. https://doi.org/10.1038/nprot.2014.110

Vancouver

Baker MJ, Trevisan J, Bassan P, Bhargava R, Butler HJ, Dorling KM et al. Using Fourier transform IR spectroscopy to analyze biological materials. Nature Protocols. 2014 Aug;9(8):1771-1791. https://doi.org/10.1038/nprot.2014.110

Author

Baker, Matthew J. ; Trevisan, Júlio ; Bassan, Paul ; Bhargava, Rohit ; Butler, Holly J. ; Dorling, Konrad M. ; Fielden, Peter R. ; Fogarty, Simon W. ; Fullwood, Nigel J. ; Heys, Kelly A. ; Hughes, Caryn ; Lasch, Peter ; Martin-Hirsch, Pierre L. ; Obinaju, Blessing ; Sockalingum, Ganesh D. ; Sulé-Suso, Josep ; Strong, Rebecca ; Walsh, Michael J. ; Wood, Bayden R. ; Gardner, Peter ; Martin, Francis L. / Using Fourier transform IR spectroscopy to analyze biological materials. In: Nature Protocols. 2014 ; Vol. 9, No. 8. pp. 1771-1791.

Bibtex

@article{2d0e38dc6dbd448dbe732fce52f6bcac,
title = "Using Fourier transform IR spectroscopy to analyze biological materials",
abstract = "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.",
author = "Baker, {Matthew J.} and J{\'u}lio Trevisan and Paul Bassan and Rohit Bhargava and Butler, {Holly J.} and Dorling, {Konrad M.} and Fielden, {Peter R.} and Fogarty, {Simon W.} and Fullwood, {Nigel J.} and Heys, {Kelly A.} and Caryn Hughes and Peter Lasch and Martin-Hirsch, {Pierre L.} and Blessing Obinaju and Sockalingum, {Ganesh D.} and Josep Sul{\'e}-Suso and Rebecca Strong and Walsh, {Michael J.} and Wood, {Bayden R.} and Peter Gardner and Martin, {Francis L.}",
year = "2014",
month = aug,
doi = "10.1038/nprot.2014.110",
language = "English",
volume = "9",
pages = "1771--1791",
journal = "Nature Protocols",
issn = "1754-2189",
publisher = "Nature Publishing Group",
number = "8",

}

RIS

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 - 1754-2189

IS - 8

ER -