Using Fourier transform IR spectroscopy to analyze biological materials

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

Research output: Contribution to journalArticle

529 Citations (Scopus)

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.

LanguageEnglish
Pages1771-1791
Number of pages21
JournalNature Protocols
Volume9
Issue number8
Early online date3 Jul 2014
DOIs
Publication statusPublished - Aug 2014

Fingerprint

Fourier Analysis
Biological materials
Infrared spectroscopy
Spectrum Analysis
Fourier transforms
Cytology
Tissue
Processing
Standardization
Quality control
Feature extraction
Labels
Information Storage and Retrieval
Data acquisition
Microscopic examination
Screening
Dermatoglyphics
Health
Quality Control
Sampling

Keywords

  • blood sampling
  • biological materials
  • IR spectroscopy

Cite this

Baker, M. J., Trevisan, J., Bassan, P., Bhargava, R., Butler, H. J., Dorling, K. M., ... 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
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 J. ; Walsh, Michael J. ; Wood, Bayden R. ; Martin, Francis L. / Using Fourier transform IR spectroscopy to analyze biological materials. In: Nature Protocols. 2014 ; Vol. 9, No. 8. pp. 1771-1791.
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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, RJ, Walsh, MJ, Wood, BR & 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

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 J.; Walsh, Michael J.; Wood, Bayden R.; Martin, Francis L.

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

Research output: Contribution to journalArticle

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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