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.
authors.affiliation: 1] Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston, UK. [2] Present address: WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Baker
authors.affiliation: 1] Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK. [2] School of Computing and Communications, Lancaster University, Lancaster, UK.
authors.forename: Júlio
authors.initials: J
authors.lastname: Trevisan
authors.affiliation: Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Bassan
authors.affiliation: Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Rohit
authors.initials: R
authors.lastname: Bhargava
authors.affiliation: Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK.
authors.forename: Holly J
authors.initials: HJ
authors.lastname: Butler
authors.affiliation: Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston, UK.
authors.forename: Konrad M
authors.initials: KM
authors.lastname: Dorling
authors.affiliation: Department of Chemistry, Lancaster University, Lancaster, UK.
authors.forename: Peter R
authors.initials: PR
authors.lastname: Fielden
authors.affiliation: 1] Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK. [2] Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster, UK.
authors.forename: Simon W
authors.initials: SW
authors.lastname: Fogarty
authors.affiliation: Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster, UK.
authors.forename: Nigel J
authors.initials: NJ
authors.lastname: Fullwood
authors.affiliation: Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK.
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Heys
authors.affiliation: Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK.
authors.forename: Caryn
authors.initials: C
authors.lastname: Hughes
authors.affiliation: Proteomics and Spectroscopy (ZBS 6), Robert-Koch-Institut, Berlin, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Lasch
authors.affiliation: Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK.
authors.forename: Pierre L
authors.initials: PL
authors.lastname: Martin-Hirsch
authors.affiliation: Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK.
authors.forename: Blessing
authors.initials: B
authors.lastname: Obinaju
authors.affiliation: Equipe MéDIAN-Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, UnitéMEDyC, CNRS UMR7369, UFR Pharmacie, SFR CAP-Santé FED4231, Reims, France.
authors.forename: Ganesh D
authors.initials: GD
authors.lastname: Sockalingum
authors.affiliation: Institute for Science and Technology in Medicine, School of Medicine, Keele University, Stoke-on-Trent, UK.
authors.forename: Josep
authors.initials: J
authors.lastname: Sulé-Suso
authors.affiliation: Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK.
authors.forename: Rebecca J
authors.initials: RJ
authors.lastname: Strong
authors.affiliation: Department of Pathology, College of Medicine Research Building (COMRB), University of Illinois at Chicago, Chicago, Illinois, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Walsh
authors.affiliation: Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria, Australia.
authors.forename: Bayden R
authors.initials: BR
authors.lastname: Wood
authors.affiliation: Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Gardner
authors.affiliation: Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK.
authors.forename: Francis L
authors.initials: FL
authors.lastname: Martin
mesh_terms: D003106:Colon / Q000473:pathology; D016591:Histocytological Preparation Techniques; D006801:Humans; D012984:Software; D017550:Spectroscopy, Fourier Transform Infrared / Q000295:instrumentation / Q000379:methods*