Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and polymer science fields. The application of Raman spectroscopy and microscopy within biology is rapidly increasing because it can provide chemical and compositional information, but it does not typically suffer from interference from water molecules. Analysis does not conventionally require extensive sample preparation; biochemical and structural information can usually be obtained without labeling. In this protocol, we aim to standardize and bring together multiple experimental approaches from key leaders in the field for obtaining Raman spectra using a microspectrometer. As examples of the range of biological samples that can be analyzed, we provide instructions for acquiring Raman spectra, maps and images for fresh plant tissue, formalin-fixed and fresh frozen mammalian tissue, fixed cells and biofluids. We explore a robust approach for sample preparation, instrumentation, acquisition parameters and data processing. By using this approach, we expect that a typical Raman experiment can be performed by a nonspecialist user to generate high-quality data for biological materials analysis.

Raman spectroscopy is an optical technique based on inelastic scattering of light by vibrating molecules and can provide chemical fingerprints of cells, tissues or biofluids. The high chemical specificity, minimal or lack of sample preparation and the ability to use advanced optical technologies in the visible or near-infrared spectral range (lasers, microscopes, fibre-optics) have recently led to an increase in medical diagnostic applications of Raman spectroscopy. The key hypothesis underpinning this field is that molecular changes in cells, tissues or biofluids, that are either the cause or the effect of diseases, can be detected and quantified by Raman spectroscopy. Furthermore, multivariate calibration and classification models based on Raman spectra can be developed on large "training" datasets and used subsequently on samples from new patients to obtain quantitative and objective diagnosis. Historically, spontaneous Raman spectroscopy has been known as a low signal technique requiring relatively long acquisition times. Nevertheless, new strategies have been developed recently to overcome these issues: non-linear optical effects and metallic nanoparticles can be used to enhance the Raman signals, optimised fibre-optic Raman probes can be used for real-time in-vivo single-point measurements, while multimodal integration with other optical techniques can guide the Raman measurements to increase the acquisition speed and spatial accuracy of diagnosis. These recent efforts have advanced Raman spectroscopy to the point where the diagnostic accuracy and speed are compatible with clinical use. This paper reviews the main Raman spectroscopy techniques used in medical diagnostics and provides an overview of various applications.

The use of near-infrared Raman spectroscopy to interrogate epithelial tissue biochemistry and hence distinguish between normal and abnormal tissues was investigated. Six different epithelial tissues from the larynx, tonsil, oesophagus, stomach, bladder and prostate were measured. Spectral diagnostic models were constructed using multivariate statistical analysis of the spectra to classify samples of epithelial cancers and pre-cancers. Tissues were selected for clinical significance and to include those which develop into carcinoma from squamous, transitional or columnar epithelial cells. Rigorous histopathological protocols were followed and mixed pathology tissue samples were discarded from the study. Principal component fed linear discriminant models demonstrated excellent group separation, when tested by crossvalidation. Larynx samples, with squamous epithelial tissue, were separated into three distinct groups with sensitivities ranging from 86 to 90% and specificities from 87 to 95%. Bladder specimens, containing transitional epithelial tissue, were separated into five distinct groups with sensitivities of between 78 and 98% and specificities between 96 and 99%. Oesophagus tissue can contain both squamous and columnar cell carcinomas. A three group model discriminated the columnar cell pathological groups with sensitivities of 84-97% and specificities of 93-99%, and an eight group model combining both columnar and squamous tissues in the oesophagus was able to discriminate pathologies with sensitivities of 73-100% and specificities of 92-100%. It is likely that any overlap between pathology group predictions will have been due to a combination of the difficulty in histologically distinguishing between pre-cancerous states and the fact that there is no biochemical boundary from one pathological group to the next, i.e. there is believed to be a continuum of progression from the normal to the diseased state.

Several techniques are under development to diagnose oesophageal adenocarcinoma at an earlier stage. We have demonstrated the potential of Raman spectroscopy, an optical diagnostic technique, for the identification and classification of malignant changes. However, there is no clear recognition of the biochemical changes that distinguish between the different stages of disease. Our aim is to understand these changes through Raman mapping studies. Raman spectral mapping was used to analyse 20-mm sections of tissue from 29 snap-frozen oesophageal biopsies. Contiguous haematoxylin and eosin sections were reviewed by a consultant pathologist. Principal component analysis was used to identify the major differences between the spectra across each map. Pseudocolour score maps were generated and the peaks of corresponding loads identified enabling visualisation of the biochemical changes associated with malignancy. Changes were noted in the distribution of DNA, glycogen, lipids and proteins. The mean spectra obtained from selected regions demonstrate increased levels of glycogen in the squamous area compared with increased DNA levels in the abnormal region. Raman spectroscopy is a highly sensitive and specific technique for demonstration of biochemical changes in the carcinogenesis of Barrett's oesophagus. There is potential for in vivo application for real-time endoscopic optical diagnosis.