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This study examines the feasibility of using tip-enhanced Raman spectroscopy (TERS) for label-free chemical characterization of nanostructures in biological systems. For this purpose, a well-defined model system consisting of calcium alginate fibers is studied. In a companion paper, calcium alginate fibers and their network structures were shown to be a good model for the extracellular polysaccharides of biofilms at the nanoscale. TERS analysis of biological macromolecules, such as alginates, is complicated by heterogeneity in their sequence, molecular weight, and conformations, their small Raman cross-section, and the large number of functional groups, which can chemically interact with the silver surface of the tip and cause significant band shifts. Due to these effects, Raman frequencies in TERS spectra of biopolymers do not necessarily resemble band positions in the normal Raman spectrum of the bulk material, as is the case for less complex samples (e.g., dye molecules) studied so far. Additionally, analyte decomposition due to laser heating can have a significant influence, and carbon contamination signals can sometimes even overwhelm the weak analyte signals. Based on the investigation of alginates, strategies for spectra correction, choice of appropriate reference samples, and data interpretation are presented. With this approach, characteristic frequency ranges and specific marker bands can be found for biological macromolecules that can be employed for their identification in complex environments. [Figure not available: see fulltext.] © 2008 Springer-Verlag.