Proteome Analysis

Marina Creydt

With a few exceptions, proteins consist of a total of 20 different amino acids and can perform a wide variety of tasks in living organisms, such as building up structures, enzymatic reactions, transport processes or messenger functions.

The analysis of ancient proteomes – the entirety of peptides (3-10 amino acids) and proteins (>100 amino acids) – using mass spectrometry (Ion Mobility Q-TOF Instrument, Orbitrap (Q Exactive) Instrument) has become increasingly important in recent years. On the one hand, this is due to the rapidly advancing technological developments in the mass spectrometric detection of peptides and proteins and, on the other hand, to the fact that the analysis of the proteome provides information about ancient artefacts that are not accessible, for example, using DNA analyses.

Furthermore, recent studies indicate that compared to ancient DNA, ancient proteoms can be more resistant to degradation processes.

Peptides and proteins are usually analysed after enzymatic digestion, mostly with trypsin (bottom-up approach), using high-resolution mass spectrometers.. On the basis of the peptide fragments obtained, conclusions can be drawn about the original protein via a comparison with databases and reference samples. This approach is also referred to as peptide mass fingerprinting or peptide fragment fingerprinting. The advantage of analysing smaller peptide fragments over proteins is twofold: (i) peptides are generally more soluble than proteins and can be separated with a higher resolution by chromatography; (ii) peptides can be detected more sensitively with the currently available mass spectrometric detectors and accordingly lower detection limits can be achieved. In addition, when analysing ancient artefacts, it can be assumed that a large part of the proteins has already been broken down into smaller fragments.

In general, proteome analyses can be divided into proteomics and metaproteomics methods: Proteomics refers to the analysis of the proteome of individual organelles, cells, tissues or an entire organism, while metaproteome analyses focus on the residues of other organisms.

Questions that can be addressed with proteomics studies include: biological identity of organic materials (genus, species), characterization of the material (e. g. egg white or egg yolk was used, which are relevant as binding agents), surface treatments, an estimation of the age and state of preservation.

Questions that can be addressed with metaproteomics studies include: microbial contamination (stains), instruction for restoration, storage / biodeterioration and information about author / reader.

References

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Buckley, M., Whitcher Kansa, S., Howard, S., Campbell, S., Thomas-Oates, J., and Collins, M. (2010). Distinguishing between archaeological sheep and goat bones using a single collagen peptide. J. Archaeol. Sci., 37, 13–20. https://doi.org/10.1016/j.jas.2009.08.020.
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Fiddyment, S., Goodison, N.J., Brenner, E., Signorello, S., Price, K., and Collins, M.J. (2021). Girding the loins? Direct evidence of the use of a medieval parchment birthing girdle from biomolecular analysis. R. Soc. Open Sci., 8, 202055. https://doi.org/10.1098/rsos.202055.
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