Curating Proteins and Fibers

Microscope image of Rhizorhabdus wittichii RW1 overlaod with a mass spectrum and the corresponding protein sequence (rearranged and cropped), by Rolf U. Halden , 2005. CC BY-SA 4.0

No 5
Proteomics: Possibilities and Limitations
Proteomic analysis has been a game changer in the identification of animal fibers, but how can the information gained from its methods be applied?

Proteomic analyses are significant for our group’s interests as they play a crucial role in advancing our understanding of biology, biological function, and evolutionary processes, and can even support or confront written sources. In our most recent reading group, we picked four readings to explore the application of proteomic approaches “Ancient Proteins Analysis in Archeology,” “Proteomics and Coast Salish Blankets: A Tale of Shaggy Dogs?,” “Proteins, Possibly Human, Found in World War II Concentration Camp Artifact” and the chapter “Biocodicology.”

We started our discussion with the review article “Ancient Protein Analysis in Archaeology” by Jessica Hendy, which focuses on the potential of various methods of protein analysis—such as providing evidence of eating habits of ancient humans—and also their limitations, for example, the dependence on sample quality. According to Hendy, scientists examining ancient materials historically favored DNA analysis over traditional proteomics methods based on amino acid analysis and immunoassays—these were considered unreliable due to the inherent difficulties of running assays and the impossibility of amplifying the analysis with different samples. However, the adoption of mass spectrometry (MS) approaches has revolutionized proteomic analysis, providing a detailed understanding of protein samples that was not available using earlier techniques. MS serves as the foundation for ZooMS (zooarchaeology by mass spectrometry), an innovative method that analyzes animal-based materials such as hair and bone extracted from archeological sites by comparing their protein signatures against other samples in a growing database, enabling the identification of specific animal taxon.

We further explored case studies that highlighted the applications of proteomic analysis. One such study focused on the Coast Salish blankets, where anthropologists and conservators at the Smithsonian Museum of the American Indian employed proteomics to gain insights into the materials used. Another case study involved proteomic analysis: forensic medical examiners analyzed World War II concentration camp artifacts to provide scientific evidence to support oral testimonies.

For a practical example, we turned to Bruce Holsinger’s chapter on biocodicology. This interdisciplinary field combines the analysis of biological materials with archival research. Holsinger’s work showcased the effectiveness of ZooMS in accurately identifying the animal species used in medieval parchment production. However, it is important to note that MS has its limitations, as demonstrated by Yang et al.’s study on Holocaust artifacts. Samples with mixed protein origins may pose challenges during identification, and the lack of reference data results in unidentified species.

Our engaging session explored the profound value of proteomic analysis in archaeological and archival research. These techniques have unlocked new perspectives on historical documents, textile traditions, and human history in general. The stimulating discussion drove us to contemplate the significance of fostering interdisciplinary studies that combine scientific methodologies with traditional research approaches.

Our thought-provoking discussions led us to raise several questions, including:

  • Considering that new technologies have produced new evidence that was impossible in the past, what else can be known through proteomics analysis?
  • If historians and scientists using proteomics methods collaborated more frequently, how might historical research change? Do historians require a deeper familiarity with the science behind proteomic methods in order to envision the possibilities of using proteomics analyses in collaboration with scientists?
  • Is there a hierarchy among the forms of evidence valued by historians?

We were happy foster this rich conversation with our reading group, which generated many questions and brought together several collaborators from various fields. The “Proteins and Fibers” Working Group will continue advancing interdisciplinary conversation during our subsequent activities.

Isabela Dornelas


Hendy, Jessica. “Ancient Protein Analysis in Archaeology.” Science Advances 7, no. 3 (2021): 1–11.

Holsinger, Bruce. “Biocodicology,” in On Parchment: Animals, Archives, and the Making of Culture from Herodotus to the Digital Age, 273–287. New Haven: Yale University Press, 2023.

Solazzo, Caroline, Susan Heald, Mary W. Ballard, David Ashford, Paula. T. DePriest, Robert J. Koestler, and Matthew J. Collins. “Proteomics and Coast Salish Blankets: A Tale of Shaggy Dogs?” Antiquity 85, no. 330 (2011): 1418–1432.

Yang, Heyi, Erin Butler, Samantha A. Monier, and Donald Siegel. “Proteins, Possibly Human, Found in World War II Concentration Camp Artifact.” Scientific Reports 2, no. 1 (2022): 1–9.


Back to Curating Proteins and Fibers