Paleoproteomics: ZooMS

Zooarchaeology by Mass Spectrometry 

NCC is now accepting submission forms for ZooMS sample processing

Zooarchaeology by Mass Spectrometry (ZooMS), more formally known as collagen peptide mass-fingerprinting by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, is a rapidly expanding analytical method designed to identify the taxa of morphologically unidentifiable animal remains; namely bone. The technique extracts peptides stored within Type I Collagen of bone, ivory, eggshell and other animal remains, runs them through a MALDI-TOF mass spectrometer, and compares the resulting peptide peaks to a pre-established database. When the peptide peak results match a set of peaks listed in the database, the species of the otherwise unknown sample is identified. These species-specific peptide peaks are called the Peptide Mass Fingerprint (PMF) for that species.   

This paleoproteomics technique has been serving the fields of archaeology, cultural heritage, ecology, and forensics for just over a decade (Buckley et al. 2009). Compared to aDNA analysis, ZooMS is minimally destructive and more cost-effective. It also produces more reliable results due to the higher survival rate of collagen than DNA in severe conditions and over long periods of time. This survivability is partially due to Type I Collagen’s abundance within animal matter, making up 95% of collagen and 80% of all proteins. These factors have driven the field of ZooMS to expand rapidly, with related publications over doubling in the past five years alone (Brown et al. 2021a).  

While this technique is useful across various fields, it was initially developed by and for archaeologists. As a result, this is where the majority of its development has centered. Examples of its uses in archaeology span from discovering symbolic expression through species selection for Iroquoian bone points (McGrath et al. 2019), to identifying hominin remains from nearly 10,000 bone fragments at Denisova cave (Brown et al. 2016, 2021b, 2021c), and species identification of leather shoe parts from medieval Denmark (Ebsen et al. 2019). Other uses include identifying remains in museum collections and identifying animal-based components in works of art (Fiddyment et al. 2015; Kirby et al. 2013). Identification of ivory (Coutu et al. 2016) and wild African bovids (Janzen et al. 2021) also opens up the potential to use ZooMS in tracking illegal trade of ivory products and bushmeat. 

Facilities and Instrumentation 

NCC’s ZooMS sample processing lab is run out of the 4Front Technology & Office Campus at 

3510 Hopkins Pl N, Oakdale, MN 55128 

NCC has an established relationship with the Center for Metabolics and Proteomics (CMSP) in the College of Biological Sciences at the University of Minnesota. Samples prepared at the ZooMS lab are brought to the CMSP labs on the U of M St. Paul campus and run through the center’s MALDI-TOF for final spectra results.  


Laura Koski, MSc, RPA
ZooMS Lab Director 

Example Publications: 

Start Here for an overview of the process and its development: 

(2022) Korzow Richter, Kristine; Codlin, Maria C.; Seabrook, Melina and Christina Warinner.
A primer for ZooMS applications in archaeology. PNAS 119(20) e2109323119 DOI 10.1073/pnas.21093323119 

(2009) Buckley, Michael; Collins, Matthew; Thomas-Oates, Jane and Julie C. Wilson. 
Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Communications in Mass Spectrometry 23:3843-3854. DOI 10.1002/rcm.4316 

(2013) Kirby, Daniel P.; Buckley, Michael; Promise, Ellen; Trauger, Sunia A. and Rose T. Holdcraft
Identification of collagen-based materials in cultural heritage. Analyst 17:4849-4858. DOI 10.1039/c3an00925d 

(2015) Fiddyment, Sarah; Holsinger, Bruce; Ruzzier, Chiara; Devine, Alexander; Binois, Annlise; Albarella, Umberto; Fischer, Roman; Nichols, Emma; Curtis, Antoinette; Cheese, Edward; Teasdale, Matthew D.; Checkley-Scott, Caroline; Milner, Stephen J.; Rudy, Kathryn M.; Johnson, Eric J.; Vnouček, Jiří; Garrison, Mary; McGrory, Simon; Bradley, Daniel G. and Matthew J. Collins
Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting. PNAS 112(24):15066-15071. DOI 10.1073/pnas.1512264112 

(2016) Brown, Samantha; Higham, Thomas; Slon, Vivane; Pääbo, Svante; Meyer, Matthias; Douka, Katerina; Brock, Fiona; Comeskey, Daniel; Procopio, Noemi; Shunkov, Michael; Derevianko, Anatoly and Michael Buckley. 
Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis. Scientific Reports 6:23559. DOI 10.1038/srep23559 

(2016) Coutu, Ashley N.; Whiteclaw, Gavin; le Roux, Petrus and Judith Sealy. 
Earliest Evidence for the Ivory Trade in Southern Africa: Isotopic and ZooMS Analysis of Seventh-Tenth Century AD Ivory from KwaZulu-Natal. African Archaeology Review 33:411-435. DOI 10.1007/s10437-016-9232-0 

(2019) Amsgaard Ebsen, Jannie; Haase, Kristine; Larsen, Rene ; Vestergaard Poulson Sommer, Dorte and Luis Orsted Brandt. 
Identifying archaeological leather – discussing the potential of grain pattern analysis and zooarchaeology by mass spectrometry (ZooMS) through a case study involving medieval shoe parts from Denmark. Journal of Cultural Heritage 39:21-31.. DOI 10.1016/j.culher.2019.04.008 

(2019) McGrath, Krista; Rowsell, Keri; Gates St-Pierre, Christina; Tedder, Andrew; Foody, George; Roberts, Carolynn; Speller, Camilla and Matthew Collins. 
Identifying Archaeological Bone via Non-Destructive ZooMS and the Materiality of Symbolic Expression: Examples from Iroquoian Bone Points. Scientific Reports 9:11027. DOI s41598-019-47299-x  

(2021a) Brown, Samantha; Douka, Katerina; Collins, Matthew J. and Kristina Korzow Richter. 
On the standardization of ZooMS nomenclature. Journal of Proteomics 235:104041. DOI 101.1016/j.jprot.2020.104041 

(2021b) Brown, Samantha; Wang, Naihui; Oertle, Annette; Kozlikin, Maxim B.; Shunkov, Michael V.; Derevianko, Anatoly P.; Comeskey, Daniel; Jope-Street, Blair; Harvey, Virginia L.; Chowdhury, Manasij Pal; Buckley, Michael; Higham, Thomas and Katerina Douka. 
Zooarchaeology through the lens of collagen fingerprinting at Denisova Cave. Scientific Reports 11:15457. DOI 10.1038/s41598-021-94731-2   

(2021c) Brown, Samantha; Massilani, Diyendo; Kozlikin, Maxim B.; Shunkov, Michael V.; Derevianko, Anatoly P.; Soessel, Alexander; Jope-Street, Blair; Meyer, Matthias; Kelso, Janet; Pääbo, Svanta; Higham, Thomas and Katerina Douka . 
The earliest Denisovans and their cultural adaptation. Nature Ecology & Evolution 6:28-35. DOI 10.1038/s41559-021-01581-2 

(2021) Janzen, Anneke; Korzow Richter, Kristine; Mwebi, Ogeto; Brown, Samantha; Onduso, Veronicah; Gatwiri, Filia; Ndiema, Emmanuel; Katongo, Maggie; Goldstein, Steven T.; Douka, Katerina and Nicole Boivin. 
Distinguishing African bovids using Zooarchaeology by Mass Spectrometry (ZooMS): New peptide markers and insights into Iron Age economies in Zambia. PloSONE 16(5). DOI 10.1371/journal.pone.0251061. 

NCC’s Current ZooMS Services Work For: 

  • Bone 
  • Ivory
  • Eggshell
  • Leather/Skins 
  • Flesh/Meat 

NCC is working on expanding to mussel shell analysis. 

Standard Timeline (~1 month)$52/sample
Rush Fee$104/sample