SPIN - Species by Proteome INvestigation

Ruether, P. L.; Husic, Immanuel; Bangsgaard, Pernille; Gregersen, Kristian Murphy; Pantmann, Pernille; Carvalho, Milena; Godinho, Ricardo Miguel; Friedl, Lukáš; Cascalheira, João; Joerkov, M. L. S.; Benedetti, Michael M.; Haws, Jonathan; Bicho, Nuno; Welker, Frido; Cappellini, Enrico; Olsen, Jesper V.

doi:10.1101/2021.02.23.432520

Cited by 6 publications

(6 citation statements)

References 59 publications

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“…Because many of the NCPs and some of the collagens have higher mutation rates than COL1, they are better targets for phylogenetic reconstructions, especially between closely related species. , Analyses of bone and dentine proteomes have successfully aided in resolving the phylogenetic relationships of extinct megafauna, ,,, including archaic hominins. , In addition, bone proteome-scale analyses using new high-throughput LC–MS/MS workflows, such as SPIN, show great promise for enabling genus and species-level taxonomic assignments of nondiagnostic bone …”

Section: Applications In Paleoproteomicsmentioning

confidence: 99%

Paleoproteomics

2022

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Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human−animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

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Section: Applications In Paleoproteomicsmentioning

confidence: 99%

Paleoproteomics

2022

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“…Recent developments in bead-based sample preparation for paleoproteomics ,− have allowed rapid separation of coextracting molecules (e.g., humic substances) that prevent detection and characterization of ancient proteomes through ion suppression, as well as host of other issues (e.g., column clogging) . Although bead-based methods have, to-date, only been paired with bottom-up MS approaches, the wide range of protein/peptide sizes that is possible to capture with this methodology , make it suitable for future use with digestion-free and top-down approaches as well.…”

Section: Future Directions In Dtppmentioning

confidence: 99%

“…Although bead-based methods have, to-date, only been paired with bottom-up MS approaches, the wide range of protein/peptide sizes that is possible to capture with this methodology , make it suitable for future use with digestion-free and top-down approaches as well. Bead-based methods have also been shown to be effective in automated sample preparation of archeological material . Automation has great potential for deep time paleoproteomics because sample preparation can be completed within a controlled environment.…”

Section: Future Directions In Dtppmentioning

confidence: 99%

“…However, to effectively utilize the bead-based methods, optimization of protein extraction for each tissue/sample type will be necessary. Recently optimized applications to bone and enamel ,, show that fossil protein extractomics is an area that has much room for development and optimization, especially with an eye toward increasing yield for samples from deep time.…”

Section: Future Directions In Dtppmentioning

confidence: 99%

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Deep Time Paleoproteomics: Looking Forward

2021

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The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.

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“…These results further demonstrate that ZooMS analyses can successfully be applied to semi-digested bone fragments which are frequently preserved in dog and human palaeofaeces [ 58 ] and may provide complementary insight into diet [ 42 ]. While ZooMS can provide species-level information for Pacific salmonids, higher resolution analyses, such as LC-MS/MS may be required for this level of taxonomic resolution for mammal species [ 59 ].…”

Section: Resultsmentioning

confidence: 99%

Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome

et al. 2021

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The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed dietary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spectrometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunalleq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes.

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SPIN - Species by Proteome INvestigation

Cited by 6 publications

References 59 publications

Paleoproteomics

Paleoproteomics

Deep Time Paleoproteomics: Looking Forward

Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome

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