Periodic Reporting for period 1 - SSPIN (Species and Sex by Proteome Investigation)
Reporting period: 2024-02-01 to 2025-07-31
The "Species and Sex by Proteome Investigation - SSPIN" project aimed to solve a critical and pervasive problem in the study of the past: the inability to perform economically viable, large-scale identification of species and sex from highly fragmented, tiny, or morphologically non-informative ancient bone and tooth specimens. Species and sex identification is highly valuable in archaeological, palaeoanthropological, and paleontological research. In these fields, which are closely linked to Social Sciences and Humanities (SSH), obtaining accurate species and sex data is essential for reconstructing ancient life and societies. Species Identification (Species-ID) allows archaeologists to reconstruct how extinct human species and prehistoric communities of our species exploited animal resources, shedding light on ancient diet, technology, and ritual practices. Sex Identification (Sex-ID) is crucial in palaeoanthropology to distinguish whether morphological variation in fossils originates from sexual dimorphism within a species or from taxonomic diversity across different species.
The objective of SSPIN is to offer rapid, low-cost, and highly reliable Species and Sex identification based on a novel, high-resolution mass spectrometry-based proteomic approach. The project addresses the bottlenecks of current technology by increasing throughput (aiming for 100-200 samples processed per day) and lowering the cost-per-sample. SSPIN will make previously prohibitively expensive research projects move within reach on a global scale. Once the project objectives will be fully reached, the project will make the routine assignment of biological sex possible for large archaeological sample sets, including challenging specimens like human subadults, and it will transform the accurate reconstruction of sexual dimorphism in hominid fossil remains into a standard practice.
The objective of SSPIN is to offer rapid, low-cost, and highly reliable Species and Sex identification based on a novel, high-resolution mass spectrometry-based proteomic approach. The project addresses the bottlenecks of current technology by increasing throughput (aiming for 100-200 samples processed per day) and lowering the cost-per-sample. SSPIN will make previously prohibitively expensive research projects move within reach on a global scale. Once the project objectives will be fully reached, the project will make the routine assignment of biological sex possible for large archaeological sample sets, including challenging specimens like human subadults, and it will transform the accurate reconstruction of sexual dimorphism in hominid fossil remains into a standard practice.
SSPIN substantially achieved its core objective of advancing its high-throughput mass spectrometry (MS)-based proteomic method from Technology Readiness Level (TRL) 3 to TRL 5-6 (Technology validated/demonstrated in a relevant environment). The core scientific work focused on technology validation by rigorously testing the analytical workflow under real-world conditions:
• Validation on Ancient Samples: The workflow, which uses a published proof-of-concept MS-based proteomic method, was applied to a large sample set of approximately 300 human remains from a Bronze Age necropolis (~5000 years old) in Europe.
• Scientific Dissemination: A peer-reviewed research article based on this extensive analysis is in preparation. This article will demonstrate the application of the technology in a relevant environment.
An aspect that still requires further development is the automation of sample preparation and data analysis. The primary expected outcome is the establishment of a high-throughput platform to democratize species and sex identification, addressing the lack of an economically viable strategy for large-scale analysis. Once fully optimised, the workflow will achieve rapid, micro-destructive MS-based proteomic analysism of 100-200 samples per day. The technology could have wider applications in forensic medicine.
• Validation on Ancient Samples: The workflow, which uses a published proof-of-concept MS-based proteomic method, was applied to a large sample set of approximately 300 human remains from a Bronze Age necropolis (~5000 years old) in Europe.
• Scientific Dissemination: A peer-reviewed research article based on this extensive analysis is in preparation. This article will demonstrate the application of the technology in a relevant environment.
An aspect that still requires further development is the automation of sample preparation and data analysis. The primary expected outcome is the establishment of a high-throughput platform to democratize species and sex identification, addressing the lack of an economically viable strategy for large-scale analysis. Once fully optimised, the workflow will achieve rapid, micro-destructive MS-based proteomic analysism of 100-200 samples per day. The technology could have wider applications in forensic medicine.
The main SSPIN outcomes are:
• Core Validation: The core analytical workflow was rigorously tested on a large sample set of approximately 300 human remains from a 5000-year-old necropolis. These results will be presented in a peer-reviewed article currently in preparation.
• Potential: The service is designed for a high throughput of 100-200 samples per day at a low cost per sample. This now makes feasible research projects previously considered prohibitive.
• Wider Applications: The technology's impact extends beyond archaeology, with potential repurposing for diagnostics in forensic medicine.
The project has identified several key needs to ensure successful uptake and commercialisation. The automation of sample preparation and data analysis needs to be further implemented to realize the full high-throughput potential. Ultimately, the project has achieved its initial objectives, successfully advancing the proteomic technology to a status of Testing/Pilot and Upscaling. The core scientific validation is complete, and a functional, beta-tested service platform is in place.
• Core Validation: The core analytical workflow was rigorously tested on a large sample set of approximately 300 human remains from a 5000-year-old necropolis. These results will be presented in a peer-reviewed article currently in preparation.
• Potential: The service is designed for a high throughput of 100-200 samples per day at a low cost per sample. This now makes feasible research projects previously considered prohibitive.
• Wider Applications: The technology's impact extends beyond archaeology, with potential repurposing for diagnostics in forensic medicine.
The project has identified several key needs to ensure successful uptake and commercialisation. The automation of sample preparation and data analysis needs to be further implemented to realize the full high-throughput potential. Ultimately, the project has achieved its initial objectives, successfully advancing the proteomic technology to a status of Testing/Pilot and Upscaling. The core scientific validation is complete, and a functional, beta-tested service platform is in place.