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Fabrizi I, Flament S, Delhon C, Gourichon L, Vuillien M, Oueslati T, Auguste P, Rolando C, Bray F. Low-Invasive Sampling Method with Tape-Disc Sampling for the Taxonomic Identification of Archeological and Paleontological Bones by Proteomics. J Proteome Res 2024. [PMID: 39042361 DOI: 10.1021/acs.jproteome.4c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Collagen from paleontological bones is an important organic material for isotopic measurement, radiocarbon analysis, and paleoproteomic analysis to provide information on diet, dating, taxonomy, and phylogeny. Current paleoproteomic methods are destructive and require from a few milligrams to several tens of milligrams of bone for analysis. In many cultures, bones are raw materials for artifacts that are conserved in museums, which hampers damage to these precious objects during sampling. Here, we describe a low-invasive sampling method that identifies collagen, taxonomy, and post-translational modifications from Holocene and Upper Pleistocene bones dated to 130,000 and 150 BC using dermatological skin tape discs for sampling. The sampled bone micropowders were digested following our highly optimized enhanced filter-aided sample preparation protocol and then analyzed by MALDI FTICR MS and LC-MS/MS for identifying the genus taxa of the bones. We show that this low-invasive sampling does not deteriorate the bones and achieves results similar to those obtained by more destructive sampling. Moreover, this sampling method can be carried out at archeological sites or in museums.
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Affiliation(s)
- Isabelle Fabrizi
- Univ. Lille, CNRS UAR 3290─MSAP─Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille F-59000, France
| | - Stéphanie Flament
- Univ. Lille, CNRS UAR 3290─MSAP─Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille F-59000, France
| | - Claire Delhon
- Université Côte d'Azur, CNRS, CEPAM (UMR 7264), Nice F-06300, France
| | - Lionel Gourichon
- Université Côte d'Azur, CNRS, CEPAM (UMR 7264), Nice F-06300, France
| | - Manon Vuillien
- Université Côte d'Azur, CNRS, CEPAM (UMR 7264), Nice F-06300, France
| | - Tarek Oueslati
- Univ. Lille, CNRS UMR 8164─HALMA─Histoire, Archéologie et Littérature des Mondes Anciens, Lille F-59000, France
| | - Patrick Auguste
- Univ. Lille, CNRS UMR 8198─EEP─Evolution, Ecology and Paleontology, Lille F-59000, France
| | - Christian Rolando
- Univ. Lille, CNRS UAR 3290─MSAP─Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille F-59000, France
- Shrieking Sixties, Villeneuve d'Ascq F-59650, France
| | - Fabrice Bray
- Univ. Lille, CNRS UAR 3290─MSAP─Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille F-59000, France
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Zilberstein G, Zilberstein S, Righetti PG. Holy Grail possibly made from clay. Electrophoresis 2024. [PMID: 38234009 DOI: 10.1002/elps.202300249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
The main goal of the work was to find biochemical protein markers specific for grapes and wine in ancient amphorae shards and fermentation pools. Grape-specific proteins are more reliable markers than tartaric acid and other small organic acids (tartaric acid natural source are not only grape but also apple, mango, and other plants). The Yavne winery (located in the Central District of Israel) is stated to be the largest known wine production complex from the Byzantine period (ca. 1500 years ago). The site has been excavated recently, and a number of wine jar have been recovered. We have applied our ethylene vinyl acetate (EVA) (EVA studded with strong cation and anion exchangers) diskettes to the inner surface of a number of jars, thus capturing residual grape proteins therein. Via mass spectrometry analyses, we have been able to identify four grape and three yeast proteins. This has been possible because the EVA films, applied to such surfaces, are able to harvest and concentrate any trace species, rendering them amenable to instrumental analysis. Our analysis makes it possible to propose an explanation for the Holy Grail phenomenon as a dish in which wine or water begins to smell pleasant. We attribute this to the slow release of terpenes, aldehydes, and ketones from the clay walls of pottery. After digital modeling, we identified that "scallop-shaped" niches in winery were used for the condensation of high percentage alcohol by passive evaporation from fermentation tanks.
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Affiliation(s)
| | | | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta, ", Milan, Italy
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3
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Zilberstein G, Zilberstein R, Zilberstein S, Maor U, Cohen-Ofri I, Shor P, Bitler T, Riestra B, Righetti PG. Proteomics and metabolomics composition of the ink of a letter in a fragment of a Dead Sea Scroll from Cave 11 (P1032-Fr0). J Proteomics 2021; 249:104370. [PMID: 34517122 DOI: 10.1016/j.jprot.2021.104370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 08/31/2021] [Indexed: 11/19/2022]
Abstract
It is well established that the ink pigment used for writing the Dead Sea Scrolls (DSS) is mainly composed of carbon soot. The ink's binder however has yet to be securely identified. By applying EVA (ethylene vinyl acetate containing strong anion and cation exchangers admixed with C8 and C18) diskettes on one fragment and analyzing the captured material, the following study was able to determine the composition of the binder. Proteins admixed of plant proteins (ribulose biphosphate carboxylase, rhamnogalacturonate lyase, α-galactosidase A, calmodulin, among those identified) as well as of a few glycoproteins with different combinations of pentosyl and hexosyl units with plant acids (stearic, palmitic, oleic, linoleic and linolenic acids) and terpenes (triacontanol, catechin, lupeol) are mixed attributes of acacia trees which suggests the use of gum Arabic as the ink's binder. SIGNIFICANCE: Whereas a huge body of reports has explored any possible aspect of the Dead Sea Scrolls, including the dating and the animal origin of the parchment, one aspect had not been investigated so far, namely which kind of ligand had been adopted to ensure a firm binding of the ink (in reality carbon soot) to the supporting parchment. In the present investigation it has been demonstrated that this "glue" is a mixture of plant proteins, as well as a few glycoproteins, together with plant acids and terpenes. These proteins and metabolites belong to two species of trees, Vachellia nilotica and Acacia Albida, widespread in this Middle East region. The EVA methodology here adopted has shown that it is possible to explore any item pertaining to the world Cultural Heritage in the absence of damage or contamination thus permititng to analyze any possible precious document stored in museum, public libraries and private collections.
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Affiliation(s)
| | | | | | - Uriel Maor
- Spectrophon Ltd, Oppenheimer 7, Rehovot 7670107, Israel
| | | | - Pnina Shor
- Israel Antiquities Authority, Jerusalem, Israel
| | | | | | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy.
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Barberis E, Manfredi M, Marengo E, Zilberstein G, Zilberstein S, Righetti PG. Fiat Lux ... how Alessandro Volta illuminated his scripts. CR CHIM 2021. [DOI: 10.5802/crchim.128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Boschetti E, Zilberstein G, Righetti PG. Combinatorial peptides: A library that continuously probes low-abundance proteins. Electrophoresis 2021; 43:355-369. [PMID: 34498305 DOI: 10.1002/elps.202100131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/31/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022]
Abstract
After a decade of experimental applications, it is the objective of this review to make a point on combinatorial peptide ligand libraries dedicated to low-abundance proteins from animals to plants and to microorganism proteomics. It is, thus, at the light of the recent technical developments and applications that we will examine the state of the art, its usage within the scientific community, and its openness to unexplored fields. The improvements of the methodology and its implementation in connection with analytical determinations of combinatorial peptide ligand library (CPLL)-treated samples are extensively reviewed and commented upon. Relevant examples covering few critical aspects describe the performance of the technology. Finally, a reflection on the technological future is attempted in particular by involving new concepts adapted to the limited availability of certain biological samples.
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Affiliation(s)
| | | | - Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
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6
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Cucina A, Cunsolo V, Di Francesco A, Saletti R, Zilberstein G, Zilberstein S, Tikhonov A, Bublichenko AG, Righetti PG, Foti S. Meta-proteomic analysis of the Shandrin mammoth by EVA technology and high-resolution mass spectrometry: what is its gut microbiota telling us? Amino Acids 2021; 53:1507-1521. [PMID: 34453585 PMCID: PMC8519927 DOI: 10.1007/s00726-021-03061-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/03/2021] [Indexed: 11/29/2022]
Abstract
During the last decade, paleoproteomics allowed us to open a direct window into the biological past, improving our understanding of the phylogenetic relationships of extant and extinct species, past human diseases, and reconstruction of the human diet. In particular, meta-proteomic studies, mainly carried out on ancient human dental calculus, provided insights into past oral microbial communities and ancient diets. On the contrary, very few investigations regard the analysis of ancient gut microbiota, which may enable a greater understanding of how microorganisms and their hosts have co-evolved and spread under the influence of changing diet practices and habitat. In this respect, this paper reports the results of the first-ever meta-proteomic analysis carried out on a gut tissue sample some 40,000 years old. Proteins were extracted by applying EVA (ethylene–vinyl acetate) films to the surface of the gut sample of a woolly mammoth (Mammuthus primigenus), discovered in 1972 close to the Shandrin River (Yakutia, Russia), and then investigated via a shotgun MS-based approach. Proteomic and peptidomic analysis allowed in-depth exploration of its meta-proteome composition. The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the “original” endogenous peptides from contaminant ones. Overall, the results of the meta-proteomic analysis here reported agreeing with the previous paleobotanical studies and with the reconstructed habitat of the Shandrin mammoth and provided insight into its diet. The data have been deposited to the ProteomeXchange with identifier < PXD025518 > .
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Affiliation(s)
- Annamaria Cucina
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Vincenzo Cunsolo
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Antonella Di Francesco
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Rosaria Saletti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | | | | | - Alexei Tikhonov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab.1, Saint-Petersburg, 199034, Russia
| | - Andrey G Bublichenko
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab.1, Saint-Petersburg, 199034, Russia
| | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering ''Giulio Natta'', Politecnico di Milano, Via Mancinelli 7, 20131, Milan, Italy
| | - Salvatore Foti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
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Yates JR. “To Infinity...and beyond”: Looking Past Model Systems. J Proteome Res 2020; 19:3593-3594. [DOI: 10.1021/acs.jproteome.0c00607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zilberstein G, Zilberstein S, Righetti PG. Stalin's "black dog": a postmortem diagnosis. Anal Bioanal Chem 2020; 412:7701-7708. [PMID: 32876722 DOI: 10.1007/s00216-020-02914-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/10/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
Abstract
Undoubtedly, the two leaders who were under enormous pressure during World War II (WWII) were Winston Churchill and Joseph Stalin' since their respective countries had to sustain most of the war weight, at least in Europe. Lord Moran recounted in his memoir Winston Churchill: The Struggle for Survival that he had diagnosed a middle-aged Churchill with bipolar disorder. Churchill himself often referred to his periods of intense and prolonged depression as his "black dog." On the contrary, not much is known about Stalin's mental conditions, although in 1927 the neurologist V. M. Bekhterev, the day prior to his sudden death, upon a long examination of the leader's mental status, declared that he had found him affected by paranoia. No chemical evidence via clinical chemistry analyses was provided for the two leaders, though. We have had access to the collection of books (stored in the Russian Government Archive of Social and Political History, RGASPI, of the former Institute of Marxism and Leninism under the Central Committee of the USSR Communist Party) that Stalin was reading during WWII, with pages containing personal annotations on the margins. Upon harvesting surface material via EVA disks (ethylene-vinyl acetate studded with strong cation and anion exchangers and C8-C18 resins) and instrumental analysis via X-ray photoelectron spectroscopy, we detected lithium levels (~ 100 ± 8 ng/cm2) compatible with those present in the sweat and/or saliva of patients treated with lithium salts for curing bipolarity and paranoia or probably gout. These data are the first clear indication that Stalin was under cure for this pathology.Graphical abstract.
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Affiliation(s)
| | | | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, 20131, Milan, Italy.
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