Introducing protein deamidation: Landmark discoveries, societal outreach, and tentative priming workflow to address deamidation

Boudier-Lemosquet, Axel; Mahler, Adrien; Bobo, Claude; Dufossée, Mélody; Priault, Muriel

doi:10.1016/j.ymeth.2021.11.012

Cited by 7 publications

(6 citation statements)

References 100 publications

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“…Analysis of PTMs, such as glutamine deamidation, provides information on the conservation status of bone. The degree of glutamine deamidation has been previously reported to hold promise as an indicator of degradation in ancient materials. ,− Older or degraded samples have a higher level of deamidation. ,− Deamidation is used in many publications to validate that proteins found in samples are ancient and are not the result of a contamination. Unfortunately, comparing deamidation data between publications is complex due to technical issues and the condition of preservation of the bones.…”

Section: Resultsmentioning

confidence: 99%

“…19,65,69 The second technical issue is that the calculation methods and software are different and do not focus on the same deamidation rate values. 48,66,67,69,71,72 Several values of deamidation are obtained according to the analytical protocol. In ZooMS based on MALDI MS analysis, only the percentage of glutamine deamidation from the peptide P1 is used.…”

Section: T H Imentioning

confidence: 99%

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Low-Invasive Sampling Method with Tape-Disc Sampling for the Taxonomic Identification of Archeological and Paleontological Bones by Proteomics

Fabrizi,

Flament,

Delhon

et al. 2024

J. Proteome Res.

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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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Section: Resultsmentioning

confidence: 99%

Section: T H Imentioning

confidence: 99%

Low-Invasive Sampling Method with Tape-Disc Sampling for the Taxonomic Identification of Archeological and Paleontological Bones by Proteomics

Fabrizi,

Flament,

Delhon

et al. 2024

J. Proteome Res.

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“…(iii) the calculation methods and software are different and do not give the same type of values. 36, 56–57, 59, 61–62 The rate of deamidation between publications for bones from the same period may be different because the procedures for demineralization of bones, extraction of proteins are variable and may induce deamidation. 54–55, 59 With regard to this last point, it is possible to obtain the percentage of glutamine deamidation from the peptide P1, the percentage of glutamine and asparagine deamidation of the peptides identified on type I collagen and other proteins.…”

Section: Resultsmentioning

confidence: 99%

“…[54][55][56][57] Older or degradated samples have a higher level of deamidation. [54][55][56][57][58][59][60][61] Deamidation is used in many publications to validate that samples and proteins are ancient.…”

Section: Tape Stripping Methods Applied To Palaeontological and Archa...mentioning

confidence: 99%

Low-invasive sampling method for taxonomic for the identification of archaeological and paleontological bones by proteomics of their collagens

Fabrizi,

Flament,

Delhon

et al. 2023

Preprint

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Collagen from paleontological bones is an important organic material for isotopic measurement, radiocarbon and paleoproteomic analyzes, to provide information on diet, dating and taxonomy. Current paleoproteomics methods are destructive and require from a few milligrams to several tenths of milligrams of bone for analysis. In many cultures, bones are raw materials for artefact which are conserved in museum which hampers to damage 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 micro-powders were digested following our highly optimized eFASP protocol, 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 performed at archaeological sites or in museums.

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“…She pioneered the description of a monodeamidated form of Bcl-xL, and of the sequential mechanism that leads to the doubly deamidated form [ 167 , 168 ]. She has now specialized her lab on protein instability and molecular aging [ 169 ], and uses Bcl-xL deamidation both as a tool and as a study object.…”

Section: Team Workmentioning

confidence: 99%

Keeping Cell Death Alive: An Introduction into the French Cell Death Research Network

et al. 2022

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Since the Nobel Prize award more than twenty years ago for discovering the core apoptotic pathway in C. elegans, apoptosis and various other forms of regulated cell death have been thoroughly characterized by researchers around the world. Although many aspects of regulated cell death still remain to be elucidated in specific cell subtypes and disease conditions, many predicted that research into cell death was inexorably reaching a plateau. However, this was not the case since the last decade saw a multitude of cell death modalities being described, while harnessing their therapeutic potential reached clinical use in certain cases. In line with keeping research into cell death alive, francophone researchers from several institutions in France and Belgium established the French Cell Death Research Network (FCDRN). The research conducted by FCDRN is at the leading edge of emerging topics such as non-apoptotic functions of apoptotic effectors, paracrine effects of cell death, novel canonical and non-canonical mechanisms to induce apoptosis in cell death-resistant cancer cells or regulated forms of necrosis and the associated immunogenic response. Collectively, these various lines of research all emerged from the study of apoptosis and in the next few years will increase the mechanistic knowledge into regulated cell death and how to harness it for therapy.

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Introducing protein deamidation: Landmark discoveries, societal outreach, and tentative priming workflow to address deamidation

Cited by 7 publications

References 100 publications

Low-Invasive Sampling Method with Tape-Disc Sampling for the Taxonomic Identification of Archeological and Paleontological Bones by Proteomics

Low-Invasive Sampling Method with Tape-Disc Sampling for the Taxonomic Identification of Archeological and Paleontological Bones by Proteomics

Low-invasive sampling method for taxonomic for the identification of archaeological and paleontological bones by proteomics of their collagens

Keeping Cell Death Alive: An Introduction into the French Cell Death Research Network

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