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      Human Bone Proteomes before and after Decomposition: Investigating the Effects of Biological Variation and Taphonomic Alteration on Bone Protein Profiles and the Implications for Forensic Proteomics

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          Abstract

          Bone proteomic studies using animal proxies and skeletonized human remains have delivered encouraging results in the search for potential biomarkers for precise and accurate post-mortem interval (PMI) and the age-at-death (AAD) estimation in medico-legal investigations. The development of forensic proteomics for PMI and AAD estimation is in critical need of research on human remains throughout decomposition, as currently the effects of both inter-individual biological differences and taphonomic alteration on the survival of human bone protein profiles are unclear. This study investigated the human bone proteome in four human body donors studied throughout decomposition outdoors. The effects of ageing phenomena ( in vivo and post-mortem) and intrinsic and extrinsic variables on the variety and abundancy of the bone proteome were assessed. Results indicate that taphonomic and biological variables play a significant role in the survival of proteins in bone. Our findings suggest that inter-individual and inter-skeletal differences in bone mineral density (BMD) are important variables affecting the survival of proteins. Specific proteins survive better within the mineral matrix due to their mineral-binding properties. The mineral matrix likely also protects these proteins by restricting the movement of decomposer microbes. New potential biomarkers for PMI estimation and AAD estimation were identified. Future development of forensic bone proteomics should include standard measurement of BMD and target a combination of different biomarkers.

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          STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

          Abstract Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein–protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein–protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.
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            The PRIDE database and related tools and resources in 2019: improving support for quantification data

            Abstract The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.
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              Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search

              We present a statistical model to estimate the accuracy of peptide assignments to tandem mass (MS/MS) spectra made by database search applications such as SEQUEST. Employing the expectation maximization algorithm, the analysis learns to distinguish correct from incorrect database search results, computing probabilities that peptide assignments to spectra are correct based upon database search scores and the number of tryptic termini of peptides. Using SEQUEST search results for spectra generated from a sample of known protein components, we demonstrate that the computed probabilities are accurate and have high power to discriminate between correctly and incorrectly assigned peptides. This analysis makes it possible to filter large volumes of MS/MS database search results with predictable false identification error rates and can serve as a common standard by which the results of different research groups are compared.
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                Author and article information

                Journal
                J Proteome Res
                J Proteome Res
                pr
                jprobs
                Journal of Proteome Research
                American Chemical Society
                1535-3893
                1535-3907
                08 March 2021
                07 May 2021
                : 20
                : 5
                : 2533-2546
                Affiliations
                []Department of Cultural Sciences, Linnaeus University , Kalmar 352 52, Sweden
                []Forensic Anthropology Center, Texas State University , San Marcos 78666, Texas, United States
                [§ ]Forensic Science Research Group, Faculty of Health and Life Sciences, Northumbria University , Ellison Building, Northumbria University Newcastle, Newcastle Upon Tyne NE1 8ST, U. K.
                []Dipartimento di Chimica, University of Turin , Via P. Giuria 7, 10125 Turin, Italy
                []Forensic Sciences Unit, School of Natural Sciences and Mathematics, Chaminade University of Honolulu , Honolulu 96816, Hawaii, United States
                Author notes
                Author information
                http://orcid.org/0000-0002-7461-7586
                Article
                10.1021/acs.jproteome.0c00992
                8155572
                33683123
                39200f37-fe81-4b97-9cd4-58e0484e23c7
                © 2021 The Authors. Published by American Chemical Society

                Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained ( https://creativecommons.org/licenses/by/4.0/).

                History
                : 08 December 2020
                Funding
                Funded by: FP7 Ideas: European Research Council, doi 10.13039/100011199;
                Award ID: 319209
                Funded by: Universiteit Leiden, doi 10.13039/501100001717;
                Award ID: 5604/30-4-2015/Byvanck
                Funded by: Royal Society, doi 10.13039/501100000288;
                Award ID: RGS/R1/191371
                Funded by: UK Research and Innovation, doi 10.13039/100014013;
                Award ID: MR/S032878/1
                Categories
                Article
                Custom metadata
                pr0c00992
                pr0c00992

                Molecular biology
                forensic proteomics,forensic taphonomy,bone mineral density,post-mortem interval estimation,age-at-death estimation,human decomposition,forensic microbiology

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