Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins

Zhang, Yao; Li, Qidan; Wu, Feilin; Zhou, Ruo; Qi, Yingzi; Su, Na; Chen, Lingsheng; Xu, Shaohang; Jiang, Tao; Zhang, Chengpu; Cheng, Gang; Chen, Xinguo; Kong, Degang; Wang, Yujia; Zhang, Tao; Zi, Jian; Wei, Wei; Gao, Yuan; Zhen, Bei; Zhi, Xiao‐Yang; Wu, Songfeng; Yang, Pengyuan; Wang, Quanhui; Wen, Bo; He, Fuchu; Xu, Ping; Liu, Siqi

doi:10.1021/acs.jproteome.5b00435

Cited by 47 publications

(73 citation statements)

References 42 publications

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“…This observation suggests that these tissues have a significant number of uniquely expressed genes or alternative transcripts not found in other tissues. Other recent publications focusing on the analysis of Testis tissue have also found this to be true 26 .…”

Section: Resultsmentioning

confidence: 61%

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

et al. 2016

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Complete annotation of the human genome is indispensable for medical research. The GENCODE consortium strives to provide this, augmenting computational and experimental evidence with manual annotation. The rapidly developing field of proteogenomics provides evidence for the translation of genes into proteins and can be used to discover and refine gene models. However, for both the proteomics and annotation groups, there is a lack of guidelines for integrating this data. Here we report a stringent workflow for the interpretation of proteogenomic data that could be used by the annotation community to interpret novel proteogenomic evidence. Based on reprocessing of three large-scale publicly available human data sets, we show that a conservative approach, using stringent filtering is required to generate valid identifications. Evidence has been found supporting 16 novel protein-coding genes being added to GENCODE. Despite this many peptide identifications in pseudogenes cannot be annotated due to the absence of orthogonal supporting evidence.

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Section: Resultsmentioning

confidence: 61%

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

et al. 2016

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“…Jumeau et al 40 (PXD002367) reported finding 89 missing proteins from human spermatozoa. Zhang et al 41 (PXD002179) identified 166 missing protein groups in testis. In Supplementary Table 3, we show that only 354 of the 879 HPA testis-enriched proteins are canonical in PeptideAtlas, leaving 525 yet to be found even after these two data sets were incorporated into PeptideAtlas 2016-01.…”

Section: Concluding Remarks and New Directionsmentioning

confidence: 99%

Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications

et al. 2016

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The HUPO Human Proteome Project (HPP) has two overall goals: (1) stepwise completion of the protein parts list—the draft human proteome including confidently identifying and characterizing at least one protein product from each protein-coding gene, with increasing emphasis on sequence variants, post-translational modifications (PTMs), and splice isoforms of those proteins; and (2) making proteomics an integrated counterpart to genomics throughout the biomedical and life sciences community. PeptideAtlas and GPMDB reanalyze all major human mass spectrometry data sets available through ProteomeXchange with standardized protocols and stringent quality filters; neXtProt curates and integrates mass spectrometry and other findings to present the most up to date authorative compendium of the human proteome. The HPP Guidelines for Mass Spectrometry Data Interpretation version 2.1 were applied to manuscripts submitted for this 2016 C-HPP-led special issue [www.thehpp.org/guidelines]. The Human Proteome presented as neXtProt version 2016-02 has 16,518 confident protein identifications (Protein Existence [PE] Level 1), up from 13,664 at 2012-12, 15,646 at 2013-09, and 16,491 at 2014-10. There are 485 proteins that would have been PE1 under the Guidelines v1.0 from 2012 but now have insufficient evidence due to the agreed-upon more stringent Guidelines v2.0 to reduce false positives. neXtProt and PeptideAtlas now both require two non-nested, uniquely mapping (proteotypic) peptides of at least 9 aa in length. There are 2,949 missing proteins (PE2+3+4) as the baseline for submissions for this fourth annual C-HPP special issue of Journal of Proteome Research. PeptideAtlas has 14,629 canonical (plus 1187 uncertain and 1755 redundant) entries. GPMDB has 16,190 EC4 entries, and the Human Protein Atlas has 10,475 entries with supportive evidence. neXtProt, PeptideAtlas, and GPMDB are rich resources of information about post-translational modifications (PTMs), single amino acid variants (SAAVSs), and splice isoforms. Meanwhile, the Biology- and Disease-driven (B/D)-HPP has created comprehensive SRM resources, generated popular protein lists to guide targeted proteomics assays for specific diseases, and launched an Early Career Researchers initiative.

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“…P, proteins and parameters. by consultation of the Tissue Atlas at www.proteinatlas.org (visited between October 2018 and January 2019; see also LC-MS/MS study by Zhang et al [2015a]). For generating BODY1 and BODY2, we selected 2 mutually exclusive sets of protein-coding genes from the according list at www.genenames.org (Human Genome Nomenclature Committee).…”

Section: Protein Setsmentioning

confidence: 99%

Intra-Protein Coevolution Is Increasingly Functional with Greater Proximity to Fertilization

Kwiatkowski

Asif

Schumacher

et al. 2020

Cytogenet Genome Res

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Intramolecular coevolution of amino acid sites has repeatedly been studied to improve predictions on protein structure and function. Thereby, the focus was on bacterial proteins with available crystallographic data. However, intramolecular coevolution has not yet been compared between protein sets along a gradient of functional proximity to fertilization. This is especially true for the potential effect of external selective forces on intraprotein coevolution. In this study, we investigated both aspects in equally sized sets of mammalian proteins representing spermatozoa, testis, entire body, and liver. For coevolutionary analyses, we derived the proportion of covarying sites per protein from amino acid alignments of 10 mammalian orthologues each. In confirmation of the validity of our coevolution proxy, we found positive associations with the nonsynonymous or amino acid substitution rate in all protein sets. However, our coevolution proxy negatively correlated with the number of protein interactants (node degree) in male reproductive protein

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Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins

Cited by 47 publications

References 42 publications

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications

Intra-Protein Coevolution Is Increasingly Functional with Greater Proximity to Fertilization

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