The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome

Paik, Young Ki; Jeong, Seul Ki; Omenn, Gilbert S.; Uhlén, Mathias; Hanash, Samir M.; Cho, Sang Yun; Lee, Hyoung Joo; Na, Keun; Choi, Eun Young; Yan, Fangfei; Zhang, Fan; Zhang, Yue; Snyder, M; Cheng, Yong; Chen, Rui; Markó-Varga, György; Deutsch, Eric W.; Kim, Hoguen; Kwon, Ja Young; Aebersold, Ruedi; Bairoch, Amos Marc; Taylor, Allen D.; Kim, Kwang Youl; Lee, Eun Young; Hochstrasser, Denis F.; Legrain, Pierre; Hancock, William S.

doi:10.1038/nbt.2152

Cited by 277 publications

(379 citation statements)

References 9 publications

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“…The biochemical characterization of the proteins encoded by the approximately 20,300 human genes is complicated by the multi-functionality of many protein molecules, the highly diverse interactions within protein complexes and the dynamic nature of protein expression patterns (Paik et al 2012). In contrast to the relatively stable genome, the global protein constellation of specific cell types or tissues is highly variably and constantly adapting to changed functional demands and environmental influences.…”

Section: From Genome To Proteomementioning

confidence: 99%

Exercise Proteomics: Review

Monika¹,

Kumar²

2017

jesp

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Aim: The aim of this review was to discuss the proteomics of exercise. Results: The sophisticated protein biochemical and mass spectrometric technologies can now be used to study subtle changes in protein concentration, isoform expression patterns, protein-protein interactions and/or post-translational modifications following physical exercise. Conclusion: Rapid advancements in molecular techniques and the streamlining of mass spectrometry-based proteomic workflows have enabled the establishment of global alterations in the concentration, isoform expression patterns, molecular interactions and posttranslational modifications of muscle proteins following physical exercise. Recent genetic advances in the field of molecular exercise science will heavily influence the design of future proteomic studies in sports science and sports medicine.

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Section: From Genome To Proteomementioning

confidence: 99%

Exercise Proteomics: Review

Monika¹,

Kumar²

2017

jesp

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“…Both resources, PeptideAtlas and GPMDB, are also joining efforts in the context of the Chromosome‐based (C‐) and Biology/Disease (B/D) Human Proteome Projects (HPP) 65, 66, together with neXtProt and the antibody‐based resource Human Proteome Atlas 67. This is a clear example of the utility of large‐scale and centralized (re‐)processing, as it can ensure consistent processing and thus comparable results.…”

Section: Introductionmentioning

confidence: 99%

Exploring the potential of public proteomics data

et al. 2015

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In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS‐based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re‐)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data.

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“…The Chromosome-Centric Human Proteome Project (C-HPP) federates teams from different countries aiming at delivering an extended catalogue of experimentally validated human proteins 1 . Its first goal is to obtain definitive proof for the existence of at least one representative protein per protein coding gene by various approaches, including direct protein sequencing, antibody or mass-spectrometry based techniques.…”

Section: Introductionmentioning

confidence: 99%

Missing Protein Landscape of Human Chromosomes 2 and 14: Progress and Current Status

et al. 2016

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Within the C-HPP, the Swiss and French teams are responsible for the annotation of proteins from chromosomes 2 and 14, respectively. neXtProt currently reports 1231 entries on chromosome 2 and 624 entries on chromosome 14; of these, 134 and 93 entries are still not experimentally validated and are thus considered as "missing proteins" (PE2−4), respectively. Among these entries, some may never be validated by conventional MS/MS approaches because of incompatible biochemical features. Others have already been validated but are still awaiting annotation. On the basis of information retrieved from the literature and from three of the main C-HPP resources (Human Protein Atlas, PeptideAtlas, and neXtProt), a subset of 40 theoretically detectable missing proteins (25 on chromosome 2 and 15 on chromosome 14) was defined for upcoming targeted studies in sperm samples. This list is proposed as a roadmap for the French and Swiss teams in the near future.

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The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome

Cited by 277 publications

References 9 publications

Exercise Proteomics: Review

Exercise Proteomics: Review

Exploring the potential of public proteomics data

Missing Protein Landscape of Human Chromosomes 2 and 14: Progress and Current Status

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