Advances of the HUPO Human Proteome Project with broad applications for life sciences research

Omenn, Gilbert S.

doi:10.1080/14789450.2017.1270763

Cited by 8 publications

(9 citation statements)

References 12 publications

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“…We strongly encourage all proteome scientists who report on human cancer proteomics studies to adhere to the clinical proteomics reporting guidelines as formulated in 2008 by an expert team for the Molecular and Cellular Proteomics journal [ 24 ] and the HPP Guidelines v2.1 (hupo.org/hpp/guidelines). This guideline mandates a protein-level FDR < 1%, careful scrutiny of the spectra, use of thresholds of 9 amino acids in length and 2 uniquely mapping peptides for peptide-to-protein matches, along with careful consideration of alternative protein matches, especially to sequence variants or isobaric PTMs of abundant proteins [ 25 ]. Finally, to achieve Cancer-HPP aims, post-publication deposition of raw data of cancer proteomics data sets in the public domain is crucial to enable meta- and pan-cancer analyses.…”

Section: The Human Cancer Proteome Projectmentioning

confidence: 99%

The cancer proteomic landscape and the HUPO Cancer Proteome Project

et al. 2018

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The Human Cancer Proteome Project (Cancer-HPP) is an international initiative organized by HUPO whose key objective is to decipher the human cancer proteome through a coordinated effort by cancer proteome researchers around the world. The ultimate goal is to map the entire human cancer proteome to disclose tumor biology and drive improved diagnostics, treatment and management of cancer. Here we report the progress in the cancer proteomics field to date, and discuss future proteomic developments that will be needed to optimally delineate cancer phenotypes and advance the molecular characterization of this significant disease that is one of the leading causes of death worldwide.Electronic supplementary materialThe online version of this article (10.1186/s12014-018-9180-6) contains supplementary material, which is available to authorized users.

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Section: The Human Cancer Proteome Projectmentioning

confidence: 99%

The cancer proteomic landscape and the HUPO Cancer Proteome Project

et al. 2018

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“…These developments have resulted in proteomics playing a role in advancing our understanding of disease biology and opened new avenues such as biomarker development, augmentation of therapeutic modalities and drug discovery. Global consortia like CPTAC (Clinical Proteomics Tumor Analysis Consortium), TCGA (The Cancer Genome Atlas) and HUPO (Human Proteome Organization) have played a major role in utilising the power of omics technologies towards understanding the underlying mechanisms of various cancers (1)(2)(3). The development of new softwares, global repositories and reproducible workflows has also played a key role in increasing the utility of proteomics methodologies for research in the last decade.…”

Section: Introductionmentioning

confidence: 99%

Multiple Reaction Monitoring-Based Targeted Assays for the Validation of Protein Biomarkers in Brain Tumors

et al. 2021

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The emergence of omics technologies over the last decade has helped in advancement of research and our understanding of complex diseases like brain cancers. However, barring genomics, no other omics technology has been able to find utility in clinical settings. The recent advancements in mass spectrometry instrumentation have resulted in proteomics technologies becoming more sensitive and reliable. Targeted proteomics, a relatively new branch of mass spectrometry-based proteomics has shown immense potential in addressing the shortcomings of the standard molecular biology-based techniques like Western blotting and Immunohistochemistry. In this study we demonstrate the utility of Multiple reaction monitoring (MRM), a targeted proteomics approach, in quantifying peptides from proteins like Apolipoprotein A1 (APOA1), Apolipoprotein E (APOE), Prostaglandin H2 D-Isomerase (PTGDS), Vitronectin (VTN) and Complement C3 (C3) in cerebrospinal fluid (CSF) collected from Glioma and Meningioma patients. Additionally, we also report transitions for peptides from proteins – Vimentin (VIM), Cystatin-C (CST3) and Clusterin (CLU) in surgically resected Meningioma tissues; Annexin A1 (ANXA1), Superoxide dismutase (SOD2) and VIM in surgically resected Glioma tissues; and Microtubule associated protein-2 (MAP-2), Splicing factor 3B subunit 2 (SF3B2) and VIM in surgically resected Medulloblastoma tissues. To our knowledge, this is the first study reporting the use of MRM to validate proteins from three types of brain malignancies and two different bio-specimens. Future studies involving a large cohort of samples aimed at accurately detecting and quantifying peptides of proteins with roles in brain malignancies could potentially result in a panel of proteins showing ability to classify and grade tumors. Successful application of these techniques could ultimately offer alternative strategies with increased accuracy, sensitivity and lower turnaround time making them translatable to the clinics.

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“…One of the immediate scientific goals of this initiative, under the frame of the biology and disease-centric strategy of the HPP (B/D-HPP) 4,5 , is to assemble prioritized lists of proteins clinically relevant in RAD using the so-called 'popular proteins' strategy and text mining software 6,7 . Remarkably, none of the tissues most affected in arthritis, such as articular cartilage, synovial tissue, or bone, are currently included in the Human Protein Atlas, even though such efforts have been initiated 8 .…”

Section: Introductionmentioning

confidence: 99%

“…The aim of the initiative is to tackle the unmet clinical needs in RADs, such as the development of improved diagnostics, the identification of novel drug targets, the establishment of targeted interventions, and improvement in clinical management using proteomics and its allied OMICs approaches. One of the immediate scientific goals of this initiative, under the frame of the biology-and-disease-centric strategy of the HPP (B/D-HPP), , is to assemble prioritized lists of proteins clinically relevant in RADs using the so-called “popular proteins” strategy and text mining software. , Remarkably, none of the tissues most affected in arthritis, such as articular cartilage, synovial tissue, or bone, are currently included in the Human Protein Atlas, even though such efforts have been initiated . Furthermore, available proteomic data are limited to the human bone and pig/horse synovial fluid from the PeptideAtlas repository .…”

Section: Introductionmentioning

confidence: 99%

Mining the Proteome Associated with Rheumatic and Autoimmune Diseases

et al. 2019

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A steady increase in the incidence of osteoarthritis and other rheumatic diseases has been observed in recent decades, including autoimmune conditions such as rheumatoid arthritis, spondyloarthropathies, systemic lupus erythematosus, systemic sclerosis and Sjögren's syndrome. Rheumatic and autoimmune diseases (RADs) are characterised by inflammation of joints, muscles, or other connective tissues. In addition to often experiencing debilitating mobility and pain, RAD patients are also at higher risk of suffering comorbidities such as cardiovascular or infectious events. Given the socioeconomic impact of RAD, broad research efforts have been dedicated to these diseases worldwide.In the present work, we applied literature mining platforms to identify 'popular' proteins closely related to RAD. The platform is based on publicly available literature. The results will not only enable the systematic prioritization of candidates to perform targeted proteomics studies, but also may lead to a greater insight into the key pathogenic processes of these disorders.

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Advances of the HUPO Human Proteome Project with broad applications for life sciences research

Cited by 8 publications

References 12 publications

The cancer proteomic landscape and the HUPO Cancer Proteome Project

The cancer proteomic landscape and the HUPO Cancer Proteome Project

Multiple Reaction Monitoring-Based Targeted Assays for the Validation of Protein Biomarkers in Brain Tumors

Mining the Proteome Associated with Rheumatic and Autoimmune Diseases

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