Advances and utility of the human plasma proteome

EW Deutsch, GS Omenn, Z Sun, M Maes… - Journal of proteome …, 2021 - ACS Publications
The study of proteins circulating in blood offers tremendous opportunities to diagnose,
stratify, or possibly prevent diseases. With recent technological advances and the urgent …

A high-stringency blueprint of the human proteome

S Adhikari, EC Nice, EW Deutsch, L Lane… - Nature …, 2020 - nature.com
Abstract The Human Proteome Organization (HUPO) launched the Human Proteome Project
(HPP) in 2010, creating an international framework for global collaboration, data sharing …

The ProteomeXchange consortium in 2020: enabling 'big data'approaches in proteomics

EW Deutsch, N Bandeira, V Sharma… - Nucleic acids …, 2020 - academic.oup.com
The ProteomeXchange (PX) consortium of proteomics resources (http://www.
proteomexchange. org) has standardized data submission and dissemination of mass …

The PRIDE database and related tools and resources in 2019: improving support for quantification data

Y Perez-Riverol, A Csordas, J Bai… - Nucleic acids …, 2019 - academic.oup.com
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 …

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

D Wang, B Eraslan, T Wieland, B Hallström… - Molecular systems …, 2019 - embopress.org
Abstract Genome‐, transcriptome‐and proteome‐wide measurements provide insights into
how biological systems are regulated. However, fundamental aspects relating to which …

What can Ribo-Seq, immunopeptidomics, and proteomics tell us about the noncanonical proteome?

JR Prensner, JG Abelin, LW Kok, KR Clauser… - Molecular & Cellular …, 2023 - Elsevier
Abstract Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of
the human genome and proteome by illuminating thousands of noncanonical sites of …

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

EW Deutsch, A Csordas, Z Sun… - Nucleic acids …, 2016 - academic.oup.com
Abstract The ProteomeXchange (PX) Consortium of proteomics resources (http://www.
proteomexchange. org) was formally started in 2011 to standardize data submission and …

The neXtProt knowledgebase in 2020: data, tools and usability improvements

M Zahn-Zabal, PA Michel, A Gateau… - Nucleic Acids …, 2020 - academic.oup.com
Abstract The neXtProt knowledgebase (https://www. nextprot. org) is an integrative resource
providing both data on human protein and the tools to explore these. In order to provide …

The 2022 report on the human proteome from the HUPO human proteome project

GS Omenn, L Lane, CM Overall, C Pineau… - Journal of proteome …, 2022 - ACS Publications
The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP)
show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 …

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

M Tardaguila, L De La Fuente, C Marti… - Genome …, 2018 - genome.cshlp.org
High-throughput sequencing of full-length transcripts using long reads has paved the way
for the discovery of thousands of novel transcripts, even in well-annotated mammalian …