Mass spectrometry-based plasma proteomics: considerations from sample collection to achieving translational data

V Ignjatovic, PE Geyer, KK Palaniappan… - Journal of proteome …, 2019 - ACS Publications
The proteomic analysis of human blood and blood-derived products (eg, plasma) offers an
attractive avenue to translate research progress from the laboratory into the clinic. However …

[HTML][HTML] Cellular interactions in the tumor microenvironment: the role of secretome

BR da Cunha, C Domingos, ACB Stefanini… - Journal of …, 2019 - ncbi.nlm.nih.gov
Over the past years, it has become evident that cancer initiation and progression depends
on several components of the tumor microenvironment, including inflammatory and immune …

A genome-wide transcriptomic analysis of protein-coding genes in human blood cells

M Uhlen, MJ Karlsson, W Zhong, A Tebani, C Pou… - Science, 2019 - science.org
INTRODUCTION Blood is the predominant source for molecular analyses in humans, both in
clinical and research settings, and is the target for many therapeutic strategies, emphasizing …

[HTML][HTML] Integrated omics: tools, advances and future approaches

BB Misra, C Langefeld, M Olivier… - Journal of molecular …, 2019 - jme.bioscientifica.com
With the rapid adoption of high-throughput omic approaches to analyze biological samples
such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can …

[HTML][HTML] Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses

T Wu, J Guan, A Handel, DC Tscharke, J Sidney… - Nature …, 2019 - nature.com
The magnitude of T cell responses to infection is a function of the naïve T cell repertoire
combined with the context and duration of antigen presentation. Using mass spectrometry …

[HTML][HTML] Quantifying the impact of public omics data

Y Perez-Riverol, A Zorin, G Dass, MT Vu, P Xu… - Nature …, 2019 - nature.com
The amount of omics data in the public domain is increasing every year. Modern science
has become a data-intensive discipline. Innovative solutions for data management, data …

[HTML][HTML] N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping

S Sun, Y Hu, M Ao, P Shah, J Chen, W Yang, X Jia… - Clinical proteomics, 2019 - Springer
Background N-linked glycoprotein is a highly interesting class of proteins for clinical and
biological research. The large-scale characterization of N-linked glycoproteins …

PDV: an integrative proteomics data viewer

K Li, M Vaudel, B Zhang, Y Ren, B Wen - Bioinformatics, 2019 - academic.oup.com
Data visualization plays critical roles in proteomics studies, ranging from quality control of
MS/MS data to validation of peptide identification results. Herein, we present PDV, an …

Human proteome project mass spectrometry data interpretation guidelines 3.0

EW Deutsch, L Lane, CM Overall… - Journal of proteome …, 2019 - ACS Publications
The Human Proteome Organization's (HUPO) Human Proteome Project (HPP) developed
Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016 …

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

JM Mudge, I Jungreis, T Hunt, JM Gonzalez… - Genome …, 2019 - genome.cshlp.org
The most widely appreciated role of DNA is to encode protein, yet the exact portion of the
human genome that is translated remains to be ascertained. We previously developed …