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ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination
TLDR
The PX submission tool simplifies the process of submitting data to PRIDE by automating the very labor-intensive and therefore time-heavy and expensive process of manually downloading and editing files.
A quantitative assessment of plasma homocysteine as a risk factor for vascular disease. Probable benefits of increasing folic acid intakes.
TLDR
Higher folic acid intake by reducing tHcy levels promises to prevent arteriosclerotic vascular disease and under different assumptions, 13,500 to 50,000 CAD deaths annually could be avoided.
Effects of a combination of beta carotene and vitamin A on lung cancer and cardiovascular disease.
TLDR
After an average of four years of supplementation, the combination of beta carotene and vitamin A had no benefit and may have had an adverse effect on the incidence of lung cancer and on the risk of death from lung cancer, cardiovascular disease, and any cause in smokers and workers exposed to asbestos.
Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression
Multiple, complex molecular events characterize cancer development and progression. Deciphering the molecular networks that distinguish organ-confined disease from metastatic disease may lead to the
Risk factors for lung cancer and for intervention effects in CARET, the Beta-Carotene and Retinol Efficacy Trial.
TLDR
Results based on the pre-specified analytic method are presented, details about risk factors for lung cancer, and analyses of subgroups and of factors that possibly influence response to the intervention are presented.
Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a
TLDR
Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs in the PPP database, and the database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides.
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data
TLDR
A new, substantially redesigned version of the tool Metscape is described that allows users to enter experimental data for metabolites, genes and pathways and display them in the context of relevant metabolic networks and visualize changes in the gene/metabolite data.
A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas*
TLDR
This work has identified 20,433 distinct peptides, from which it inferred a highly nonredundant set of 1929 protein sequences at a false discovery rate of 1%, and compiled a high-confidence human plasma proteome reference set with well over twice the identified proteins of previous high- confidence sets.
A common open representation of mass spectrometry data and its application to proteomics research
TLDR
The 'mzXML' format is introduced, an open, generic XML (extensible markup language) representation of MS data that will facilitate data management, interpretation and dissemination in proteomics research.
An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis
TLDR
Overall, MASCOT, a probabilistic search algorithm, correctly identified most peptides based on a specified FP rate, and the rescoring algorithm, PeptideProphet, enhanced the overall performance of the SEQUEST algorithm, as well as provided predictable FP error rates.
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