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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 Cross-platform Toolkit for Mass Spectrometry and Proteomics
TLDR
The ProteoWizard Toolkit is developed, a robust set of open-source, software libraries and applications designed to facilitate proteomics research that implements the first-ever, non-commercial, unified data access interface for proteomics, bridging field-standard open formats and all common vendor formats.
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
TLDR
The PeptideAtlas Project is described, its contents and components are described, and it is shown how together they provide a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics.
A guided tour of the Trans‐Proteomic Pipeline
TLDR
The full workflow of the TPP is described, along with an example on a sample data set, demonstrating that the setup and use of the tools are straightforward and well supported and do not require specialized informatic resources or knowledge.
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
TLDR
The ProteomeXchange Consortium of proteomics resources was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics data worldwide and is supporting a change in culture of the proteomics field.
The PeptideAtlas project
TLDR
A summary of the process and details about the Human, Drosophila and Yeast PeptideAtlas builds are presented and a uniform statistical validation ensures a consistent and high-quality set of peptide and protein identifications.
Design and implementation of microarray gene expression markup language (MAGE-ML)
TLDR
MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier.
Development and validation of a spectral library searching method for peptide identification from MS/MS
TLDR
An open‐source, functionally complete, high‐throughput and readily extensible MS/MS spectral searching tool, SpectraST, developed, which vastly outperforms the sequence search engine SEQUEST in terms of speed and the ability to discriminate good and bad hits.
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.
TLDR
In comparing the physiologies of the two halophilic archaea, in addition to the expected extensive similarity, it is discovered several differences in their metabolic strategies and physiological responses such as distinct pathways for arginine breakdown in each halophile.
The minimum information about a proteomics experiment (MIAPE)
TLDR
The processes and principles underpinning the development of guidance modules for reporting the use of techniques such as gel electrophoresis and mass spectrometry are described and the ramifications for various interest groups such as experimentalists, funders, publishers and the private sector are discussed.
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