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Downloads and Upgrades: Skyline Software; Genedata Expressionist MSX; Proteome Discoverer 2.0; and more


Researchers at the University of Washington, Seattle, have released a new version of the Skyline proteomics software that supports Bruker’s maXis series ultra-high resolution ESI-Qq-TOF mass spectrometers.

Genedata has released Genedata Expressionist MSX software for use in academic proteomics and metabolomics research.

According to the company, the software offers the same algorithms and data visualization capabilities that are included in the enterprise version of Genedata Expressionist for Mass Spectrometry.

It provides support for a variety of proteomic and metabolomic MS setups, including gas chromatography mass spectrometry and stable isotope labeling with amino acids in cell culture. The software can be used in biomarker discovery and validation; protein profiling; peptide identification and quantification; protein-protein interaction studies; metabolic profiling within drug development; and plant breeding studies.

Thermo Fisher Scientific has released version 2.0 of its Proteome Discoverer software, which is used for analyzing qualitative and quantitative proteomics data.

The release combines spectral library searching with classical database searching to help researchers identify true positive peptide spectrum matches. It also includes a multi-threaded Sequest search engine that speeds up database searches; a peptide and protein false discovery rate and probability feature, which provides high-confidence identification of proteins and peptides; and it generates reports automatically, which is especially useful for large studies where hundreds of files are interpreted.

Thermo Fisher has also signed a non-exclusive agreement with Protein Metrics allowing it to license the company’s Byonic database search software, adding the capability to streamline analysis of glycopeptides and other post-translational modification data.

The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium has launched a data portal to host all the data that is currently being produced by the consortium and from a previous program.

The total amount of hosted data exceeds over 500 gigabytes of raw data in over 800 files. These data include characterization of the proteome and phosphoproteome in experiments that demonstrate the capabilities of each of the mass spectrometry platforms that will be used to analyze genomically characterized biospecimens from sources including the Cancer Genome Atlas Project. Furthermore, model systems were used to address questions about protein stability in excised tissues, preservation of material before mass spectrometry analyses, and detection of proteomic signatures from tumors.

The Scan

Support for Moderna Booster

An FDA advisory committee supports authorizing a booster for Moderna's SARS-CoV-2 vaccine, CNN reports.

Testing at UK Lab Suspended

SARS-CoV-2 testing at a UK lab has been suspended following a number of false negative results.

J&J CSO to Step Down

The Wall Street Journal reports that Paul Stoffels will be stepping down as chief scientific officer at Johnson & Johnson by the end of the year.

Science Papers Present Proteo-Genomic Map of Human Health, Brain Tumor Target, Tool to Infer CNVs

In Science this week: gene-protein-disease map, epigenomic and transcriptomic approach highlights potential therapeutic target for gliomas, and more