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

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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

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.