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MetaMorpheus is a proteomics search software developed at the University of Wisconsin-Madison with integrated calibration, post-translational modification discovery, bottom-up and top-down proteomics search, cross-linking mass spectrometry (XL-MS) search, proteogenomic search, and label-free quantification (LFQ) capabilities. [7] MSFragger Freeware
Top-down vs bottom-up proteomics. Top-down proteomics is a method of protein identification that either uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry (MS/MS) analysis [1] [2] or other protein purification methods such as two-dimensional gel electrophoresis in conjunction with MS/MS. [3] Top-down proteomics is capable ...
Genedata is a bioinformatics company that develops enterprise software solutions to accelerate biopharmaceutical research and development. Founded in 1997 by Othmar Pfannes, Genedata has since grown to approximately 400 employees.
In addition, BIOBASE has developed the ExPlain system for the biological interpretation of gene expression and proteomics data by integrated functional, promoter and pathway analysis. The "Gene Regulation Portal" offers a number of earlier revisions of company products free of charge to users from non-profit organizations.
Skyline is an open source software for targeted proteomics [1] [2] and metabolomics [3] data analysis. It runs on Microsoft Windows and supports the raw data formats from multiple mass spectrometric vendors. It contains a graphical user interface to display chromatographic data for individual peptide or small molecule analytes.
PEAKS is commonly used for peptide identification (Protein ID) through de novo peptide sequencing assisted search engine database searching. [1] PEAKS has also integrated PTM and mutation characterization through automatic peptide sequence tag based searching (SPIDER) [2] and PTM Identification.
NanoString's research tools are based on the nCounter Analysis System, which is a modification of the DNA microarray technology. [11] The nCounter system allows for the simultaneous profiling of hundreds of genes, proteins, miRNAs, or copy number variations with high sensitivity and precision, using molecular barcodes and microscopic imaging in a hybridization reaction.
Integromics was founded in 2002 as a spin-off of the National Center for Biotechnology (CNB / CSIC) in Spain and the University of Malaga.Principal founder Dr. Jose Maria Carazo was motivated by a market need to develop new computational methods for analyzing data, with the company's first product addressing the needs of the microarray data analysis market.