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Human Protein Atlas (HPA [10]): a public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues, cells, subcellular compartments, and cancer tumors. Legume Information System (LIS): genomic database for the legume family [11]
The earliest conception of ProteomeXchange stems from a meeting at the HUPO 2005 conference in Munich, [18] where the main proteomics data repositories at the time agreed in principle to exchange their data, and thus provide a means for the user to find public proteomics data at any of the participating databases. Due to the rapid development ...
The Human Protein Atlas (HPA) is a Swedish-based program started in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology.
2011 Integromics launches OmicsHub Proteomics 2.0, a data management and analysis tool for mass spectrometry laboratories and core facilities 2011 Integromics publication in Mol Cell Proteomics describes Multiplexed homogeneous proximity ligation assays for high-throughput protein biomarker research in serological material.
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.
Cellosaurus is an online knowledge base on cell lines, which attempts to document all cell lines used in biomedical research. [1] It is provided by the Swiss Institute of Bioinformatics (SIB). It is an ELIXIR Core Data Resource [ 2 ] [ 3 ] as well as an IRDiRC's Recognized Resource. [ 4 ]
The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet, [2] ProteinProphet, [3] ASAPRatio, XPRESS and Libra.
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.