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Tools for Proteomics Investigation
Cardiac Organellar Protein Atlas Knowledgebase (COPaKB) serves as an essential tool box to support the translation of proteomics data into the advancement of cardiovascular biology and medicine. It bridges the gap between traditional data-driven proteomics studies and hypothesis-driven investigations widely employed by the cardiovascular community, propelling innovation and new discoveries. iCOPa V1.1 is now available at Apple App store. It delivers global access to the COPaKB knowledgebase to your fingertips. Enjoy cardiovascular proteomics, intuitively! https://itunes.apple.com/us/app/icopa/id568723410?mt=8
High-throughput mass spectrometry data from shotgun proteomics experiments necessitate an efficient and automated way to analyze large amounts of quantitative data. We introduce a software tool called Census that facilitates automated quantitative analysis using either stable isotope labeling or an isotope free strategy. Using high-resolution and high mass accuracy data from an LTQ-Orbitrap hybrid mass spectrometer as input for Census, we were able to quantify roughly three times as many peptides as our previous software (i.e., RelEx). While some of the increase can be attributed to the benefits inherent to the instrumentation, improvements in Census are also responsible. One of the reasons for the increase in accurately quantified peptides is that Census minimizes the contributions of interfering peaks and chemical noise by taking advantage of the high mass accuracy of the Orbitrap using a small mass accuracy tolerance for each isotopic peak. In addition, a dynamic peak finding algorithm is employed that makes use of database search results for improved accuracy and quantification efficiency. Finally, a weighted means of the peptides are calculated to determine the protein ratios.
The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data. It has been developed to provide the proteomics community with a public repository for protein and peptide identifications together with the evidence supporting these identifications. PRIDE is also able to capture details of post-translational modifications coordinated relative to the peptides in which they have been found.
The Human Protein Atlas portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in 46 different normal human tissues and 20 different cancer types, as well as 47 different human cell lines. The data is released together with application-specific validation performed for each antibody, including immunohistochemisty, Western blot analysis and, for a large fraction, a protein array assay and immunofluorescent based confocal microscopy. The database has been developed in a gene-centric manner with the inclusion of all human genes predicted from genome efforts. Search functionalities allow for complex queries regarding protein expression profiles, protein classes and chromosome location.
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