Bioinformatics Tools for Cardiac Proteome Biology

COPaKB Related Tools

  • COPaKB Client is a versatile tool that allows you to process and analyze a large batch of raw proteomic datasets. Its latest version (V2.0) was built in Java; therefore, it functions in Windows, OS X (Mac) or Linux with Java 7 environment. COPaKB Client provides an integrated hub for task management, file management, data transfer and result display. The program thus provides a reliable access to COPaKB via robust web services.
  • iCOPa is the very first mobile App created for proteomic analyses. The latest version (V2.1) is available for download from the Apple's App store, and it functions on iPad devices with iOS 5 or 6 operating system. You can access COPaKB via iCOPa if there is available network connection.
  • ProteoWizard Converter is an open source application developed by the ProteoWizard Software Foundation. This application converts raw mass spectral files into mzML format, the standard XML format established by PSI. COPaKB Client has an option to streamline the processes of file converstion and analysis by utilzing ProteoWizard Converter.

Resources from EBI

  • ProteomeXchange - The mission of the ProteomeXchange consortium, as stated in its website, is to "provide a coordinated submission of MS/MS proteomics data to the main existing proteomics repositories, and to encourage optimal data dissemination."
  • PRIDE - The PRIDE (PRoteomics IDEntifications) database, according to its website, is "a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence."
  • IntAct - IntAct, according to its website, "provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available."
  • UniProt - The mission of UniProt, according to its website, is to "provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information."

Resources from KTH

  • HPA - The HPA (Human Protein Atlas), according to its website, 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."

Resources from TSRI

  • RawExtractor - RawExtractor is a program to extract MS and MS/MS spectra from RAW files generated by Thermo mass spectrometers, such as LCQ, LTQ and LTQ-Orbitrap. Extracted spectra data are saved in ms1, ms2 or mzXML formats.
  • SEQUEST - SEQUEST performs protein identification and peptide sequencing by comparing fragmentation patterns of mass spectral datasets with those of theoretical mass spectral datasets derived from protein or nucleotide databases.
  • ProLuCID - ProLuCID, according to TSRI website, is "a fast and sensitive tandem mass spectra-based protein identification algorithm."
  • DTASelect - DTASelect organizes and filters the results of SEQUEST/ProLuCID analyses. The output for the protein identification process will meet a pre-set threshold value for false discovery rate.
  • Census - Census supports quantitative analysis of individual proteins in mass spectrometry-based proteomic datasets. It can be used for both stable isotope labeling and label-free studies.