|COPaKB Related Tools
- COPaKB Client -
batch of raw proteomic datasets can be processed with COPaKB Client. Its latest
release (2.0) is built with Java, therefore, it functions in Windows, OS X (Mac)
or Linux with Java 6 or 7 environment. COPaKB Client prvoides an integrated hub for task management, file management,
data transfer and result presentation. Via robust web services, it
caters reliable access to COPa Knowledgebase.
- iCOPa -
the very first mobile App for proteomic analyses. The latest built (V2.0) is
available to download at Apple's APP store and it functions on iPad devices with
iOS 5 or 6 operating system. Via iCOPa, the resources at COPaKB are accessible wherever network reaches.
This is an open source application developed by the ProteoWizard Software Foundation.
This application converts
raw spectral files into mzML format, the standard XML format established by PSI.
In COPaKB Client, a slot has been pre-implemented where ProteoWizard Converter can
plug in to streamline the processes of file conversion and
Resources from EBI
- ProteomeXchange -
ProteomeXchange consortium has been set up to provide a single point of
submission of MS proteomics data to the main existing proteomics repositories,
and to encourage the data exchange between them for optimal data dissemination.
- PRIDE -
PRIDE (PRoteomics IDEntifications) database is a centralized, standards
compliant, public data repository for proteomics data, including protein and
peptide identifications, post-translational modifications and supporting
IntAct - IntAct 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 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) 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 are saved in ms1, ms2 or mzXML formats.
- SEQUEST -
SEQUEST deduces protein identities from mass spectral datasets using theoratical
spectra dervied from protein or nucleotide databases as reference.
- ProLuCID -
ProLuCID 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
will meet a preset threshold of false discovery rate.
- Census -
Census supports quantitative analysis of individual proteins in mass
spectrometry-based proteomic datasets. It supports both stable isotope
labeling or label-free studies.