Proteomics

The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparision, exchange and verification.

A proteomics analyzation software capable of extracting information from the online universal protein resource database UniProt. ProteinID Finder imports your mass spectrometer analyzed protein lists (uniprot accession numbers) into experiments and organizes your proteomics experiments into...

EigenMS is a stand-alone (or Matlab) bottom-up proteomics data normalization algorithms. EigenMS utilized SVD to detect significant trends in the data and eliminates those attributable to bias. EigenMS eliminates effects from known and unknown factors.


Platforms: Windows, Mac, Linux

JBioFramework (JBF) is a set of simulations of three different chemical separations applications (ion exchange chromatography, 1D electrophoresis and 2D electrophoresis) that are frequently used in chemistry, biochemistry and proteomics research.


Platforms: Windows, Mac, Linux

Open2Dprot is an open-source proteomics project for the development of bioinformatic tools for n-dimensional protein expression data analysis of quantified protein expression across multiple samples from research experiments.


Platforms: Windows, Mac, Linux

An open source framework for LC-MS based proteomics. OpenMS offers datastructures and algorithms for the processing of mass spectrometry data. The library is written in C++.


Platforms: Windows, Mac, BSD, Linux

A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.)


Platforms: Windows, Mac, Linux

The goal of Picklist Editor is to display and modify pick lists before spot picking (in proteomics).


Platforms: Windows, Mac, Linux

A Java-based tool to visualize, integrate and analyze LC-MS/MS proteomics data.


Platforms: Windows, Mac, Linux

Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files


Platforms: Windows, Mac, Linux

Software for storing and distributing proteomics data


Platforms: Windows, Mac, Linux

This tool enhances signal detection for broad-mass TOF spectra by accounting for changing peak width and providing peak-shape-dependent filtering capabilities. A set of input TOF spectra is processed to produce aligned peak list and array of corresponding signal intensities. Signal processing...


Platforms: Matlab

pIcarver is a tool to visualize theoretical distributions of peptide pI on a given pH range, and proposes a fractionation scheme that generates fractions with similar peptide frequencies. This tool has been developed as a service of the Bioinformatics Core Facility for Proteomics, within a...


Platforms: Mac

Abacus is a tool for extracting adjusted spectral counts from the result XML files generated by the Trans-Proteomic Pipeline (TPP). Abacus outputs a tab-delimited file that can be used for label-free quantification or simply viewing proteomics results across multiple experimental runs. A...


Platforms: Mac

Open2Dprot is an open-source proteomics project for the development of bioinformatic tools for n-dimensional protein expression data analysis of quantified protein expression across multiple samples from research experiments.


Platforms: *nix

msInspect allows you to process and view mass spectrometry (MS1) data in an mzXML file. You can use msInspect's built-in tools to inspect data, identify peptide features, generate peptide arrays using data from multiple runs, and export data to external applications for further analysis and...


Platforms: Windows

A powerful and user-friendly graphical software designed to conduct large scale exploration of biological sequence databanks and related information (functional, taxonomy, pathways, mutations, etc). KoriBlast can be used for a wide range of applications in genomics and proteomics, such as: full...


Platforms: Mac

Annotated Gel Markup Language is a simple markup language that is being proposed to markup data obtained by 2D gel electrophorosis.The goal of AGML is to enable proteomics research move into the browsing mode of searching through existing databases.


Platforms: Windows, Mac, Linux

Maltcms is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research. * Changed build system to Maven 2. Access to maven repository can be requested by contacting the project owner. * Fixed a bug in the...


Platforms: Mac

BlastViewer provides an interactive graphical user interface for the analysis of the reports produced by the BLAST sequence database search system. BlastViewer is an easy to use software designed for everyday biological sequence analysis relying on BLAST. It allows an easy visualisation and...


Platforms: Mac, Java 1.5 or later