PepNovo is a high throughput de novo peptide sequencing tool for tandem mass spectrometry data. PepNovo typically runs in less than 0.2 seconds per spectrum. PepNovo uses a probabilistic network to model the peptide fragmentation events in a mass spectrometer.
Lutefisk takes MS/MS spectra files and does de novo sequencing to directly figure out what the amino acid sequence of the peptide is. Lutefisk is well regarded de novo sequencing programs that is available for free.
DanteR is an entirely R-based program that provides a graphical front-end for common data analysis tasks in "omics", with an emphasis on proteomics. It is the successor to DAnTE, providing all of the previous features plus new functionality.
Census is a quantitative analysis software tool for mass spectrometry based proteomics. Census facilitates automated quantitative analysis using either stable isotope labeling or an isotope free strategy.
Using a web portal, ProSight PTM allows identification and characterization of intact proteins (and their post- translational modifications, PTMs) using the Top-Down Approach. This site has many tools and graphical features to facilitate analysis of single (recombinant) proteins, proteins in mixtures, and proteins fragmented in parallel. Our ProSight Warehouses are annotated with all known post-translational modifications (PTMs), alternative splicing events and single nucleotide polymorphisms (S
GutenTag is a hybrid software that combines in a single program the capability of de novo tag sequences and search databases to identify peptides. The GutenTag analysis starts with the inference of short sequence tags derived directly from tandem mass spectra and continues by launching an error-tolerant database search.
msInspect is an open source application written in Java that allows you to process and view mass spectrometry (MS1) data in an mzXML file. You can inspect data, identify peptide features, generate peptide arrays using data from multiple runs, and export data to external applications for further analysis and collaboration.
GenePattern is a powerful genomic analysis platform that provides access to more than 150 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
MZmine 2 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data and with the main goal to provide a user-friendly, flexible and easily extendable framework with a complete set of modules covering the entire LC-MS data analysis workflow.
The ProMAT (Protein Microarray Analysis Tool) is a data analysis application for protein microarray data. The software was developed for use with ELISA microarray experimental data by the Statistics Group and the Cell Biology and Biochemistry Group at Pacific Northwest National Laboratory.
OpenMS is an open-source software C++ library for LC/MS data management and analyses, developed by researchers at three German Universities in Tübingen, Berlin and Saarbrücken. It offers an infrastructure for the development of mass spectrometry related software. OpenMS is free software available under the LGPL.
The APEX Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data (Lu et al., Nature Biotech., 25(1):117-124, 2007). The underlying technique improves upon label free quantitation techniques such as MS/MS spectral counting. This technique uses machine learning algorithms to help correct for variable peptide detection related to certain peptide physicochemical properties which fav
MSight, created by the Proteome Informatics Group, was specifically developed for the 2-D representation of mass spectra along with data from the separation step. The software allows graphical exploration inside huge dataset and gives the scientist access to information that previously was hidden.