Protein inference software tools | Mass spectrometry-based untargeted proteomics
Assembling peptides identified from tandem mass spectra into a list of proteins, referred to as protein inference, is a critical step in proteomics research. Due to the existence of degenerate peptides and 'one-hit wonders', it is very difficult to determine which proteins are present in the sample.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
An algorithm for peptide identification using tandem mass spectrometry and protein sequence databases. ProLuCID uses a three tier scoring scheme. First, a binomial probability is used as a preliminary scoring scheme to select candidate peptides. The binomial probability scores generated by ProLuCID minimize molecular weight bias and are independent of database size. A modified cross-correlation score is calculated for each candidate peptide identified by the binomial probability. This cross-correlation scoring function models the isotopic distributions of fragment ions of candidate peptides which ultimately results in higher sensitivity and specificity than that obtained with the SEQUEST XCorr. Finally, ProLuCID uses the distribution of XCorr values for all of the selected candidate peptides to compute a Z score for the peptide hit with the highest XCorr.
Assembles SEQUEST identifications and highlights the most significant matches. The accompanying Contrast tool compares DTASelect results from multiple experiments. The two programs improve the speed and precision of proteomic data analysis.
Recognizes and quantifies protein in biologic complex samples. Proteome Discoverer covers a wide range of possible proteomic investigations from proteins and peptides identification to post-translational modification. It searches in many databases and several dissociation technics for performing complete studies. This tool automatizes data analyze and allows researchers to represent results thanks to modules like gene ontology (GO) enrichment.
An open-source protein assembly tool that derives a minimum protein list from peptide identifications filtered to a specified false discovery rate. By segregating peptide identifications for thresholding using both the precursor charge state and the number of tryptic termini, IDPicker retrieves more peptides for protein assembly. The new version is more robust against false positive proteins, especially in searches using multispecies databases, by requiring additional novel peptides in the parsimony process.