Finds all the spectra that correspond to a specific compound across different databases. SPLASH is a database-independent spectrum identifier that contains separate blocks for defining different layers of information, separated by dashes. The software was developed and refined on a dataset of more than 563000 mass spectra from MassBank, GNPS, HMDB, ReSpect, FiehnLib and NIST. It can be used for cross-reference identification and also allows for coarse similarity comparisons.
Allows automated peptide and protein identification via tandem mass spectrometry (MS/MS). pFind is a search engine that includes several modules, workflows and algorithms, such as Open-pFind. An automatic estimation of false positive rate (FPR) is provided, based on the target-decoy database search strategy. A toolbox is incorporated to index protein databases for high-throughput application. Third parties can develop their own algorithms modules.
A software tool for identification and characterization of proteoforms at the whole proteome level by top-down tandem mass spectra using database search. TopPIC efficiently identifies proteoforms with unexpected mutations and post-translational modifications and accurately estimates statistical significance of identifications. It uses several techniques, such indexes, spectral alignment, and a generation function method, to increase its speed, sensitivity, and accuracy.
An open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. DIA-Umpire enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation.
Permits untargeted and sensitive peptide identification in data-independent acquisition (DIA) data. MSPLIT-DIA is a spectral matching tool that uses spectrum projections to match library spectra to each DIA spectrum. This method also evaluates the similarity of the matched peaks between library spectra and multiplexed spectra across multiple consecutive DIA spectra. Assay libraries for targeted extraction tools are automatically generated by MSPLIT-DIA to facilitate coupling of sensitive identification with accurate quantification from DIA data.
Allows top-down data analysis. Informed-Proteomics is composed of a liquid chromatography mass spectrometry (LC-MS) feature-finding algorithm, a database-search algorithm, and an interactive results viewer. It is used to proceed sensitive and comprehensive high-throughput analysis of complex mixtures of intact proteins. This tool is able to identify differently expressed LC-MS features and proteoforms from breast cancer samples.
Detects peptides by searching MS/MS spectra against sequences present in protein sequence databases. Comet is a tandem mass spectrometry (MS/MS) sequence database search engine that existed as the University of Washington's academic version of the SEQUEST database search tool. The software implements a cross-correlation algorithm to score peptide sequences against experimental tandem mass spectra.
A database-searching algorithm for peptide and protein identification in shotgun proteomics. Hybrid Message Passing Interface/OpenMP parallelism of the new Sipros architecture allowed its computation to be scalable from desktops to supercomputers.
Permits users to analyze a variety of types of shotgun proteomics data. Crux is a toolkit that offers extensive confidence estimates, including false discovery rate and posterior error probability estimates at the spectrum, peptide, and protein levels with additional functionalities. It supports a variety of workflows, providing users with flexibility to tailor their analysis to their experimental goals.
An MS2 peak intensity prediction server that computes MS2 charge 2+ and 3+ spectra from peptide sequences for the most common fragment ions. The server integrates the Unimod public domain post-translational modification database for modified peptides. The prediction model is an improvement of the previously published MS2PIP model for Orbitrap-LTQ CID spectra. Predicted MS2 spectra can be downloaded as a spectrum file and can be visualized in the browser for comparisons with observations.
Serves for site localization analysis of phosphorylation events using tandem mass spectrometry (MS/MS) data. LuciPHOr consists of a target-decoy framework specifically designed for phospho-site localization. It can be used for estimating false localization rate (FLR) for any PTMs of a fixed mass. Moreover, this program constructs a probability model of peak intensity and mass accuracy across all spectra for correct and incorrect localizations respectively. It also computes the likelihood ratio as the localization score for each candidate site.
Allows users to perform false rate discovery (FDR) assessment. Passatutto intends to help in determining fitted scoring parameters for large scale tandem mass spectrometry (MS/MS) projects. It contains features to (i) create and browse decoy databases; (ii) estimate q-values by using means of the target-decoy approach or by empirical Bayes estimation or (iii) to use fragmentation trees to perform noise-filtering reference spectra.
Permits to create and search spectrum libraries. BiblioSpec is a flexible spectrum comparison program that could be used in other applications such as for rapid detection of specific peptides of interest, for finding spectra in common between two experiments. It consists of several independent programs. The three mains are (i) BlibBuild, which creates a spectral library of mass spectra, (ii) BlibFilter, which modifies an existing spectrum library to contain only one spectrum per peptide, and (iii) BlibSearch, which matches query spectra to library spectra.
Provides a unified interface for resources dealing with proteomics. SearchGUI is an open source software which provides a mean to query: (i) a tool for file conversion; (ii) eight search engines including MS-GF+, Comet or Andromeda (iii) two de novo engines such as Novo and (iv) an application for post processing. It aims to simplify the detection of proteins and peptides by performing multiple simultaneous researches.
Assigns accurate spectrum-specific statistical significance to peptide hits. RAId_DbS is a peptide identification software that takes into account the integrated information of annotated single amino acid polymorphisms (SAPs) and/or post-translational modifications (PTMs) and diseases while performing peptide searches. It offers flexibility for users to add SAPs/PTMs information to various proteins.
Investigates and compares the results of several experiments on known proteins. MassSorter increases the number of reasonable matches between experimental and theoretical m/z values. It can consider several types of modifications, missed cleavages, and potentially unexpected cleavages. This tool can cleave only at the theoretically correct sites of the enzyme selected during the digestion of an amino acid sequence.
An R package providing a complete and modular analysis pipeline for quantitative analysis of mass spectrometry data. MALDIquant is specifically designed with application in clinical diagnostics in mind and implements sophisticated routines for importing raw data, preprocessing, non-linear peak alignment and calibration. It also handles technical replicates as well as spectra with unequal resolution.