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Software that can analyze terminal and internal fragments in top-down mass spectrometry.

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Agilent ExDViewer software is a freeware tool for analyzing and visualizing peptide and protein fragmentation data. The software deconvolutes data from collision-induced dissociation (CID), electron capture dissociation (ECD), electron transfer dissociation (ETD), and other types of fragmentation to interpret complex, isotopically resolved spectra from top- and middle-down experiments.

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FLASHIda is an intelligent online data acquisition algorithm for top-down proteomics that ensures the real-time selection of high-quality precursors of diverse proteoforms. It ensures the real-time selection of high-quality precursors of diverse proteforms, using an instant m/z-intensity to mass-quality spectral transformation coupled with a machine learning-based quality assessment.

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The MASH software series is a freely available collection of data analysis tool for both native and denatured top-down proteomics.  MASH Explorer can process data from various vendors and incorporates multiple algorithms for deconvolution and database searching. MASH Native is an all-in-one software for native top-down proteomics, complex-down analysis, native intact MS, and denatured top-down.

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Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities

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MS-Align+ is a software tool for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications. MS-Align+ is fast in identifying unexpected post-translational modifications. In addition, MS-Align+ reports statistical significance of top-down protein identifications.

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MS-Deconv is a software tool for top down spectral deconvolution. MS-Deconv uses a combinatorial algorithm. The algorithm first generates a large set of candidate isotopomer envelopes for a spectrum, then represents the spectrum as a graph, and finally selects its highest scoring subset of envelopes as a heaviest path in the graph. In contrast with other approaches, the algorithm scores sets of envelopes rather than individual envelopes.

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MSPathFinder is a database search engine for top-down proteomics, part of the Informed Proteomics package.

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ProSight Lite is a free Windows application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations.

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ProSight PTM 2.0 allows identification and characterization of both intact proteins and peptides. ProSight Warehouses are annotated with all known post-translational modifications (PTMs), alternative splicing events and single nucleotide polymorphisms (SNPs) using Shotgun Annotation. ProSightPTM allows the user to search their tandem MS data against proteome warehouses containing the known biological complexity present in UniProt.

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This tool (beta) was developed for scoring proteoforms of multiply-modified proteins. The input is: (i) an intact mass, (ii) a fragment ion dataset, (iii) a protein sequence, and (iv) the specific kinds of PTMs to be considered. The output is given as a [Phrap] score, where the higher scores are better.

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Software for constructing, quantifying, and visualizing proteoform families.

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The ability to integrate and visualize experimental proteomic evidence in the context of rich protein feature annotations represents an unmet need of the proteomics community. Protter is a web-based tool that supports interactive protein data analysis and hypothesis generation by visualizing both annotated sequence features and experimental proteomic data in the context of protein topology. Protter supports numerous proteomic file formats and automatically integrates a variety of reference protein annotation sources, which can be readily extended via modular plug-ins.

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pTop is a software dedicated for the analysis of intact protein using mass spectrometry. It can support the complex data sets with ultra-modifications.

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Here we combine the CORUM and UniProt databases to create candidates for an error-tolerant search engine designed for hierarchical top-down analyses, identification, and scoring of multi-proteoform complexes by native mass spectrometry.

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SpectroGene is a tool for top-down protein identification using unannotated bacterial genome. SpectroGene could be used for disocvery of previously unannotated genes as well as correction of known genes coordinates (especially, Start codons). Almost all PrSMs which are found with a standard search with a known proteome could be also identified with SpectroGene without proteome reference.

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TopFIND is the Termini oriented protein Function Inferred Database (TopFIND), an integrated knowledge-base focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases.s.

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TopPIC Suite consists of five software tools for the analysis of top-down mass spectrometry data:

TopFD converts isotopic envelopes to monoisotopic neutral masses.
TopIndex generates index files for protein sequence databases.
TopPIC identifies and characterizes proteoforms by searching against a protein sequence database.
TopMG  is a tool for identifying highly modified proteoforms.
TopDiff  finds differentially expressed proteoforms.

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UniDec is a Bayesian deconvolution program for deconvolution of mass spectra and ion mobility-mass spectra.

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YADA 3.0 is the newest version of Yet Another Deconvolution Algorithm (Y.A.D.A) tool to perform fast deconvolution.