• Capabilities:

    • Top-down and bottom-up search capabilities
    • Modification Fine Control for fast and accurate identification, even with 20+ types of modification
    • Wildcard Search for unknown modifications
    • Intact glycopeptide identification
    • Scoring models for all types of fragmentation spectra: CID, TOF-TOF, QTOF HCD, ETD/ECD, and EThcD
    • Sequence variant search and modification site localization

MASH Suite

  • Ying Ge’s group developed MASH Suite, a user-friendly and versatile software interface for processing high-resolution mass spectrometry data. MASH Suite contains a wide range of features that allow users to easily navigate through data analysis, visualize complex high-resolution mass spectrometry data and manually validate automatically processed results. See paper here.


  • 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.


  • 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.


  • Similar to database search engines for bottom-up, it takes a fasta file, a spectrum file, and a list of modifications as an input and reports proteoform spectrum matches (PrSMs) and their scores.

ProSight Lite

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

ProSight PTM 2

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

ProSightPC 3.0



  • ProteinGoggle is an intact protein database search engine using our novel search algorithm, isotopic mass-to-charge ratio & envelope fingerprinting (iMEF)! iMEF intrinsically interpret tandem mass spectral data in situ (without deconvolution or deisotoping) with two unique strength. One is to accurately and efficiently resolve overlapping isotopic envelopes; and the other is to unambiguously separate matching product ions with ideal isotopic envelopes from non-matching product ions with non-ideal isotopic envelopes. These two strength together with strict quality (tolerance) control of m/z and relative abundance down to every isotopic peak in every isotopic envelope (both precursor & product ions), ProteinGoggle delivers confident identification of proteoforms (amino acid sequence plus post-translational modifications) .

Proteoform Characterization Tool

1.0 BETA

  • From our Consortium Paper in Proteomics.

    "The issue of proteoform and PTM scoring arose during workshops and consortium meetings and was identified as a key ambiguity in the field that needs to be addressed."

    "An initial tool 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. Initial use of the tool (available on the website of the Consortium for Top Down Proteomics) is in progress. This software is ongoing in its development and represents our initial attempt to address the pressing issue of formalizing confidence in proteoform characterization."


  • 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. A built-in export function produces publication-quality customized proteoform illustrations, also for large datasets. Protter is of specific utility for the integrated visual analysis of membrane proteins and peptide selection for targeted proteomics.



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

Search Engine for Multi-Proteoform Complexes


  • Efforts to map the human protein interactome have resulted in information about hundreds to thousands of multi-protein assemblies housed in public repositories, but the molecular characterization and stoichiometry of their protein subunits remains widely unknown. 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.


  • 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.


  • TopFIND is the Termini oriented protein Function Inferred Database (TopFIND) is an integrated knowledgebase 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.


  • TopPIC (TOP-Down Mass Spectrometry Based Proteoform Identification and Characterization) is a software tool for identification and characterization of proteoforms at the whole proteome level by top-down tandem mass spectra using database search. It 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.


  • Description: YADA can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra). YADA also enables a pipeline consisting of ProLuCID and DTASelect for analyzing large-scale middle-down proteomics data.