Our Discovery Tools:

Educational Materials and Tutorials

The following two videos on the topic, Bioinformatics for Prohormone and Neuropeptide Discovery, are both publicly accessible via the link above.

Part 1: Introduction and Identification of the Molecular Complement
Part 2: Sequence Modeling, Analysis, and Applications

Human Proteoform Atlas

The Human Proteoform Atlas is a FAIR community-driven resource for experimentally-derived proteoform annotation. Representing a large-scale effort, the first Human Proteoform Atlas provides a resource linking experimentally identified proteoforms to human cells, tissues, and disease, and is managed by the Northwestern team.

microMS

microMS, for microscopy-guided mass spectrometry, is written in Python and provides an intuitive graphical user interface to simplify image-guided MS for novice users. The class hierarchy of instrument interactions was designed to easily integrate new MS systems while retaining the feature-rich image analysis framework. microMS provides a versatile platform for researchers to perform targeted profiling experiments using a series of mass spectrometers. The flexibility in mass analyzers greatly simplifies serial analysis of the same targets by different instruments.

Mouse Brain Proteoform Atlas

The Mouse Brain Proteoform Atlas catalogs all proteoforms observed during top-down proteomics experiments in murine brain tissue. This online database is managed by the Northwestern team.

MSModDetector

MSModDetector is Python package that deconvolutes overlapping proteoforms within a single landscape using individual ion mass spectrometry (I2MS) and a list of possible PTMs. This tool was developed by Marjan Faizi (Faizi et al., Bioinformatics 40:btae335, 2024) as part of a collaboration between Harvard and Northwestern University.

NeuroPred

NeuroPred is a web-based application that integrates models and repositories to accurately predict prohormone cleavage sites and annotate the resulting peptides in human and a number of biomedical species. NeuroPred provides the research community with the most likely set of resulting peptides, including sequence, mass and post-translational modifications.

PepShop

PepShop is a web-based application to facilitate annotation and identification of neuropeptides and prohormones across multiple species. In addition to a searchable database of prohormones, PepShop provides bioinformatics tools for homology searches, multiple sequence alignment and cleavage prediction sites, and proteomic tools for searches for neuropeptides and fragment ion prediction.

ProSight Annotator

ProSight Annotator is a free Windows application allowing researchers to enhance their targeted proteoform searches using the Center’s Discovery Tools. Users add novel specific features to existing public data such as PTMs, glycans, disulfide bonds, or endogenous cleavages that researchers have identified. This new information is then used by other Center Discovery Tools to discover novel proteoforms from their top-down data. This online toolset is managed by the Northwestern team.

ProSightPD™

ProSightPD™ enables the identification and characterization of intact proteins and their post-translational modifications and can be used to analyze top-down proteomics data with speed, accuracy, and precision using our ProSight search engine.

Protocols

The published protocols presented here have been developed and published by the Center so that all in the research community may benefit from these discovery toolsets.

Songbird Neuroanatomy Webpages

The images on the Songbird Neuroanatomy webpages show the expression distribution of 15 prohormone genes across sections from an adult male zebra finch brain. You will find links for viewing brain sections stained for each of these genes and the option to view all sections from one brain with some neuroanatomical annotation (“Whole brain”).

Stretched Imaging

This is a set of computational tools to use when employing the stretched imaging method developed by members of the Sweedler group.

TD Portal and TD Viewer

TDPortal is a high-throughput top-down proteomics engine running on the Northwestern Quest High Performance Computing cluster, with access available on request. This portal runs on the Galaxy framework and provides access to multithreaded top-down proteomics data analysis. Results from the TDPortal are viewable using the TDViewer, a Windows application created under the Windows Presentation Foundation framework. This visual tool allows users to profile proteins identified and proteoforms characterized within a top-down proteomics experiment. This online toolset is managed by the Northwestern team.

Retired Discovery Tools

SequenceGazer, used to characterize intact proteins, neuropeptides, and their post-translational modifications, has been replaced with ProsightLite.

neuroProSight is no longer supported and has been replaced with ProSightPD™.

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