top of page

Table of Content Graphic of the cNPDB database paper

cNPDB
A Comprehensive Empirical Crustacean Neuropeptide Database

cNPDB, the first centralized resource dedicated to the subphylum Crustacea, promisingly accelerating crustacean neuropeptidome research and offering a blueprint for cross-species translational studies of neuropeptide signaling. cNPDB is comprised of 1516 published neuropeptides from 30 crustacean species, each annotated with corresponding taxonomic information, computed physicochemical properties, spatial localization, and predicted three-dimensional structure.

Table of Content Graphic of the MSIght paper

MSIght
A Modular Platform for Improved Confidence in Global, Untargeted Mass Spectrometry Imaging Annotation

MSIght is a modular and accessible platform designed to simplify and accelerate routine, untargeted mass spectrometry imaging (MSI) analysis. It addresses a major challenge in the field by integrating histology, MSI, and LC-MS/MS data into a single automated workflow, removing the need for manual cross-referencing. This platform opens opportunities for large-scale clinical studies, helping researchers and pathologists discover novel biomarkers and improve clinical insights.

Table of Content Graphic of the MOTIF-QUEST paper

MotifQuest

An Automated Pipeline for Motif Database Creation to Improve Peptidomics Database Searching Programs

MotifQuest, our novel motif database generation algorithm, is designed to work in partnership with EndoGenius, a program optimized for database searching of endogenous peptides and that is powered by a motif database to capitalize on biological context to produce identifications. MotifQuest aims to quickly develop motif databases without any prior knowledge, a laborious task not possible with traditional sequence alignment resources.

Table of Content Graphic of the Endogenius paper

Endogenius
An Open-Source Software for Optimized Neuropeptide Identification from Mass Spectrometry Datasets

EndoGenius, a database searching strategy designed specifically for elucidating neuropeptide identifications from mass spectra by leveraging optimized peptide–spectrum matching approaches, an expansive motif database, and a novel scoring algorithm to achieve broader representation of the neuropeptidome and minimize reidentification.

Table of Content Graphic of the MSI Parser paper

MSI Parser
An Open-Source Software for Analysis of Single-Cell Mass Spectrometry Imaging Data

MSI-Parser is a program designed to define regions of interest (ROI) for single cell mass spectrometry analysis, followed by average spectra extraction, and machine learning classification of cell types.

Table of Content Graphic of the HyPep paper

HyPep

An Open-Source Software for Identification and Discovery of Neuropeptides Using Sequence Homology Search

HyPep is an open-source Python based algorithm designed for hybrid analysis of neuropeptide mass spectral data through sequence homology searching and accurate mass matching. HyPep aligns de novo sequenced peptides, generated through PEAKS software, with neuropeptide database sequences and identifies neuropeptides based on the alignment score. Users can upload their data files following the instructions in the manual and the results can be downloaded for use.

Table of Content Graphic of the Metandem paper

Metandem

A Data Analysis Tool for Isobaric Labeling-based Metabolomics

Metandem is a free online data analysis platform for mass spectrometry-based isobaric labeling metabolomics. It allows users to upload and process MS or hyphenated MS data files for isobaric-labeling-based quantitative and qualitative metabolomics analyses, including feature extraction, metabolite quantification, metabolite identification, batch processing of multiple data files, parameter optimization, median normalization, and statistical analysis. Results can be downloaded or visualized online.

Cite

Table of Content Graphic of the PRESnovo paper

PRESnovo

Prescreening prior to de novo sequencing

Prescreening Prior to de novo sequencing tool using peptide motif homology for improved de novo sequencing of peptides. PRESnovo works by searching tandem mass spectrometry data against a predefined motif database consisting of known peptides from the species of interest or related species. The software assigns the most probable motif to each precursor using a sophisticated scoring function. Results can then be used in conjunction with other de novo sequencing software to improve the accuracy of the de novo sequences.

More coming soon!

bottom of page