FlashLFQ is a program that quantifies peptides, proteins, and proteoforms in mass spectrometry data. This step is performed after these analytes have been identified by a search program, such as MetaMorpheus. As the name implies, it is orders of magnitude faster than existing quantification software. The primary goal of the software is to provide a fast, high-quality, quantitative platform to quantify any search software’s identifications.



MetaMorpheus is a software tool that identifies peptides, proteins, and proteoforms from mass spectrometry fragmentation (MS/MS) data. It is capable of searching both bottom-up (peptide) and top-down (intact proteoform) data. Currently, five graduate students and several undergraduates work on improving MetaMorpheus, making it one of our most collaborative and dynamic projects. Often, the motivation for adding a feature to MetaMorpheus is the need to analyze new types of data that existing software simply cannot handle. We use computer programming as a tool to solve these problems, much like traditional chemical biology uses organic chemistry to probe biological systems. MetaMorpheus was specifically designed to identify the “dark matter” of proteomics; where most search programs attempt to identify mostly unmodified peptides, we provide the capability of identifying peptides with a wide range of post-translational modifications. Recently, we have added the ability to identify proteoforms, chemically crosslinked peptides, and isotopically-labeled peptides. We also focus on providing this tool to the proteomics community as a free, open-source, easy-to-use tool. We have a community of over 200 users, which grows every day. We are constantly adding new features to the software, and release new versions of MetaMorpheus every few weeks.

mzLib: A library for mass spectrometry projects.

    Proteoform Suite

Proteoform Suite is a software program that performs intact-mass analysis and quantification of proteoforms in mass spectrometry MS1-only data. In a typical top-down analysis, more proteoforms are observed in the MS1 spectra than identified by MS2; Proteoform Suite increases the number of proteoform identifications in top-down analyses by identifying proteoforms by accurate intact mass. Proteoform Suite also constructs and automates the visualization of proteoform families by grouping together related proteoforms based on mass differences and liquid chromatography elution time. Proteoform Suite can integrate both bottom-up and top-down data to maximize the number of proteoform identifications.


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