“Over 330 Publications”

Human Proteome Project

Hear about the Top Down version of the Human Proteome Project!

The tectonic collision of biology with separation science, MS, and informatics occurred over the past 15 years and was driven by contributions from more than 100 laboratories. Like budding yeast, MS is sprouting emergent approaches for the direct profiling and MS/MS analysis of heterogeneous proteins in ever more complex mixtures. Such approaches promise to determine molecular indicators of complex diseases and deepen our understanding of dynamic regulatory mechanisms in cell biology.

The TedX Talk at Northwestern University

Neil's TEDx Talk, A Plan to Weigh Every Protein in the Human Body: The Cell- Based Human Proteome Project presents a "big science" project with huge implications for how proteins in the human body are catalogued and used for drug therapies and treatments.
Since 2011, Dr. Kelleher has served as the director of the Proteomics Center of Excellence at Northwestern University, where dozens of Northwestern laboratories are supported and beyond state-of-the-art in Top Down proteomics is developed. Dr. Kelleher was elected Treasurer of the American Society for Mass Spectrometry in 2012 and established the Consortium for Top Down Proteomics that same year With more than 200 papers published over the course of his career and teaching duties in two departments, Dr. Kelleher is a trans-disciplinary investigator with visible streaks of international impact in mass spectrometry-based proteomics and the discovery of new natural products from the microbial world. Validation of protein-based biomarkers in organ transplantation and cancers of the blood are among the focused areas currently being pursued in clinical research at Northwestern.

Neil Kelleher's Lab: Studying Top Down Proteomics

The core of the Kelleher Team is built around expertise in technology development for complex mixture analysis using Fourier-Transform Mass Spectrometry for targeted applications in proteomics and metabolomics.

Making Sense of Proteins to Improve Cancer Detection

Northwestern molecular biosciences professor Neil Kelleher discusses the need for precision measurement of proteins — using top-down proteomics — in order to better understand and detect cancer and other diseases.


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.

In 2015, Prof. Kelleher was awarded an NIH P41 grant, establishing the National Resource for Translational and Developmental Proteomics (NRTDP). A major objective of the Resource is the dissemination of software to the scientific community. This includes ProSightLite, a free Windows application for single protein characterization.

Native Top Down MS

The evolution of technology to determine the composition of protein molecules with complete molecular specificity continues. As we move forward, one can frame the use of mass spectrometry and associated methods into a three-level enterprise: bottom up, top down and native proteomics. Native TDMS requires robust solutions to the challenges that arise when shifting to analyze proteins when ionized by electrospray at approximately neutral pH. Such a simple change creates many ripple effects in the separations, mass spectrometry and informatics that have been demonstrated by many over the past years to be of high value.

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International Influence