Proteomics  Data Mining Challenge 2020 


Proteomic informatics is rapidly improving, but is it finally ready to help in human disease research? 

This challenge is a test of where we are now in identifying protein post-translational modifications (PTMs) that are relevant in human diseases. 


Over 25 teams around the world have signed up for this challenge to pit their data processing pipelines for PTMs


A recently described LCMS analysis of the CSF of ALS patients and matched controls.

The goal of this challenge is to find the best pipelines for identifying PTM biomarkers in global proteomics data. 



The details you need for this study can be found in this powerpoint you can download here. 

Attention: The powerpoint was updated on 2/25/20 to correct an error in the RAW file assignment list. 

Do you want to participate in this challenge? We are accepting data until April 15, 2020. Email us at:


Further details on the dataset we will be re-analyzing can be found here.

Bereman et al., 2018 ((Scientific Reports volume 8, Article number: 16334 (2018))

All data can be downloaded from Chorus Project #1439 (

Scientist in the Lab

Lou Gherig's disease, or ALS, is a condition with no current cure and limited diagnostics.

You can read a recent open review of the disease at the New England Journal of Medicine here


Challenge Judges

We have assembled a team of judges with expertise in proteomics, post-translational modifications, and ALS. 
Emphasis will be on two levels:
The technical results and their quality
The impact of the presented results to forward ALS research.


Matthew Elliott, MD

Medical Director
UVA ALS Clinic

Matthew is a practiciing neurologist and recently became the medical director of the ALS Clinic at the University of Viriginia.


Ben Neely, Ph.D.


Ben is a specialist in mass spectrometry and proteomics informatics.

Michael Bereman, Ph.D.

Assistant Professor

NC State

Michael Bereman is an expert in both proteomic informatics and ALS research adn the originator of this dataset.


Miranda Darby, Ph.D.

Assistant Professor
Hood College Bioinformatics

Miranda directs the Bioinformatics MS and Certificate programs at Hood College and specializes in neurological diseases.


Participants are from*

*Participation is on a voluntary basis and does not necessarily include the endorsement of these institutions.