View Josh Elias’ and Brian DeFelice’s full list of publications on Google Scholar. Below is some recent, relevant work.

Rapid QC-MS – Interactive Dashboard for Synchronous Mass Spectrometry Data Acquisition Quality Control Icon
February 1, 2024

Rapid QC-MS actively listens for newly created LC-MS raw files and automatically quantifies internal, external, and reference standards producing interactive plots on a browser based dashboard.  These visualizations allow researchers to quickly verify and interrogate the quality of the data being generated by their LC-MS system.

PLOS Biology: Systems Biology Elucidates the Distinctive Metabolic Niche Filled by the Human Gut Microbe <em>Eggerthella lenta</em> Icon
May 19, 2023

CZ Biohub SF Investigator Peter Turnbaugh’s team and the SF Biohub Mass Spec Platform collaborated to investigate the unique metabolism of the prevalent and disease-linked Actinobacterium Eggerthella lenta. The application of stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP.

eLife: Intermittent fasting induces rapid hepatocyte proliferation to restore the hepatostat in the mouse liver Icon
January 31, 2023

In the first demonstration of diet-induced liver regeneration, this study with Stanford Medicine shows that intermittent fasting spurs rapid liver cell proliferation in mice.

Molecular Cell: Increasing cell size remodels the proteome and promotes senescence Icon
September 1, 2022

It is commonly assumed that protein concentrations generally remain constant across cells of a given type. CZ Biohub postdoctoral fellow, Mike Lanz demonstrated this is not the case, revealing new dimensions of cellular regulation. This work resulted from a close collaboration with CZ Biohub Investigator Jan Skotheim at Stanford.

Molecular & Cellular Proteomics: Tuning DO:DM Ratios Modulates MHC Class II Immunopeptidomes Icon
March 1, 2022

Our study bridges a gap in understanding and predicting MHC-II antigen presentation.

Joshua E. Elias
Nature Communications: An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease Icon
February 16, 2022

Here, we develop a liquid chromatographic-mass spectrometric workflow for untargeted sequence analysis of the urinary peptidome.

Joshua E. Elias
Nature: A metabolomics pipeline for the mechanistic interrogation of the gut microbiome Icon
July 14, 2021

Collectively, our microbiome-focused metabolomics pipeline and interactive metabolomics profile explorer are a powerful tool for characterizing microorganisms and interactions between microorganisms and their host.

Brian C. DeFelice
ACS Publications: Automated Ligand Purification Platform Accelerates Immunopeptidome Analysis by Mass Spectrometry Icon
December 20, 2020

Here, we describe our efforts to optimize purification and mass spectrometer parameters, ultimately allowing us to identify as many as almost 5000 pMHC I and 7400 pMHC II from as little as 2.5 × 107 Raji cells each.

Joshua E. Elias
Nature Biotechnology: TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets Icon
April 1, 2019

Here, we describe TagGraph, a computational tool that overcomes both challenges with an unrestricted string-based search method that is as much as 350-fold faster than existing approaches, and a probabilistic validation model that we optimized for PTM assignments.

Joshua E. Elias
ACS Publications: Mass Spectral Feature List Optimizer (MS-FLO): A Tool To Minimize False Positive Peak Reports in Untargeted Liquid Chromatography–Mass Spectroscopy (LC-MS) Data Processing Icon
February 22, 2017

To demonstrate the effectiveness of MS-FLO, we processed 28 biological studies and uploaded raw and results data to the Metabolomics Workbench website, encompassing 1481 chromatograms produced by two different data processing programs used in-house (MZmine2 and later MS-DIAL).

Brian C. DeFelice
Journal of Clinical Oncology: Diacetylspermine Is a Novel Prediagnostic Serum Biomarker for Non–Small-Cell Lung Cancer and Has Additive Performance With Pro-Surfactant Protein B Icon
August 17, 2015

We have investigated the potential of metabolomics to discover blood-based biomarkers relevant to lung cancer screening and early detection.

Brian C. DeFelice
Nature Methods: LipidBlast in silico tandem mass spectrometry database for lipid identification Icon
June 30, 2013

We provide a freely available computer-generated tandem mass spectral library of 212,516 spectra covering 119,200 compounds from 26 lipid compound classes, including phospholipids, glycerolipids, bacterial lipoglycans and plant glycolipids.

Brian C. DeFelice