About the PI

Simone Sidoli

Simone Sidoli is an Assistant Professor at the Department of Biochemistry at the Albert Einstein College of Medicine.

He approached mass spectrometry (MS) as a trainee in the laboratory of Prof. Careri at the University of Parma (Italy), his hometown. There, he established methods to detect allergens in aliments, as food and food safety are critical aspects of the economy of Parma. Next, he moved to the University of Southern Denmark (Odense, DK) for his PhD, joining the prestigious Protein Research Group. In the group of Ole N. Jensen, he developed methods for protein analysis, processing large datasets and learned to maintain state-of-the-art instrumentation. Together with the Biotech Research & Innovative Center (BRIC) in Copenhagen, he studied the histone PTM landscape of embryonic stem cells using his own developed middle-down MS workflow. Middle-down MS performs unbiased identification and quantification of co-existing histone marks.

In 2014, he joined Ben Garcia’s lab, located within the Epigenetics Institute at the University of Pennsylvania (Philadelphia, PA, USA). In this amazing environment, hosting many worldwide famous experts in epigenetics, he investigated human disease systems by developing a proteomics and computational pipeline to link cell signaling cascades (protein phosphorylation) with chromatin changes (histone modifications). He also applied this methodology to identify the regulated proteome during host viral infection. These methods include improvements in quantification accuracy of histone PTMs and follow-up optimization of the middle-down MS strategy. Moreover, he is now working on a new method to assess the chromatin state of all histone marks in a single experiment and establishing a workflow to analyze histone marks in <1 min, paving the way to high throughput epigenomics screening.

Selected publications (full list in PubMed)

One minute analysis of histone post-translational modifications by direct injection mass spectrometry Sidoli S, Kori Y, Lopes M, Yuan ZF, Kim HJ, Kulej K, Janssen K, Agosto L, Cunha JPC and Garcia BA (Genome Research, 2019)

Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code Sidoli S, Lu C, Coradin M, Wang X, Karch KR, Ruminowicz C and Garcia BA (Epigenetics & Chromatin, 2017)

Low resolution data-independent acquisition (DIA) in an LTQ-Orbitrap allows for simplified and fully untargeted analysis of histone samples Sidoli S, Simithy-Williams J, Karch KR, Kulej K and Garcia BA (Analytical Chemistry, 2015)

Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones Sidoli S, Schwämmle V, Ruminowicz C, Hansen TA, Wu X, Helin K and Jensen ON (Proteomics, 2014)