Principal Investigator


Dr. Ying Ge

PhD: Chemistry, Cornell University

Dr. Ge is a Professor in the Department of Cell & Regenerative Biology and in the Department of Chemistry at the University of Wisconsin-Madison. She also serves as the Director of Mass Spectrometry for the Human Proteomics Program in the School of Medicine and Public Health. Dr. Ge has extensive experience in mass spectrometry-based proteomics and protein chemistry. She has devoted the past eighteen years to developing and applying top-down high-resolution mass spectrometry (MS)-based proteomics for biomedical research. To address the challenges in the data analysis in top-down proteomics, she has assembled a bioinformatics team (since 2009) and developed two software packages: MASH Suite for top-down MS characterization of single proteins, and MASH Suite Pro for top-down proteomics, which serves as foundation to establish MASH Explorer.



Dr. Irene Ong

PhD: Computer Science, UW-Madison

Dr. Ong is an Assistant Professor at the University of Wisconsin Departments of Obstetrics and Gynecology with a joint appointment in Biostatistics and Medical Informatics and the Associate Director of the University of Wisconsin Carbone Cancer Center's Cancer Informatics Shared Resource. Irene received her PhD in Computer Science with minor in Biology. She has extensive experience in the development of databases, cloud computing and web applications. She also has over 10 years of experience with analysis of various omics data. Irene will provide efforts and guidance in the development of MASH Explorer Portal, a web-based platform.


Dr. Sean McIlwain

PhD: Computer Science, UW-Madison

Dr. McIlwain is an Assistant Scientist (equivalent to Research Assistant Professor in other institutions) in the Department of Biostatistics and Medical Informatics and Carbone Cancer Center at the University of Wisconsin-Madison. He has received a PhD in Computer Science and post-doc training in computational proteomics. Prior to his current position at UW-Madison, Sean worked as a post-doctoral fellow in William Noble’s lab in collaboration with Mike MacCoss and David Goodlett at University of Washington. He has strong expertise in the development and application of algorithms for processing proteomics/mass spectrometry data. Sean will lead the development of MASH Explorer App.



Dr. Xiaowen Liu

PhD: Computer Science, City University of Hong Kong

Dr. Liu is an Assistant Professor in the School of Informatics at Indiana University-Purdue University and Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University. Dr. Liu is a leading expert in top-down computational proteomics. He has developed algorithms for deconvolution and database search such as MS-Deconv and MS-Align . Dr. Liu and Dr. Ge’s group have collaborated for the past a few years and have published collaborative papers in Mol. Cell. Proteomics (2014 2014, 13, 2752-2764; and 2016, 15, 703-714). Dr. Liu will continue to collaborate with the team on the development of MASH Explorer.


Dr. Ruixiang Sun

PhD: Computer Science, Xi’an JiaoTong University

Dr. Sun is an Associate Professor in the National Institute of Biological Sciences, Beijing. Dr. Sun is currently in Dr. Ge’s lab as a visiting scholar. Dr. Sun has devoted his past 4 years in developing software algorithms for top-down proteomics. He will help Dr. Ge’s group to incorporate pParseTD (for deconvolution) and pTop (for database search) into the new MASH Explorer.

Software Developers


Kent Wenger

Kent received his B.S. in computer sciences from the University of Wisconsin-Madison in 1990 (after also studying at UW-Green Bay and Northwestern University). Kent joined the lab in September 2018, and is working on the development of the MASH Explorer software, with plans to also work on metabolomics software in the future. He has over 30 years of software development experience (in both the academic and commercial sectors), including past work on commercial FT/ICR software. He was born in Pittsburgh, but mostly grew up in Green Bay, and has called Madison home for three decades. In his free time, Kent enjoys cycling and international travel (preferably combined); model railroading; long walks with his wife, Sue; and playing with his miniature schnauzer, Theo.


Melissa Pergande

Melissa Pergande

PhD: Chemistry, University of Illinois at Chicago

Melissa received her BS and MS from the University of Wisconsin-Milwaukee. She earned her Ph.D. in Chemistry from the University of Illinois at Chicago, where she focused on characterizing protein and lipid alterations in a mouse model of Niemann-Pick, type C. She joined the Ge group in 2022 and is focusing on multiomic analyses. She was born and raised in Wisconsin and loves cooking, nature and animals, especially dogs.

Graduate Students


Jake Melby

Jake received his B.S. in Chemistry from the University of Pittsburgh and then joined the Chemistry PhD program in Fall 2018 as an analytical chemistry student. He is currently interested in the characterization of the human heart proteome and improving separation methods for top-down proteomics. His hobbies include biking, reading, rooting for Pittsburgh sports teams and hanging out with friends.


Eli Larson

Eli received his B.A. in chemistry at Gustavus Adolphus College in 2018 before joining the Ge lab in the fall of 2018. He is interested in biotherapeutic characterization and developing new strategies for intact protein separations using online multidimensional liquid chromatography. He enjoys cycling, woodworking, and Nordic skiing.

Research Interns

Michelle Moss

Michelle Moss

Michelle received her B.S. in Biological Sciences from the University of Maryland in 2022 and then joined the Ge lab in the summer of 2022 as a research intern. She is interested in using top-down proteomics to study cardiac disease and translational medicine. Outside of the lab, she enjoys espresso, music, reading, and history. 



Zhijie Wu

PhD: Chemistry, University of Wisconsin-Madison

Abe completed his PhD in chemical biology in 2020, graduating from the Ge group. Prior to his graduate career, Abe double majored in Chemistry and Mathematics at the University of Rochester. During his time in the Ge group, Abe contributed heavily to the transition from MASH Suite Pro to MASH Explorer v1.0 and v2.0. Currently, Abe is working as a Scientist at Regeneron Pharmaceuticals.


Molly Wetzel

Molly is a Research Intern who graduated from UW-Madison in 2018 with a B.S. in biochemistry. Molly joined the Ge Lab in April 2018 and is assisting Sean and Kent with MASH Explorer GUI and command line development. Specifically, she has developed MASH Explorer's Workflow Manager to facilitate easier database searching. Molly is also responsible for website maintenance and assisting Abe with user support. She is hoping to go to graduate school next year to pursue a career in bioinformatics.


Wenxuan Cai

PhD: Molecular and Cellular Pharmacology, University of Wisconsin - Madison

A previous graduate student in the Ge Lab, Vege received her PhD in Molecular and Cellular Pharmacology in 2018. She is the co-first author of the MASH Suite Pro paper published in Mol. Cell. Proteomics (2016, 15, 703-714). She helped with MASH Explorer development and worked on allowing MASH Explorer to process more types of raw data files.


Yiwen Gu

Yiwen obtained her master degree in Biophysics at UW-Madison and is now interested in pursuing a degree in Computer Science. Yiwen will work on the website design and development for MASH Explorer. She worked with Sean on importing multiple data formats and to develop new functionalities for the Explorer software. She also worked with Irene in the development of web-based MASH Explorer Portal.


Sudharshanan Govindaraj Ramanathan

While pursuing his undergraduate degree in Computer Engineering and Computer Science at UW-Madison, Sudharshanan worked with Sean on incorporating new functionalities into MASH Explorer software and worked with Irene on managing LabKey server user accounts.