Executive Director, Principal Investigator

Nuno Bandeira

Nuno Bandeira is an Associate Professor at both Computer Science and Engineering and at the  Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California in San Diego. He is also the Executive Director of the UCSD/NIH Biomedical Research Center for Computational Mass Spectrometry, where he leads a team of developers who created and implemented the ProteoSAFe platform for computational mass spectrometry (MS) that has already enabled searching over tens of billions of spectra from thousands of users in >200,000 search jobs. ProteoSAFe is also the platform supporting the MassIVE repository for proteomics MS data and the GNPS repository and knowledge base for small molecules MS data. These have resulted in the data-networking of thousands of researchers in 150+ countries, integrating public data with numerous ongoing research projects and consequently improving annotation of public datasets by over 10-fold since the time of original deposition. The ultimate goal of the Bandeira lab is to enable reliable, reproducible and automated identification of any class of molecules suitable for analysis with mass spectrometry instruments.

Nuno Bandeira

Contact Info

Email Address: bandeira@ucsd.edu
Phone Number: (858) 534-8666
Location: CSE 4210
Computer Science and Engineering
University of California, San Diego
9500 Gilman Drive, Mail Code 0404
La Jolla, CA 92093-0404, USA

Key Publications

Mass spectral molecular networking of living microbial colonies. Watrous J, Roach P, Alexandrov T, Heath BS, Yang JY, Kersten RD, van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC. Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1743-52. doi: 10.1073/pnas.1203689109. Epub 2012 May 14.
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking Mingxun Wang, Jeremy J Carver, [...], Pieter C Dorrestein, Nuno Bandeira. "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking." Nature biotechnology 34.8 (2016): 828-837
MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets Meena Choi, Jeremy Carver, [...], Nuno Bandeira, Olga Vitek. "MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets", Nat Methods 2020 Oct;17(10):981-984
View All CCMS Publictions

Research Interests

The Bandeira Lab research focuses on the development of algorithms and systems for interpretation of proteomics and metabolomics mass spectrometry data from endogenous and digested peptides, discovery and localization of post-translational modifications, protein-protein interactions, sequencing of non-linear peptides with unknown amino acids and characterization of microbial, marine, reptile and plant natural products.

Major research areas and related software tools:

Current lab members:

  • Benjamin Pullman, CSE Ph.D. student
  • Duong Nguyen, CSE Ph.D. student
  • Wout Bittremieux, Postdoctoral researcher
  • Tiago Leao, Postdoctoral researcher
  • Jeremy Carver, CCMS software architect
  • Julie Wertz, CCMS applications developer

Alumni and previous lab members: