Jonathan Goya

I am a PhD student in Quantitative and Computational Biology at Princeton University. My research advisor is Olga Troyanskaya and I also work with Josh Rabinowitz and Ben Garcia. I frequently collaborate with the Mass Spectrometry Center.

Before coming to Princeton I was a research technician at the University of Chicago for Steve Kron, Sam Volchenboum, and Evgeny Berdyshev. My undergraduate advisor at the University of Arizona was Vicki Wysocki.


Rapid technological advances in nucleic acid sequencing and mass spectrometry have made possible a wide variety of methods to explore the molecular composition and kinetics of biological systems. The goal of my research is to extract the most meaningful information from these methods by considering them in the context of our current understanding of the system. In particular, I am interested in combining orthogonal analytical technologies to discover novel regulatory relationships between gene expression and splicing and protein translation, modification, and degradation. This work applies traditional methods in statistics and signal processing with cutting-edge techniques for the analysis of large, heterogeneous, and streaming datasets.



Quantitator takes peptide sequence and retention time information in the form of PeptideProphet pepXML or Scaffold spectrum reports, LC-MS mass spectra in mzXML format, and a user-created parameter file as inputs. For each peptide in the pepXML or spectrum report, Quantitator estimates the signal intensity derived from each isotopic labeling group as defined by the labeling strategy, and reports these estimates along with the estimated standard error and other statistical data. For complete details, see Quantitator.


Infiltrator uses pairwise patterns of co-elution between peptides to predict retention times for unidentified peptides in LCMSMS experiments. Documentation for Infiltrator is forthcoming, for prompt assistance please contact me directly at


Rbitrary is a tool for Galaxy that takes an R script and any number of input files, and returns one output file (user-specfied numbers of output files would be nice if someone wants to figure it out...). To install, just save the Rbitrary Tool XML somewhere in the galaxy-dist/tools directory and make an entry in the tool_conf.xml file. NOT RECOMMENDED FOR PRODUCTION SERVERS! USE AT YOUR OWN RISK!


For all publications, see PubMed or Google Scholar.