Depending on the type of sample that are analyzed, you may find these links useful. Our facility uses each of these programs on a regular basis, and maintains the required licensing to upgrade as updates become available. 


For basic protein ID or qualitative comparisons, raw LC/MS/MS data are processed and searched using the latest version of Mascot, and the .dat files are loaded into Scaffold (Proteome Software). This program allows users to visualize their list of proteins, compare samples, and identify post translational modifications. You can easily select and open the spectra as well, for additional information.  Download the viewer here:

Proteome Discoverer

We use Proteome Discoverer, not only to run our Mascot searches, but also to process our complex quantitative samples. Currently, using PD 2.4, we process and evaluate TMT labeled experiments, up to 16-plex (16 samples, quantitatively compared in one project simultaneously).  When you download the demo, you have complete control of your project. You are able to select lists of proteins of interest, view volcano plots and heat maps, statistical variations, export protein lists or raw peptide spectral matches. For these projects, our staff will give users a comprehensive overview of the program and how to interpret their results. Please register with Thermo Scientific and download the demo version 2.4 here:


Skyline is a freely -available and open source Windows client application developed by the MacCoss Lab. We use it for developing Multiple reaction Monitoring (MRM), Parallel Reaction monitoring (PRM) and Data Independent Acquisition (DIA), as well as MS1 quantitative methods. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large scale quantitative mass spectrometry studies in life sciences. Their website contains an abundance of highly detailed instructional videos and tutorials. Learn more, and download their most recent software version here:


Our facility uses various programs for identifying Post-translational Modifications (PTMs). We use the BYONIC (Protein-Metrics) embedded in Proteome Discover to help detect complex, custom or multiple PTMs. Download the viewer here:


We routinely use PEAKS (Bioinformatics Solutions) to identify and detect PTMs and non-specific cleavage sites, and occasionally ragged ends from non-enzymatic cleavages. PEAKS uses and initial de novo search to supplement their search algorithm.  PEAKS display the coverage map slightly differently than other search software and the spectral annotation is clear and concise. Please register to request a trial activation key:



The Johns Hopkins Mass Spectrometry and Proteomic Facility

Director Robert Cole Ph.D. 

Phone: 410-614-6968


725 N. Wolfe Street

Wood Basic Science Building, Room 512

Baltimore, MD 21205