PMCP: Peptide Mass Comparison Program

What is it?

PMCP is a program that helps biologists evaluate the output of mass spectrometry experiments. In particular, if you have data from control and experiments, and are looking for a simple way to see a pattern in the distribution of masses, this program helps visualize the mass spec data.

The purpose of this program is to compare peptide mass data among three types of data: the masses of (tryptic) peptides from a known protein, to the masses of a putative match, to masses from the same protein that has been subjected to some potential modification. Given a set of text files containing lists of peptide masses, this data analysis program allows users to compare peptide masses between known proteins and control and experimental data. In addition to several textual mass comparisons, it generates graphs that illustrate the percentage of total files that contain a peptide of the known protein, allowing the user to observe peptides that are present in control data and significantly absent in experimental data (peptides whose masses have been modified by treatment). If the user elects to input a known protein with peptide masses in the order of the primary sequence, this information is retained in the graph, allowing the user to observe regions of the protein that are particularly modified. This information can be used in conjunction with NCBI Cn3D software to visualize the location of modifications in the structure of the protein.

PMCP was written by Pria Anand (NSF REU summer student) and Rahul Simha. The project was supervised by Profs. Rahul Simha (Computer Science) and Rob Donaldson (Biology). This project was partially supported by a National Science Foundation REU site awarded to GWU (PI: Rob Donaldson).

Where do I get it and what do I need to run it?

PMCP is written in Java and should execute on any operating system that supports recent releases of Java. These include most common Linux, Windows or MAC-OSX PC's.

Download and installation instructions:

How do I run and use it?