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.

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.

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:

Download pcmp.zip and unzip.

This will create a directory called pcmp.

Add this directory to your CLASSPATH variable so that Java can find it.

Run the MassSpec class in the directory.

How do I run and use it?

Generating data. First, your data. PMCP accepts data igenerated by the ExPASy PeptideMass program (select "chronological order" retain information about the primary sequence of the protein) in plain text format and copied to a text file. Experimental data may be generated by mass spectrometry, and a list of peaks may be copied to a text file.

Data Input into PMCP. (See the figure below) Files must be saved in text (.txt, not .rtf) format and inputted in order: Add the known protein first (1), followed by all control files (2), and finally all experimental files (3). To change the degree to which peptide masses must match to be counted as identical, enter a number in the epsilon field (4) -- 1.0 matches peptide masses to the whole number, 0.1 to the tenths place, etc. As files are added to the program, the file name will appear in the panel to the left (5), while the text of the file will appear in the main panel (6). Text at the top of the window monitors the files as they are added (7). Select "merge" to view the output (8). When prompted for whether or not you would like to view text files, choose "no" to only view graphs (9) or "yes" (10) to view all outputs. To quit the entire program, select the "quit" button at the bottom of the window (11)

Text Output. The text outputs are as follows:

Numerical: All files are sorted by numerical order in adjacent columns in the same window. Matching peptide masses appear on the same line.
Chronological: The "known" input remains in its original order. For each subsequent file, only those peptide masses that match a peptide mass in the known protein are retained in adjacent columns in the same window. Again, matching peptide masses appear on the same line across columns.
Non-matching: One window is created for each file containing only the peptides that appeared in the experimental data but not the known protein. The non-matching outputs may be saved as text files and directly read back into the program with another known protein.

Each window has a "save" button that allows it to be saved as a separate text file. To change the file name, change the text in the field at the bottom of the window, making sure to keep the ".txt" postfix. The default file output location is the directory where the program is saved.

Graphical Output. The two graphs produced by PMCP illustrate the following:

The percentage of total inputted files that contain each peptide of the known protein, with control and experimental samples appearing side-by-side on the same axes.
The difference in this percentage between the control and experimental samples for each peptide.

The x-axis of each graph assigns a number to each peptide of the known protein, and retains the order of the peptides in the original file. The y-axis refers to the percentage of total experimental or control files that contain each of these peptides. In the original graph, blue bars correspond to the experimental data, whereas red bars correspond to control data.

Each of the two graphs (See Figure below) is accompanied by a smaller window (1) that allows it to be saved as a "png" file. To change the file name, change the text in the field in the center of this window (2), making sure to keep the "png" postfix (file type). The default file output location is the directory where the program is saved.