XMapper Manual

1. Introduction
XMapper is a software tool used to map and score the cross-links in proteins
and peptides by use of MassMatrix[1] database search results. The results are
displayed in scaled color maps, called X-Maps, and also in .CSV[2] files
which you may open them in Excel for further analysis.

XMapper is free and open source software. You can redistribute it and/or
modify it under the terms of the GNU General Public License as published
by the Free Software Foundation. The software is distributed in the hope that
it will be useful, but WITHOUT ANY WARRANTY; See the GNU General
Public License for more details.

Author:
Hua Xu, Ph.D.
hxx58@case.edu
Center for Proteomics & Bioinformatics
Case Western Reserve University

Note:
[1] MassMatrix is a database search program for tandem mass spectrometric data that is
capable of searching intact disulfide bonds and/or cross-links in peptides and proteins.
It is available at:
http://www.massmatrix.net/
http://www.massmatrix.org/
[2] A .CSV, i.e. comma separated values file is used for storing data in a formatted table.
See more details at http://en.wikipedia.org/wiki/Comma-separated_values.
2. Installation and Uninstallation
To Install:
1. Download XMapper installation file at
https://sourceforge.net/projects/xmapper4protein/
2. Double click to run the XMapper installation file.
3. Follow the directions of the setup wizard (Fig 1) to install XMapper
on your computer.

Fig 1. The XMapper Setup Wizard.

To Uninstall:
Uninstall XMapper through start -> All Programs -> XMapper ->
Uninstall.
3. User Manual
3.1 To Use XMapper

Using XMapper is extremely easy.

1. Download MassMatrix search results from the MassMatrix server

and unzip the results.

2. Grab one or more MassMatrix search result html files and drop on
the XMapper program on your desktop (Fig 2).

XMapper

Fig 2. The usage to XMapper program.

3. A DOS window will be prompted to process the files one by one (Fig
3). For each file, you need to specify the maximum scale of the color
map. You may press enter to skip this and the maximum scale will be
determined by the program automatically.

Fig 3. The DOS window of XMapper.

4. One .PNG figure and one .CSV file will be generated for each protein
match in each MassMatrix result file. The results are placed in the
folder where the original MassMatrix html file is.
3.2 XMapper Results

One .PNG figure and one .CSV file will be generated for each protein
match in each MassMatrix result file and placed in the folder where the
original MassMatrix html file is. The .PNG figure can be viewed in any
type of image viewer, such Windows Picture Viewer. The .CSV file
contains the original data that are used to plot the .PNG figure and can
be opened in Excel for further analysis. The .PNG figure is a scaled color
map, called X-Map. There are two types of X-Maps as shown in Fig 4.

Chain label for multi-chained protein or Each cell represents a cross-link

Row labels protein label for a protein complex. between its row label and column label

Column
labels

Bold white bars separate different The scaled colors represent the
protein chains or different proteins scores of cross-links in the XMap

(a) (b)
Fig 4. Two types of X-Maps: (a) an X-Map of disulfide bonds in Insulin,
(b) an X-Map of Cys-Lys cross-links of Cytochrome C and Lysosome.

AC6 AC7 AC11 AC20 BC7 BC19

AC6 0 0 64.3 0 0 0
AC7 0 0 0 0 67.7 0
AC11 64.3 0 0 0 0 0
AC20 0 0 0 0 0 701.9
BC7 0 67.7 0 0 0 0
BC19 0 0 0 701.9 0 0
Fig 5. The original map for a search of disulfide bonds in Insulin whose
lower part is plotted as an X-Map shown in Fig 4a.
The first type of X-Maps is for the searches of cross-links between the
same amino acid residues, such as disulfide bonds and Lys-Lys cross-
links generated by BS3. As shown in Fig 5, this type of cross-link maps is
symmetric and only the lower part of the maps is created as X-Maps in a
triangle shape.

The second type of X-Maps in a rectangle shape is for the searches of

cross-links between two different amino acid residues, such as Cys-Lys
cross-links generated by Sulfo-SMCC.

An X-Map is a scaled color map containing many cells that are separated
by thin white bars. Each cell represents a cross-link between the amino
acid residues labeled by its row and column labels. For example, the top
cell in Fig 4a represents the cross-link between amino acid C7 on chain
A and amino acid C6 on chain A of the Insulin.

The scaled colors of the cells represent the scores of the cross-links. The
score of a cross-link is the sum of pp values of all the peptide matches
assigned to the cross-link. More sophisticated scoring algorithms are
under development and will be included and implemented in the future
releases of XMapper.

For an X-Map of a protein with multiple chains or multiple proteins, the

X-Map is split into sections that are separated by bold white bars. For
example, the top section of the X-Map in Fig 4a contains the cross-links
within the chain A of Insulin, the left bottom section contains the cross-
links between chain A and chain B of Insulin, and the right bottom
section contains one cross-link within chain B of Insulin. The X-Map in
Fig 4b contains four sections of cross-links within protein A (upper
left), between protein A and B (lower left and upper right), and within
protein B (lower right).

The maximum value of the color bar scale of an X-Map can be specified
(Step 3 in Section 3.1), if the step is skipped, the maximum scale value
will be determined by the program in accordance with the highest
scores of the cross-links. Sometimes, the pattern of an X-Map can be
dominated by one or two cells. This can be solved by manually
specifying a maximum scale value that is lower than the actually highest
score of the cross-links in the X-Map.