Bioinformatics Toolbox™

mzxmlread - Read data from mzXML file

Syntax

mzXMLStruct = mzxmlread(File)

Arguments

File

String containing a file name, or a path and file name, of an mzXML file that conforms to the mzXML 2.1 specification or earlier specifications.

If you specify only a file name, that file must be on the MATLAB^® search path or in the current directory.

Return Values

mzXMLStruct

MATLAB structure containing information from an mzXML file. It includes the following fields:

scan — Structure array containing the data pertaining to each individual scan, such as mass spectrometry level, total ion current, polarity, precursor mass (when it applies), and the spectrum data.
index — Structure containing indices to the positions of scan elements in the XML document.
mzXML — Structure containing:
- Information in the root element of the mzXML schema, such as instrument details, experiment details, and preprocessing method
- URLs pointing to schemas for the individual scans
- Indexing approach
- Digital signature calculated for the current instance of the document

Description

mzXMLStruct = mzxmlread(File) reads an mzXML file, File, and then creates a MATLAB structure, mzXMLStruct.

File can be a file name, or a path and file name, of an mzXML file. The file must conform to the mzXML 2.1 specification or earlier specifications. You can view the mzXML 2.1 specification at:

http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/Doc/mzXML_2.1_tutorial.pdf

mzXMLStruct includes the following fields.

Field Description

scan Structure array containing the data pertaining to each individual scan, such as mass spectrometry level, total ion current, polarity, precursor mass (when it applies), and the spectrum data.

index Structure containing indices to the positions of scan elements in the XML document.

Field	Description
`scan`	Structure array containing the data pertaining to each individual scan, such as mass spectrometry level, total ion current, polarity, precursor mass (when it applies), and the spectrum data.
`index`	Structure containing indices to the positions of scan elements in the XML document.
`mzXML`	Structure containing: Information in the root element of the mzXML schema, such as instrument details, experiment details, and preprocessing method URLs pointing to schemas for the individual scans Indexing approach Digital signature calculated for the current instance of the document

mzXML

Structure containing:

Information in the root element of the mzXML schema, such as instrument details, experiment details, and preprocessing method
URLs pointing to schemas for the individual scans
Indexing approach
Digital signature calculated for the current instance of the document

Tip LC/MS data analysis requires extended amounts of memory from the operating system. If you receive any errors related to memory or Java™ heap space, try the following:

Increase the virtual memory (or swap space) of your operating system or set the 3GB switch (32-bit Windows^® XP only) as described at:
```
 http://www.mathworks.com/support/tech-notes/1100/1107.html
```

Increase your Java heap space as described at:

 http://www.mathworks.com/support/solutions/data/1-18I2C.html

Examples

out = mzxmlread('results.mzxml');
% view a scan
m = out.scan(1).peaks.mz(1:2:end); 
z = out.scan(1).peaks.mz(2:2:end); 
bar(m,z)

Note The file results.mzxml is not provided. Sample mzXML files can be found at: