mzxmlread

Read data from mzXML file

Syntax

mzXMLStruct = mzxmlread(myFile)

mzXMLStruct = mzxmlread(myFile,Name,Value)

Description

mzXMLStruct = mzxmlread(myFile) returns a MATLAB^® structure, mzXMLStruct, from an mzXML file, myFile.

mzXMLStruct = mzxmlread(myFile,Name,Value) reads an mzXML file, myFile, and then returns a MATLAB structure, mzXMLStruct, using additional options specified by one or more Name,Value pair arguments.

Examples

Create a MATLAB Structure from an mzXML File

In this example, the file results_1.mzxml is not provided. You can find sample mzXML files at:

• Peptide Atlas Repository at the Institute for Systems Biology (ISB)

Read an mzXML file into a MATLAB structure.

out = mzxmlread('results_1.mzxml')

out = 

     scan: [2000x1 struct]
    mzXML: [1x1 struct]
    index: [1x1 struct]

View the first scan in the mzXML file by creating separate variables containing the mass-to-charge ratio (mz_ratio) and intensity (Y) values respectively. Then plot these values.

mz_ratio = out.scan(1).peaks.mz(1:2:end); 
Y = out.scan(1).peaks.mz(2:2:end); 
stem(mz_ratio,Y,'marker','none')

Extract One or Multiple Scans from an mzXML Structure

In this example, the file results_2.mzxml is not provided. You can find sample mzXML files at:

• Peptide Atlas Repository at the Institute for Systems Biology (ISB)

Read an mzXML file into a MATLAB structure, extracting a scan at index 1000.

out1 = mzxmlread('results_2.mzxml','ScanIndices',1000)

out1 = 

     scan: [1x1 struct]
    mzXML: [1x1 struct]
    index: [1x1 struct]

Read an mzXML file into a MATLAB structure, extracting multiple scans at indices 1000, 1500, and 2000.

out2 = mzxmlread('results_2.mzxml','ScanIndices',[1000 1500 2000])

out2 = 

     scan: [3x1 struct]
    mzXML: [1x1 struct]
    index: [1x1 struct]

Read an mzXML file into a MATLAB structure, extracting a range of scans from indices 1000 to 2000.

out3 = mzxmlread('results_2.mzxml','ScanIndices',[1000:2000])

out3 = 

    scan: [1001x1 struct]
    mzXML: [1x1 struct]
    index: [1x1 struct]

Input Arguments

myFile — Input file

character vector | string

Input file, specified as a character vector or string containing an mzXML file name. The file must conform to the mzXML 2.1 or earlier specifications. You can read the mzXML 2.1 specification here: http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Before R2021a, use commas to separate each name and value, and enclose Name in quotes.

Example: 'TimeRange',[5.0 10.0],'Verbose',true

Levels — Spectra levels

positive integer | vector of integers

Spectra levels, specified as a positive integer or vector of integers indicating which scans to extract scans from myFile. By default, mzxmlread reads all spectra levels.

For summary information about the levels of spectra in an mzXML file, use the mzxmlinfo function.

If you are using the 'Levels' name-value pair argument, then you cannot use 'ScanIndices'.

Example: 'Levels',5

TimeRange — Range of time

two-element numeric array

Range of time, specified as a two-element numeric array, such as [Start End] indicating which scans to extract from myFile. The Start and End scalar values must be between the startTime and endTime attributes of the msRun element in myFile. The Start scalar value must be less than End. By default, mzxmlread reads all scans.

For summary information about the time ranges in an mzXML file, use the mzxmlinfo function.

If you are using 'TimeRange' name-value pair argument, then you cannot use 'ScanIndices'.

Example: 'TimeRange',[5.1 10.2]

ScanIndices — Scan indices

positive integer | vector of positive integers

Scan indices, specified as a positive integer or vector of positive integers indicating which scans to extract from myFile. Use an integer to specify a single scan, or a vector of integers to specify multiple scans. By default, mzxmlread reads all scans.

For summary information about the time ranges in an mzXML file, use the mzxmlinfo function.

If you are using the 'ScanIndices' name-value pair argument, then you cannot use 'Levels' or 'TimeRange'.

Example: 'ScanIndices',7000

Verbose — Verbose mode

false (default) | 0 | true | 1

Verbose mode, specified as true (1), or false (0). When 'Verbose' is set to true, mzxmlread displays the progress while reading myFile.

Example: 'Verbose',true

Output Arguments

mzXMLStruct — Structure from mzXML file

MATLAB structure

Structure from an mzXML file, returned as a MATLAB structure. mzXMLStruct has 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.
mzXML	Structure containing all of the following: Information in the root element of the mzXML schema, such as instrument details, experiment details, and preprocessing methods URLs pointing to schemas for each scan Indexing approach Digital signature calculated for the current instance of the document

Tips

LC/MS data analysis requires extended amounts of memory from the operating system.

• If you receive errors related to memory, try the following:

  • Increase the virtual memory (swap space) for your operating system as described in Resolve “Out of Memory” Errors.

• If you receive errors related to Java^® heap space, increase your Java heap space:

  • If you have MATLAB version 7.10 (R2010a) or later, see Java Heap Memory Preferences.

  • If you have MATLAB version 7.9 (R2009b) or earlier, see https://www.mathworks.com/matlabcentral/answers/92813-how-do-i-increase-the-heap-space-for-the-java-vm-in-matlab.

Version History

Introduced in R2006b