A parse what you need mzML parser library

dp-mzml is a java library for quickly parsing spectrum data from an mzML file via sequential iteration or random access.

Features:

Random access of spectra via scan start time range, reference id, or index of spectrum in file.
Easily load your own Spectrum instances, and parse what you need.

To parse an mzML file, construct an MzMLStAXParser with the factory method reference, XMLSpectrumBuilder::new. The parser instance allows for iterating over Spectrum in the file, and random access via index or reference id. For random access via scan start time, construct an instance of the parser with the scan start time flag on. See com.digitalproteomics.parsers.mzml.cli.Example, for a working example.

Spectrum and SpectrumHeader are provided by default in the com.digitalproteomics.parsers.mzml.model package, and corresponding builders for Spectrum and SpectrumHeader are found in com.digitalproteomics.parsers.mzml.builders. You can implement your own handlers by implementing MzMLStAXParser.FromXMLStreamBuilder, which passes over each XMLStream event within a spectrum tag, and will build an object of your choosen type T.

Benchmarks

Running a single thread on Ubuntu 16.04 system with an Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz and 32 GB of RAM.

Datasets tested on indexedMzML files generated by msconvert:

The benchmarks were ran against jmzml 1.7.8, and pymzml 0.7.8 on the same desktop.

	Code	UPS1_50000amol_R3.mzML time (Minutes:Seconds)	UPS1_50000amol_R3.mzML max memory (Kb)	small.pwiz.1.1.mzML time (Minutes:Seconds)
mzmlparser (SpectrumHeader only)	java	0:04.64, 0:04.68, 0:04.59, 0:04.59, 0:04.76	266784, 249424, 239664, 267432, 254616	0:00.47, 0:00.44, 0:00.44, 0:00.54, 0:00.52
mzmlparser (Spectrum)	java	0:17.81, 0:17.82, 0:18.39, 0:17.99, 0:17.77	3535408, 3553576, 3544656, 3533604, 3535884	0:00.57, 0:00.51, 0:00.58, 0:00.59, 0:00.55
pymzml	python	0:35.68, 0:35.53, 0:35.83, 0:35.64, 0:35.09	146060, 146612, 146192, 145952, 145916	0:01.15, 0:01.05, 0:00.88, 0:01.04, 0:01.04
jmzml	java	1:45.10, 1:43.87, 1:45.38, 1:44.03, 1:41.48	5851512, 6095684, 5644776, 5635264, 5836852	0:01.44, 0:01.39, 0:01.48, 0:01.63, 0:01.54

	Code	UPS1_50000amol_R3.mzML time (Minutes:Seconds) of 10000 random indices	UPS1_50000amol_R3.mzML max memory (Kb) of 10000 random indices	UPS1_50000amol_R3.mzML time (Minutes:Seconds) of 5000 random indices
mzmlparser (SpectrumHeader only)	java	0:02.35, 0:02.57, 0:02.31, 0:02.34, 0:02.48	392392, 385660, 383504, 388208, 386984	0:01.66, 0:01.57, 0:01.51, 0:01.58, 0:01.57
mzmlparser (Spectrum)	java	0:05.50, 0:05.68, 0:05.46, 0:05.37, 0:05.33	1379292, 1381508, 1388480, 1389672, 1386696	0:03.20, 0:03.02, 0:03.16, 0:03.09, 0:03.19
pymzml	python	0:06.60, 0:06.73, 0:06.57, 0:06.69, 0:06.67	99792, 99480, 99416, 99392, 99740	0:04.01, 0:03.90, 0:03.82, 0:03.96, 0:03.93
jmzml	java	1:22.41, 1:23.47, 1:23.18, 1:21.68, 1:23.05	3032636, 3029300, 3029692, 3028772, 3032184	1:18.57, 1:19.36, 1:16.57, 1:18.97, 1:23.21

Note, these will be installed automatically if you are using Maven.

To use this library, add the following to your pom.xml file.

<dependency>
  <groupId>com.digitalproteomics</groupId>
  <artifactId>dp-mzml</artifactId>
  <version>1.1.0-RELEASE</version>
</dependency>

Apache License 2.0