Mass-Up Configuration File

Here we describe in detail the Mass-Up Configuration File so that you can create your own .muc files to import datasets into Mass-Up.

	<?xml version="1.0" encoding="UTF-8"?>
	
	<!-- Dataset definition indicating whether it is labeled or not and the data type: RAW Spectra, Peak lists or Aligned peak lists --!>
	<massupdatasetloader labeled="true" type="RAW Spectra">
	
	  <!-- Absolute paths to data files --!>
	  <files>
	    <file>D:\Mass-Up-Data\sample1_replicate1.csv</file>
	    <file>D:\Mass-Up-Data\sample1_replicate2.csv</file>
	    <file>D:\Mass-Up-Data\sample1_replicate3.csv</file>
	    <file>D:\Mass-Up-Data\sample2_replicate1.csv</file>
	    <file>D:\Mass-Up-Data\sample2_replicate2.csv</file>
	    <file>D:\Mass-Up-Data\sample2_replicate3.csv</file>
	    <file>D:\Mass-Up-Data\sample3_replicate1.csv</file>
	    <file>D:\Mass-Up-Data\sample3_replicate2.csv</file>
	    <file>D:\Mass-Up-Data\sample3_replicate3.csv</file>
	    <file>D:\Mass-Up-Data\sample4_replicate1.csv</file>
	    <file>D:\Mass-Up-Data\sample4_replicate2.csv</file>
	    <file>D:\Mass-Up-Data\sample4_replicate3.csv</file>
	  </files>
	  
	  <!-- Names of samples in dataset --!>	  
	  <samplenames>
	    <samplename>sample1</samplename>
	    <samplename>sample2</samplename>
	    <samplename>sample3</samplename>
	    <samplename>sample4</samplename>
	  </samplenames>
	  
	  <!-- Names of classes (labels) in dataset --!>	  
	  <classes>
	    <class>A</class>
	    <class>B</class>
	  </classes>
	  
	  <!-- Mappings of files to samples --!>	  
	  <filesamplemappings>
	    <mapping>0</mapping>
	    <mapping>0</mapping>
	    <mapping>0</mapping>
	    <mapping>1</mapping>
	    <mapping>1</mapping>
	    <mapping>1</mapping>
	    <mapping>2</mapping>
	    <mapping>2</mapping>
	    <mapping>2</mapping>
	    <mapping>3</mapping>
	    <mapping>3</mapping>
	    <mapping>3</mapping>
	  </filesamplemappings>
	  
	  <!-- Mappings of samples to classes --!>	  
	  <sampleclassmappings>
	    <mapping>0</mapping>
	    <mapping>0</mapping>
	    <mapping>1</mapping>
	    <mapping>1</mapping>
	  </sampleclassmappings>
	</massupdatasetloader>

The file above corresponds to a .muc file with:

• <files>: twelve RAW spectra files in .csv format.
• <samplenames>: four samples (sample1, sample2, sample3 and sample4).
• <classes>: two classes (A, B).

Each file must be mapped to a sample and each sample must be mapped to a class, using <filesamplemappings> and <sampleclassmappings> respectively. The following image illustrates this mapping.

Labeled and unlabeled experiments

The file format defined corresponds to a labeled experiment. If your experiment is unlabeled and there are no classes, just omit <classes> and <sampleclassmappings> blocks.