Usage And Examples
- Introduction
- How to parse the peptide hits
- Running the SpectrumViewer graphical user interface (GUI)
- Using MascotDatfile as a Maven dependency
- Example code
Introduction
This library was developed as a tool for the large scale analysis of all data inside one or more complex Mascot MS/MS datfiles for a variety of purposes.
The main functionality consists of retrieving a Mascot datfile from multiple sources (a harddisk, database or MascotServer URL) and transforming into a functional object model.
A MascotDatfile instance captures all the data from PeptideHits and Queries into easy accessible objects. Standard methods are integrated into the objects to analyse small details like:
- threshold calculation of an MS/MS spectrum versus ionscore of a peptide identification
- sequence coverage of a peptide identification in a MS/MS spectrum
- processing of modified aminoacid residues on peptide identifications
- processing of MS/MS spectra
- etc ..
In summary, this library makes the raw data inside Mascot datfiles easily accessible for research purposes.
The library was written by Kenny Helsens (kenny.helsens@UGent.be) and you can contact the author for any questions concerning this library.
Also feel free to contact the developers if you have suggestions/enhancements/comments to library.
How to parse the peptide hits
com.compomics.mascotdatfile.research.script.PeptideHitParser
Print usage by running the JAR without parameters
$ java -jar mascotdatfile-X.Y.Z.jar
SimpleParser arguments: <alpha> <output> <input 1> [<input 2> <input 3> ... <input n>]
Input Structure:
<alpha> alpha=0.05 reports peptide hits above 95% probability threshold
<output> output file
<input> one or more MascotDatfile input files
Output structure:
<MascotDatfile> <query number> <spectrum title> <charge state> <peptide> <peptide+PTM> <ionscore> <rank>
Example usage
$ java -jar mascotdatfile-X.Y.Z.jar 0.05 /tmp/test_peptidehitparser.txt /tmp/mascot/results/directory/F004071.dat
Processing /tmp/mascot/results/directory/F004071.dat
Successfully parsed 77 PSMs from 56 (1000) Queries above alpha 0.05
Example output
F004071.dat;3;51008_1.6.1mox_9087_210.mgf;3+;PAQEVYR;Ace-PAQ<Dam>EVYR-COOH;6.66;1;
F004071.dat;3;51008_1.6.1mox_9087_210.mgf;3+;PAQEVYR;PAQEVYR-COOH;6.66;2;
Note
If you want to include -ALL- the PeptideHits, then set alpha to ‘100000000’ which will produce a negative confidence threshold. As the IonScore is by definition positive, all PeptideHits will be included.
Running the SpectrumViewer graphical user interface (GUI)
$ java -cp mascotdatfile-X.Y.Z.jar com.compomics.mascotdatfile.research.tool.spectrumviewer.spectrumviewer_gui.Spectrumviewer_gui
Using MascotDatfile as a Maven dependency
MascotDatfile is hosted at our public maven repository.
Add the following code into your pom.xml file:
Repository
<repositories>
<!-- Compomics Genesis Maven 2 repository -->
<repository>
<id>genesis-maven2-repository</id>
<name>Genesis maven2 repository</name>
<url>http://genesis.UGent.be/maven2</url>
<layout>default</layout>
</repository>
<!-- old EBI repository -->
<repository>
<id>ebi-repo</id>
<name>The EBI internal repository</name>
<url>http://www.ebi.ac.uk/~maven/m2repo</url>
</repository>
<!-- EBI repository -->
<repository>
<id>pst-release</id>
<name>EBI Nexus Repository</name>
<url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
</repository>
</repositories>
Dependency
<dependencies>
<dependency>
<groupId>com.compomics</groupId>
<artifactId>mascotdatfile</artifactId>
<version>X.Y.Z</version>
<type>jar</type>
</dependency>
</dependencies>
Update the version number (X.Y.Z) to latest released version.
Note that the repository can be manually accessed to download the src or javadocs.
Example code
public class ExampleWiki1 {
public ExampleWiki1(String aFileName) {
String file = aFileName;
// Define the separator
char separator = ',';
// Ready to go!
MascotDatfileInf iMascotDatfile = null;
// log the status.
System.out.println("Processing " + file);
// Create a new MascotDatfile instance for each filename in the Input array.
iMascotDatfile = MascotDatfileFactory.create(file, MascotDatfileType.MEMORY);
// Fetch the QueryToPeptideMap. This indexes all queries.
// From 1 to n number of spectra in the corresponding datfile.
QueryToPeptideMapInf lQueryToPeptideMap = iMascotDatfile.getQueryToPeptideMap();
// Also explore other methods on the QueryToPeptideMap!!!
ArrayList list = null;
// This Vector retrieves the best PeptideHit for each Query.
// The Vector is zero based.
// ex: Vector[0] contains the peptidehit of Query 1, etc.
Vector lBestPeptideHits = lQueryToPeptideMap.getAllPeptideHitsAboveIdentityThreshold();
// A - Iterate over all ProteinIDs
Iterator iter = iMascotDatfile.getProteinMap().getProteinIDIterator();
ProteinID lProteinID = null;
while (iter.hasNext()) {
String item = "";
String lAccession = iter.next().toString();
lProteinID = iMascotDatfile.getProteinMap().getProteinID(lAccession);
// Collect information for current protein.
item = "PROTEIN" + separator
+ lAccession + separator
+ lProteinID.getQueryNumbers().length + separator
+ lProteinID.getDescription();
// Print to system outputstream
System.out.println(item);
}
// B - Iterate over all PeptideHits.
for (int j = 0; j < lBestPeptideHits.size(); j++) {
PeptideHit lPeptideHit = (PeptideHit) lBestPeptideHits.elementAt(j);
// CSV output array.
if (lPeptideHit != null) {
// 1. MS/MS Spectrum filename.
// 2. Modified PeptideSequence
// 3. IonScore
// 4. 95% Identity Threshold
// 5. Number of ProteinHits
// 6a. Protein i accession
// 6b. Protein i description
// etc. for n proteins.
// As a Peptide can come from multiple proteins, it can have multiple proteinhits.
ArrayList lProteins = lPeptideHit.getProteinHits();
for (int k = 0; k < lProteins.size(); k++) {
list = new ArrayList();
ProteinHit lProteinHit = (ProteinHit) lProteins.get(k);
String lAccession = lProteinHit.getAccession();
// The protein description come from another part of the Mascot Result file.
// The ProteinMap also keeps track how many peptides refer to a Protein, mind that protein inference is not regarded at all!
// 6a.
list.add(lAccession);
list.add("PEPTIDE");
// 1.
list.add(((Query) iMascotDatfile.getQueryList().get(j)).getFilename());
// 2.
list.add(lPeptideHit.getModifiedSequence());
// 3.
list.add(lPeptideHit.getIonsScore());
// 4.
list.add(lPeptideHit.calculateIdentityThreshold(0.05));
String lResult = "";
for (Object item : list) {
lResult = lResult + item + separator;
}
System.out.println(lResult);
}
}
}
iMascotDatfile.finish();
}
public static void main(String[] args) {
new ExampleWiki1("/home/myfolder/mydatfile.dat");
}
}