Related Experiment Video
Updated: Jun 16, 2026
10:59
Analysis of SEC-SAXS data via EFA deconvolution and Scatter
Published on: January 28, 2021
XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results.
Thilo Muth1, Marc Vaudel, Harald Barsnes
1Leibniz-Institut für Analytische Wissenschaften - ISAS - eV- Institute for Analytical Sciences, Dortmund, Germany.
Proteomics
|February 9, 2010
Summary
This study introduces XTandem Parser, an open-source Java library for processing X!Tandem mass spectrometry results. It simplifies peptide identification from MS/MS spectra for proteomics research.
Area of Science:
- Proteomics
- Bioinformatics
- Computational Biology
Background:
- Protein identification via mass spectrometry (MS) is vital in proteomics.
- Accurate peptide identification from MS/MS spectra is a critical bottleneck.
Purpose of the Study:
- To develop an open-source Java library for parsing X!Tandem XML output files.
- To create a user-friendly object model for accessing and utilizing proteomics data.
- To provide a graphical user interface for demonstration and visualization.
Main Methods:
- Developed an open-source Java library named XTandem Parser.
- Implemented functionality to parse X!Tandem XML result files.
- Created a graphical user interface (GUI) as a usage example and visualization tool.
Main Results:
- XTandem Parser successfully parses X!Tandem XML files into an accessible object model.
- The provided GUI serves as a practical demonstration and visualization tool for end-users.
- The library facilitates easier downstream analysis of proteomics data.
Conclusions:
- XTandem Parser enhances the accessibility and usability of X!Tandem search engine results.
- The library and GUI support efficient peptide and protein identification in proteomics workflows.
- This open-source tool contributes to the advancement of bioinformatics in mass spectrometry-based proteomics.
Related Concept Videos
01:21Tandem Mass Spectrometry
Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
01:33Peptide Identification Using Tandem Mass Spectrometry
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
01:13Mass Analyzers: Overview
The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
01:19MALDI-TOF Mass Spectrometry
Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
01:21Mass Spectrometry: Complex Analysis
Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
01:24Mass Spectrum: Interpretation
An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...