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Related Concept Videos

Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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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...
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Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass. One common type of ionization, known as electron ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave behind a...
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Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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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...
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Mass Spectrometry: Isotope Effect01:13

Mass Spectrometry: Isotope Effect

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Most elements exist in nature as a mixture of isotopes. The isotopes differ in weight due to their respective number of neutrons. The molecular weight of a molecule is different depending on the specific isotope of its elements involved. As a result, the mass spectrum of the molecule exhibits peaks from the same fragment at multiple positions. The positions of these mass signals depend on the mass differences between isotopes. Furthermore, the intensity of these signals is dependent on the...
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Mass Spectrometry of Amines01:15

Mass Spectrometry of Amines

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In mass spectroscopy, amines undergo fragmentation to give parent ions with odd molecule weights. This observed mass spectrum follows the nitrogen rule; a molecule with an odd number of nitrogen atoms produces a molecular ion with an odd molecular weight. Amines undergo fragmentation through α cleavage, producing nitrogen-containing cations—iminium ions—and alkyl radicals. Mass spectra of aromatic and cyclic aliphatic amines exhibit strong molecular ion peaks, but acyclic...
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Chemical Ionization (CI) Mass Spectrometry01:21

Chemical Ionization (CI) Mass Spectrometry

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The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ionization can lead to the rapid dissociation of some molecular ions before they reach the detector. A milder ionization method is required to increase the lifetime of such ionized analyte molecules. Chemical ionization (CI) is a gas-phase protonation reaction useful for mass-analyzing analyte molecules that are easily protonated to yield the...
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Updated: Feb 8, 2026

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis
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Complete Data Analysis Workflow for Quantitative DIA Mass Spectrometry Using Nextflow.

Mats Perk1, Sami Pietilä1, Tommi Välikangas1

  • 1Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland.

Journal of Proteome Research
|February 6, 2026
PubMed
Summary
This summary is machine-generated.

We developed glaDIAtor-nf, a Nextflow workflow for analyzing complex data-independent acquisition (DIA) mass spectrometry proteomics data. This tool efficiently reanalyzes public datasets, revealing hidden proteome patterns, such as in breast cancer research.

Keywords:
data analysisdata-independent acquisitionmass spectrometrynextflowquantitative proteomics

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Data-independent acquisition (DIA) mass spectrometry offers comprehensive protein profiling but generates large, complex datasets.
  • Analyzing DIA data requires robust computational tools to manage complex pipelines and high-performance computing.

Purpose of the Study:

  • To introduce glaDIAtor-nf, a Nextflow-based workflow for untargeted DIA mass spectrometry proteomics data analysis.
  • To demonstrate the utility of glaDIAtor-nf in reanalyzing public datasets and uncovering previously hidden biological insights.

Main Methods:

  • Development of glaDIAtor-nf using the Nextflow workflow management system.
  • Rigorous technical validation using gold-standard datasets.
  • Application to public breast cancer proteomics data.

Main Results:

  • glaDIAtor-nf demonstrated technical accuracy in analyzing DIA mass spectrometry data.
  • Reanalysis of public breast cancer data using glaDIAtor-nf revealed previously undetected proteome patterns.
  • The study highlights the potential of reanalyzing existing public data with efficient tools.

Conclusions:

  • glaDIAtor-nf provides an efficient and automated solution for large-scale DIA proteomics data analysis.
  • The workflow facilitates the discovery of novel biological insights from public repositories.
  • There is a significant need for user-friendly tools to enable widespread reanalysis of public proteomics data.