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Related Concept Videos

Tandem Mass Spectrometry01:21

Tandem 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...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide 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...
Mass Spectrometry: Complex Analysis01:21

Mass 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...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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MALDI-TOF Mass Spectrometry01:19

MALDI-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...
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Mass Spectrometry: Overview

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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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Instrument-Software Synergy in Proteomics: Systematic Evaluation across Mass Spectrometry Platforms, Search Engines,

Sander Heyndrickx1,2, Robbin Bouwmeester1,2, Arthur Declercq1,2

  • 1CompOmics, VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9000, Belgium.

Journal of Proteome Research
|July 14, 2026
PubMed
Summary

Proteomics advancements in mass spectrometry instruments and software work together synergistically. Machine learning software improves data analysis, but deeper proteome coverage may reduce quantification accuracy.

Keywords:
data analysisevaluationinstrumentsmachine learningmass spectrometrypeptide identificationpeptide quantificationproteomics

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Published on: April 11, 2019

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Mass spectrometry-based proteomics has seen parallel advancements in instrumentation and software.
  • The synergistic effects or diminishing returns of these co-evolving technologies remain unclear.

Purpose of the Study:

  • To systematically evaluate the coevolution of mass spectrometry instrumentation and data analysis software.
  • To understand the synergistic interactions between instrument improvements and software algorithms over time.

Main Methods:

  • Evaluated 72 instrument-software combinations across eight mass spectrometry platforms and three generations of search engines (2004-2024).
  • Assessed the impact of machine learning-based rescoring on identifying low-intensity precursors and challenging spectra.

Main Results:

  • Instrumentation and software improvements demonstrate synergistic, not substitutive, benefits.
  • Machine learning rescoring effectively identifies peptides from noisy spectra, especially from modern instruments with increased sensitivity.
  • Expanded proteome coverage through enhanced detection depth introduces higher quantification error for low-abundance peptides.

Conclusions:

  • Instrument and software advances have jointly shaped proteomics performance over two decades.
  • A fundamental trade-off exists between proteome coverage and quantification accuracy.
  • Machine learning plays a crucial role in maximizing proteome coverage with advanced mass spectrometry.