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Tandem Mass Spectrometry01:21

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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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This lesson details the instrumentation of a mass spectrometer—a physical instrument to perform mass spectrometry on analyte molecules and record the characteristic mass spectra. This is achieved via three chief functions:
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The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
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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...
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Updated: Jan 12, 2026

Sample Preparation for Mass-spectrometry-based Proteomics Analysis of Ocular Microvessels
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OpenSpec Enables Detecting Unexpected Modifications from Proteomics Data Generated by Orbitrap Astral Mass

Min Tang1, Zhao Sun2,3, Chengpin Shen4

  • 1School of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing 100191, China.

Analytical Chemistry
|November 3, 2025
PubMed
Summary

OpenSpec is a new computational workflow for identifying novel, unexpected modifications in proteomics data from Orbitrap Astral mass spectrometers. This method enhances shotgun proteomics by enabling comprehensive analysis of complex biological and chemical systems.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Computational Biology

Background:

  • Orbitrap Astral mass spectrometers offer high-performance data-independent acquisition (DIA) for deep proteomic profiling.
  • Existing search engines struggle to identify novel, unexpected post-translational modifications (PTMs) in complex biological systems using this data.

Purpose of the Study:

  • To develop a computational workflow, OpenSpec, for comprehensive identification of unexpected modifications in Orbitrap Astral DIA datasets.
  • To enable advanced open search strategies on DIA data, overcoming limitations of current search engines.

Main Methods:

  • Developed OpenSpec, a workflow utilizing a Transformer-based model for precursor-fragment grouping.
  • Deconvoluted DIA data into DDA-like pseudo-MS/MS spectra for open searching.
  • Benchmarked OpenSpec using synthetic peptides and compared DIA vs. DDA acquisition modes.

Main Results:

  • OpenSpec successfully identified unexpected modifications, including those on cysteine residues, across various sample pretreatments.
  • The workflow demonstrated effective deconvolution of DIA data for open search analysis.
  • Benchmarking confirmed the capability to detect diverse modification patterns.

Conclusions:

  • OpenSpec provides a robust solution for comprehensive identification of unexpected modifications in Orbitrap Astral DIA proteomics data.
  • This advancement expands the scope of proteomic analysis, facilitating the discovery of novel biological and chemical insights.
  • The workflow is publicly available, promoting further research in the field.