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Sample Preparation for Analysis: Advanced Techniques01:08

Sample Preparation for Analysis: Advanced Techniques

Accurate analysis of complex samples often requires advanced preparation techniques to achieve reliable and reproducible results. Samples containing inorganic or organic materials can be challenging to dissolve or decompose effectively. Standard sample preparation methods include acid digestion, fusion, dry ashing, and wet digestion.
Acid digestion with strong acids is commonly used to dissolve inorganic materials that are insoluble (do not dissolve) in water. This method can be useful for...

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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite.

Evgeniy V Petrotchenko1, Christoph H Borchers

  • 1University of Victoria Genome British Columbia Protein Centre, Department of Biochemistry & Microbiology, University of Victoria, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC, Canada.

BMC Bioinformatics
|January 30, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a software suite for analyzing mass spectrometry data from isotopically-coded cleavable crosslinkers. The tool enhances automated, high-accuracy identification of peptide crosslinks in protein complex studies.

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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Quantitative Detection of DNA-Protein Crosslinks and Their Post-Translational Modifications

Published on: April 21, 2023

Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Protein crosslinking coupled with mass spectrometry (MS) is crucial for studying protein structures and interactions.
  • Isotopically-coded, cleavable crosslinking reagents offer analytical advantages for MS-based protein analysis.
  • These reagents facilitate distinguishing crosslinked peptides and increase identification confidence.

Purpose of the Study:

  • To develop and describe a software suite for analyzing mass spectrometry data generated using isotopically-coded cleavable crosslinkers.
  • To provide a computational tool for enhancing the accuracy and automation of crosslink identification.

Main Methods:

  • Development of a three-program software suite: DX, DXDX, and DXMSMS.
  • DX program: Detects ion signal doublets from light and heavy isotopic forms of the crosslinker.
  • DXDX program: Identifies mass matches between cleaved and uncleaved crosslinks based on cleavage chemistry.
  • DXMSMS program: Assigns crosslinks to protein sequences using MS/MS fragmentation data.

Main Results:

  • The software suite is designed for analyzing mass spectrometry data from isotopically-coded cleavable crosslinkers.
  • Individual programs (DX, DXDX, DXMSMS) perform specific tasks in the crosslink identification workflow.
  • The combined suite enables automated identification of crosslinks.

Conclusions:

  • The integrated software suite offers a powerful tool for automated, high-accuracy peptide crosslink identification.
  • The programs are specifically tailored to the analytical features of isotopically-coded cleavable crosslinking reagents.
  • This approach enhances confidence and efficiency in studying protein complexes via crosslinking mass spectrometry.