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Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

Infrared multiphoton dissociation for quantitative shotgun proteomics.

Aaron R Ledvina¹, M Violet Lee, Graeme C McAlister

¹Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States.

Analytical Chemistry

|April 7, 2012

Summary

Infrared multiphoton dissociation (IRMPD) in a dual-cell ion trap enhances peptide identification. This method outperforms collisional-activated dissociation for complex peptide mixtures and isobaric-tagged peptides.

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Published on: November 15, 2017

Area of Science:

Analytical Chemistry
Mass Spectrometry
Proteomics

Background:

Linear ion traps are widely used for peptide analysis.
Collisional-activated dissociation (CAD) is a common fragmentation technique.
Optimizing fragmentation methods is crucial for large-scale proteomics.

Purpose of the Study:

To adapt and evaluate infrared multiphoton dissociation (IRMPD) in a dual-cell linear ion trap (QLT) for peptide analysis.
To compare the performance of IRMPD with CAD for complex peptide mixtures.
To assess the compatibility of IRMPD with isobaric-tagged peptides for quantitative proteomics.

Main Methods:

Modification of a dual-cell QLT mass spectrometer to incorporate IRMPD.
Optimization of IRMPD parameters including precursor q-value, irradiation time, and photon flux.
Analysis of yeast tryptic digests and isobaric-tagged peptides using both IRMPD and CAD.

Main Results:

Optimized IRMPD significantly outperformed CAD for peptide identification at a 1% false-discovery rate.
IRMPD demonstrated compatibility with isobaric-tagged peptides, enabling simultaneous identification and quantitation.
Variable IRMPD irradiation times were required for consistent results with isobaric-tagged peptides due to fixed QLT rf amplitude.

Conclusions:

IRMPD in a dual-cell ion trap is an effective technique for large-scale peptide analysis.
This method offers advantages over CAD for both unmodified and isobaric-tagged peptides.
The study highlights the potential of IRMPD for advancing quantitative proteomics.