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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
Published on: November 15, 2017
Segmentation of precursor mass range using "tiling" approach increases peptide identifications for MS1-based
Catherine E Vincent1, Gregory K Potts, Arne Ulbrich
1Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States.
Analytical Chemistry
|January 29, 2013
Summary
This study introduces a novel "binning" or "tiling" method for mass spectrometry-based protein quantification. This approach enhances proteome coverage and identifies more proteins without extra time or sample prep.
Area of Science:
- Proteomics
- Analytical Chemistry
- Biochemistry
Background:
- Label-free quantification (LFQ) using mass spectrometry is crucial for measuring protein abundance.
- Optimizing MS(1)-based methods requires balancing survey scans, fragmentation spectra, and extracted ion chromatograms (XIC) for maximum identification.
- Current methods face limitations in proteome coverage depth without increased instrument time or sample prefractionation.
Purpose of the Study:
- To present a novel method for increasing proteome coverage in label-free quantification experiments.
- To enhance the depth of quantifiable protein identifications without additional instrument time or sample prefractionation.
- To enable comprehensive label-free quantification across the full MS(1) mass range.
Main Methods:
- A new strategy termed "binning" or "tiling" was developed for MS(1)-based label-free quantification.
- Precursor selection was restricted to a fraction of the full MS(1) mass range for each replicate.
- Collectively, the m/z segments of all replicates covered the entire MS(1) mass range, obtaining full MS(1) spectra throughout.
Main Results:
- The "binning" or "tiling" method significantly increased the number of quantifiable yeast peptides by 31% and proteins by 52% compared to standard data-dependent experiments.
- This approach achieved greater proteome coverage without requiring additional instrument time or sample prefractionation.
- Full MS(1) chromatograms were obtainable across the entire mass range, facilitating label-free quantification for any peptide.
Conclusions:
- The proposed "binning" or "tiling" method is an effective strategy to enhance proteome coverage in label-free quantification.
- This technique offers a significant improvement in identifying quantifiable proteins and peptides, particularly in complex samples like yeast proteomes.
- The method provides a valuable advancement for mass spectrometry-based proteomics, enabling deeper insights into protein abundance.
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