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Optimizing Accuracy and Depth of Protein Quantification in Experiments Using Isobaric Carriers.

Harrison Specht1,2, Nikolai Slavov1,2,3

  • 1Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States.

Journal of Proteome Research
|November 16, 2020
PubMed
Summary

Isobaric carriers improve peptide identification in mass spectrometry for small samples like single cells. Optimizing carrier amounts and parameters balances trade-offs for applications in proteomics and single-cell analysis.

Keywords:
benchmarkingdata reliabilityisobaric carrieroptimizing mass spectrometry analysisquantification accuracysingle-cell proteomics

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Single-Cell Analysis

Background:

  • The isobaric carrier approach is vital for ultrasensitive mass spectrometry of minute biological samples.
  • Its application is expanding, particularly in single-cell analysis.

Purpose of the Study:

  • To systematically characterize the trade-offs associated with using isobaric carriers.
  • To provide guidelines for optimizing experimental design and data analysis in mass spectrometry.

Main Methods:

  • Controlled experiments using complex human proteomes.
  • Analysis of peptide sequence identification and protein quantification.
  • Evaluation of parameters like isobaric carrier amount and ion accumulation time.

Main Results:

  • Isobaric carriers enhance peptide identification without increasing sampled protein copies from small samples.
  • Optimization strategies exist for balancing quantification accuracy and the number of identified proteins.
  • Reliability estimation for protein quantification is crucial for downstream analyses.

Conclusions:

  • Characterized trade-offs enable tailored isobaric carrier experiments for diverse applications.
  • Guidelines facilitate experimental design and transparent error propagation in data analysis.
  • This work supports applications from limited biopsies to single-cell atlases and network modeling.