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Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry
Published on: April 4, 2018
Isobaric peptide termini labeling utilizing site-specific N-terminal succinylation
Christian J Koehler1, Magnus Ø Arntzen, Margarita Strozynski
1The Biotechnology Centre of Oslo, University of Oslo, Gaustadalleen 21, 0349 Oslo, Norway.
Analytical Chemistry
|May 3, 2011
Summary
This study presents a faster, cost-effective method for protein quantification using isobaric peptide termini labeling (IPTL). The optimized technique and new data analysis algorithm significantly improve protein identification in proteomics research.
Area of Science:
- Proteomics
- Analytical Chemistry
- Biochemistry
Background:
- Quantitative proteomics is crucial for understanding cellular processes.
- Existing methods for protein quantification can be time-consuming and costly.
- Isobaric peptide termini labeling (IPTL) offers a promising approach for multiplexed quantitative proteomics.
Purpose of the Study:
- To develop a rapid and cost-effective procedure for isobaric peptide termini labeling (IPTL).
- To enhance protein quantification accuracy and scope using a novel data analysis algorithm.
- To apply the optimized IPTL method to investigate proteome changes in apoptotic HeLa cells.
Main Methods:
- Developed a one-pot, 15-minute two-step chemical modification for peptide termini labeling.
- Utilized succinic anhydride for N-terminal modification and dimethylation for lysine derivatization.
- Implemented the 'force-find' algorithm within IsobariQ software for improved peak matching in MS/MS spectra.
Main Results:
- Achieved a >50% increase in quantified proteins compared to standard analysis using the 'force-find' algorithm.
- Identified over 50 differentially expressed proteins in HeLa cells undergoing STLC-induced apoptosis.
- Demonstrated coelution of isotopic labels during LC and unaffected quantification linearity in complex backgrounds.
Conclusions:
- The optimized IPTL procedure combined with the IsobariQ software and 'force-find' algorithm provides a straightforward and rapid quantitative proteomics approach.
- This method significantly enhances protein identification and quantification capabilities.
- The approach is suitable for analyzing complex biological samples and identifying quantitative proteome changes.
