Improved 6-Plex Tandem Mass Tags Quantification Throughput Using a Linear Ion Trap–High-Energy Collision Induced Dissociation MS^3 Scan
Abstract
The use of tandem mass tags (TMT) as an isobaric labeling strategy is a powerful method for quantitative proteomics, yet its accuracy has traditionally suffered from interference. This interference can be largely overcome by selecting MS^2 fragment precursor ions for high-energy collision induced dissociation (HCD) MS^3 analysis in an Orbitrap scan. While this approach minimizes the interference effect, sensitivity suffers due to the high AGC targets and long acquisition times associated with MS^3 Orbitrap detection. We investigated whether acquiring the MS^3 scan in a linear ion trap with its lower AGC target would increase overall quantification levels with a minimal effect on precision and accuracy. Trypsin-digested proteins from Saccharomyces cerevisiae were tagged with 6-plex TMT reagents. The sample was subjected to replicate analyses using either the Orbitrap or the linear ion trap for the HCD MS^3 scan. HCD MS^3 detection in the linear ion trap vs Orbitrap increased protein identification by 66% with minor loss in precision and accuracy. Thus, the use of a linear ion trap–HCD MS^3 scan during a 6-plex TMT experiment can improve overall identification levels while maintaining the power of multiplexed quantitative analysis.
Additional Information
© 2016 American Chemical Society. Received: March 17, 2016; Accepted: July 5, 2016; Published: July 5, 2016. This work was supported by Pomona College, the Beckman Institute, and the Gordon and Betty Moore Foundation through Grant GBMF775. We thank Tanya Porras-Yakushi for providing yeast whole cell lysates and are grateful to Annie Moradian and Roxana Eggleston-Rangel for their assistance with obtaining the mass spectra. The manuscript was written through contributions of all authors. The authors declare no competing financial interest.Attached Files
Supplemental Material - ac6b01067_si_001.pdf
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Additional details
- Eprint ID
- 70073
- DOI
- 10.1021/acs.analchem.6b01067
- Resolver ID
- CaltechAUTHORS:20160831-123727848
- Pomona College
- Caltech Beckman Institute
- GBMF775
- Gordon and Betty Moore Foundation
- Created
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2016-08-31Created from EPrint's datestamp field
- Updated
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2021-11-11Created from EPrint's last_modified field