ArticleJournal of biomolecular techniques : JBT2013
Optimization of data-dependent acquisition parameters for coupling high-speed separations with LC-MS/MS for protein identifications.
Article in Journal of biomolecular techniques : JBT, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Immunogenic peptides putatively from intratumor microbes: Opportunities for colorectal cancer treatment.iScience · 2024Article
- Proteomics for Microalgae Extracts by High-Resolution Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Eight key rules for successful data-dependent acquisition in mass spectrometry-based metabolomics.Mass spectrometry reviews · 2023Review
- Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS).Biomolecules · 2021Review
- Data-Independent Acquisition for the Quantification and Identification of Metabolites in Plasma.Metabolites · 2020Article
- ESTIMATION AND INFERENCE IN METABOLOMICS WITH NON-RANDOM MISSING DATA AND LATENT FACTORS.The annals of applied statistics · 2020Article
- Aconitase Functions as a Pleiotropic Posttranscriptional Regulator in Helicobacter pylori.Journal of bacteriology · 2015Article
- On an aerodynamic mechanism to enhance ion transmission and sensitivity of FAIMS for nano-electrospray ionization-mass spectrometry.Journal of the American Society for Mass Spectrometry · 2014Article
- The use of ammonium formate as a mobile-phase modifier for LC-MS/MS analysis of tryptic digests.Journal of biomolecular techniques : JBT · 2013Article
- Superficially porous silica particles with wide pores for biomacromolecular separations.Journal of chromatography. A · 2012Article
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Authors and funding
5 authors.
Funding
Abstract
Recent developments in chromatography, such as ultra-HPLC and superficially porous particles, offer significantly improved peptide separation. The narrow peak widths, often only several seconds, can permit a 15-min liquid chromatography run to have a similar peak capacity as a 60-min run using traditional HPLC approaches. In theory, these larger peak capacities should provide higher protein coverage and/or more protein identifications when incorporated into a proteomic workflow. We initially observed a decrease in protein coverage when implementing these faster chromatographic approaches, due to data-dependent acquisition (DDA) settings that were not properly set to match the narrow peak widths resulting from newly implemented, fast separation techniques. Oversampling of high-intensity peptides lead to low protein-sequence coverage, and tandem mass spectra (MS/MS) from lower-intensity peptides were of poor quality, as automated MS/MS events were occurring late on chromatographic peaks. These observations led us to optimize DDA settings to use these fast separations. Optimized DDA settings were applied to the analysis of Trypanosome brucei peptides, yielding peptide identifications at a rate almost five times faster than previously used methodologies. The described approach significantly improves protein identification workflows that use typical available instrumentation.
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