ArticleJournal of the American Society for Mass Spectrometry2009
Optimized Orbitrap HCD for quantitative analysis of phosphopeptides.
Article in Journal of the American Society for Mass Spectrometry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Revisiting resonance-excitation collision-induced dissociation for data-independent acquisition.bioRxiv : the preprint server for biology · 2026Article
- Leveraging HILIC/ERLIC separations for online nanoscale LC-MS/MS analysis of phosphopeptide isoforms from RNA polymerase II C-terminal domain.Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2025Article
- Optimization of Higher-Energy Collisional Dissociation Fragmentation Energy for Intact Protein-Level Tandem Mass Tag Labeling.Journal of proteome research · 2023Article
- Multimodal Tandem Mass Spectrometry Techniques for the Analysis of Phosphopeptides.Journal of the American Society for Mass Spectrometry · 2022Article
- Article
- Tailoring to Search Engines: Bottom-Up Proteomics with Collision Energies Optimized for Identification Confidence.Journal of proteome research · 2021Article
- In vitro analysis of RNA polymerase II elongation complex dynamics.Genes & development · 2019Article
- High Sensitivity Quantitative Proteomics Using Automated Multidimensional Nano-flow Chromatography and Accumulated Ion Monitoring on Quadrupole-Orbitrap-Linear Ion Trap Mass Spectrometer.Molecular & cellular proteomics : MCP · 2017Article
- Mechanistic analysis of a copper-catalyzed C-H oxidative cyclization of carboxylic acids.Chemical science · 2017Article
- A calibration routine for efficient ETD in large-scale proteomics.Journal of the American Society for Mass Spectrometry · 2015Article
- Complementary IMAC enrichment methods for HLA-associated phosphopeptide identification by mass spectrometry.Nature protocols · 2015Article
- Multiplexed peptide analysis using data-independent acquisition and Skyline.Nature protocols · 2015Article
- Protected amine labels: a versatile molecular scaffold for multiplexed nominal mass and sub-Da isotopologue quantitative proteomic reagents.Journal of the American Society for Mass Spectrometry · 2014Article
- Quantification of competing H3PO4 versus HPO3 + H2O neutral losses from regioselective 18O-labeled phosphopeptides.Journal of the American Society for Mass Spectrometry · 2014Article
- Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications.Nature protocols · 2014Article
- Current algorithmic solutions for peptide-based proteomics data generation and identification.Current opinion in biotechnology · 2013Review
- iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.Molecular & cellular proteomics : MCP · 2012Article
- MS(M), an efficient workflow for metabolite identification using hybrid linear ion trap Orbitrap mass spectrometer.Journal of the American Society for Mass Spectrometry · 2012Article
- Structural Characterization of Carbohydrates by Fourier Transform Tandem Mass Spectrometry.Current proteomics · 2011Article
- Online nanoflow multidimensional fractionation for high efficiency phosphopeptide analysis.Molecular & cellular proteomics : MCP · 2011Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite the tremendous commercial success of radio frequency quadrupole ion traps for bottom-up proteomics studies, there is growing evidence that peptides decorated with labile post-translational modifications are less amenable to low-energy, resonate excitation MS/MS analysis. Moreover, multiplexed stable isotope reagents designed for MS/MS-based quantification of peptides rely on accurate and robust detection of low-mass fragments for all precursors. Collectively these observations suggest that beam-type or tandem in-space MS/MS measurements, such as that available on traditional triple quadrupole mass spectrometers, may provide beneficial figures of merit for quantitative proteomics analyses. The recent introduction of a multipole collision cell adjacent to an Orbitrap mass analyzer provides for higher energy collisionally activated dissociation (HCD) with efficient capture of fragment ions over a wide mass range. Here we describe optimization of various instrument and post-acquisition parameters that collectively provide for quantification of iTRAQ-labeled phosphorylated peptides isolated from complex cell lysates. Peptides spanning a concentration dynamic range of 100:1 are readily quantified. Our results indicate that appropriate parameterization of collision energy as a function of precursor m/z and z provides for optimal performance in terms of peptide identification and relative quantification by iTRAQ. Using this approach, we readily identify activated signaling pathways downstream of oncogenic mutants of Flt-3 kinase in a model system of human myeloid leukemia.
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