ArticleJournal of the American Society for Mass Spectrometry2013
Factorial experimental designs elucidate significant variables affecting data acquisition on a quadrupole Orbitrap mass spectrometer.
Article in Journal of the American Society for Mass Spectrometry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Factorial-Design-Based Optimization of a Commercial MALDI-2 timsTOF Mass Spectrometer for Lipid Analysis.Journal of the American Society for Mass Spectrometry · 2025Article
- Definitive Screening Designs to Optimize Library-Free DIA-MS Identification and Quantification of Neuropeptides.Journal of proteome research · 2023Article
- Boost-DiLeu: Enhanced IsobaricAnalytical chemistry · 2022Article
- Multiplexed quantitative neuropeptidomics via DiLeu isobaric tagging.Methods in enzymology · 2022Article
- Mass Spectrometric Profiling of Neuropeptides in Response to Copper Toxicity via Isobaric Tagging.Chemical research in toxicology · 2021Article
- Accelerating Lipidomic Method Development throughAnalytical chemistry · 2019Article
- Optimization of mass spectrometric parameters improve the identification performance of capillary zone electrophoresis for single-shot bottom-up proteomics analysis.Analytica chimica acta · 2018Article
- The PeptideAtlas of the Domestic Laying Hen.Journal of proteome research · 2017Article
- Optimizing Mass Spectrometry Analyses: A Tailored Review on the Utility of Design of Experiments.Journal of the American Society for Mass Spectrometry · 2016Review
- Global Proteomic Analysis of Functional Compartments in Immature Avian Follicles Using Laser Microdissection Coupled to LC-MS/MS.Journal of proteome research · 2015Article
- Definitive Screening Design Optimization of Mass Spectrometry Parameters for Sensitive Comparison of Filter and Solid Phase Extraction Purified, INLIGHT Plasma N-Glycans.Analytical chemistry · 2015Article
- Multiplexed peptide analysis using data-independent acquisition and Skyline.Nature protocols · 2015Article
- Comprehensive lipidome analysis by shotgun lipidomics on a hybrid quadrupole-orbitrap-linear ion trap mass spectrometer.Journal of the American Society for Mass Spectrometry · 2015Article
- Article
- The Q Exactive HF, a Benchtop mass spectrometer with a pre-filter, high-performance quadrupole and an ultra-high-field Orbitrap analyzer.Molecular & cellular proteomics : MCP · 2014Article
- Accurate identification of deamidated peptides in global proteomics using a quadrupole orbitrap mass spectrometer.Journal of proteome research · 2014Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Instrument parameter values for a quadrupole Orbitrap mass spectrometer were optimized for performing global proteomic analyses. Fourteen factors were evaluated for their influence on data-dependent acquisition with an emphasis on both the rate of sequencing and spectral quality by maximizing two individually tested response variables (unique peptides and protein groups). Of the 14 factors, 12 factors were assigned significant contrast values (P < 0.05) for both response variables. Fundamentally, when optimizing parameters, a balance between spectral quality and duty cycle needs to be reached in order to maximize proteome coverage. This is especially true when using a data-dependent approach for sequencing complex proteomes. For example, maximum ion injection time, automatic gain control settings, and minimum threshold settings for triggering MS/MS isolation and activation all heavily influence ion signal, the number of spectra collected, and spectral quality. To better assess the effect these parameters have on data acquisition, all MS/MS data were parsed according to ion abundance by calculating the percent of the AGC target reached for each MS/MS event and then compared with successful peptide-spectrum matches. This proved to be an effective approach for understanding the effect of ion abundance on successful peptide-spectrum matches and establishing minimum ion abundance thresholds for triggering MS/MS isolation and activation.
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Registered trials
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