ArticleJournal of the American Society for Mass Spectrometry2011
Improving proteome coverage on a LTQ-Orbitrap using design of experiments.
Article in Journal of the American Society for Mass Spectrometry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 63 citations in OpenAlex.
- A planar quadrupole device for transmitting and trapping ions in high vacuum.Rapid communications in mass spectrometry : RCM · 2023Article
- Establishing Quality Control Procedures for Large-Scale Plasma Proteomics Analyses.Journal of the American Society for Mass Spectrometry · 2023Article
- Definitive Screening Designs to Optimize Library-Free DIA-MS Identification and Quantification of Neuropeptides.Journal of proteome research · 2023Article
- Discovery Proteomics and Absolute Protein Quantification Can Be Performed Simultaneously on an Orbitrap-Based Mass Spectrometer.ACS omega · 2023Article
- Non-target molecular network and putative genes of flavonoid biosynthesis inFrontiers in plant science · 2022Article
- Multiplexed quantitative neuropeptidomics via DiLeu isobaric tagging.Methods in enzymology · 2022Article
- Developing mass spectrometry for the quantitative analysis of neuropeptides.Expert review of proteomics · 2021Review
- Identification, characterization and control of a sequence variant in monoclonal antibody drug product: a case study.Scientific reports · 2021Article
- Mass Spectrometric Profiling of Neuropeptides in Response to Copper Toxicity via Isobaric Tagging.Chemical research in toxicology · 2021Article
- Deducing the presence of proteins and proteoforms in quantitative proteomics.Nature communications · 2018Article
- Optimization of mass spectrometric parameters improve the identification performance of capillary zone electrophoresis for single-shot bottom-up proteomics analysis.Analytica chimica acta · 2018Article
- Expanding Lipidome Coverage Using LC-MS/MS Data-Dependent Acquisition with Automated Exclusion List Generation.Journal of the American Society for Mass Spectrometry · 2017Article
- Improved Quantitative Plant Proteomics via the Combination of Targeted and Untargeted Data Acquisition.Frontiers in plant science · 2017Article
- Optimizing Mass Spectrometry Analyses: A Tailored Review on the Utility of Design of Experiments.Journal of the American Society for Mass Spectrometry · 2016Review
- Shotgun Proteomics of Tomato Fruits: Evaluation, Optimization and Validation of Sample Preparation Methods and Mass Spectrometric Parameters.Frontiers in plant science · 2016Article
- Performance comparisons of nano-LC systems, electrospray sources and LC-MS-MS platforms.Journal of chromatographic science · 2014Article
- Factorial experimental designs elucidate significant variables affecting data acquisition on a quadrupole Orbitrap mass spectrometer.Journal of the American Society for Mass Spectrometry · 2013Article
- A tool to evaluate correspondence between extraction ion chromatographic peaks and peptide-spectrum matches in shotgun proteomics experiments.Proteomics · 2013Article
- Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers.Journal of proteome research · 2013Article
- Optimization of data-dependent acquisition parameters for coupling high-speed separations with LC-MS/MS for protein identifications.Journal of biomolecular techniques : JBT · 2013Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Design of experiments (DOE) was used to determine improved settings for a LTQ-Orbitrap XL to maximize proteome coverage of Saccharomyces cerevisiae. A total of nine instrument parameters were evaluated with the best values affording an increase of approximately 60% in proteome coverage. Utilizing JMP software, 2 DOE screening design tables were generated and used to specify parameter values for instrument methods. DOE 1, a fractional factorial design, required 32 methods fully resolving the investigation of six instrument parameters involving only half the time necessary for a full factorial design of the same resolution. It was advantageous to complete a full factorial design for the analysis of three additional instrument parameters. Measured with a maximum of 1% false discovery rate, protein groups, unique peptides, and spectral counts gauged instrument performance. Randomized triplicate nanoLC-LTQ-Orbitrap XL MS/MS analysis of the S. cerevisiae digest demonstrated that the following five parameters significantly influenced proteome coverage of the sample: (1) maximum ion trap ionization time; (2) monoisotopic precursor selection; (3) number of MS/MS events; (4) capillary temperature; and (5) tube lens voltage. Minimal influence on the proteome coverage was observed for the remaining four parameters (dynamic exclusion duration, resolving power, minimum count threshold to trigger a MS/MS event, and normalized collision energy). The DOE approach represents a time- and cost-effective method for empirically optimizing MS-based proteomics workflows including sample preparation, LC conditions, and multiple instrument platforms.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.