ArticleJournal of the American Society for Mass Spectrometry2010
Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer.
Article in Journal of the American Society for Mass Spectrometry, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 28 citations in OpenAlex.
- Optimization of mass spectrometric parameters improve the identification performance of capillary zone electrophoresis for single-shot bottom-up proteomics analysis.Analytica chimica acta · 2018Article
- Organophosphate Hydrolase Is a Lipoprotein and Interacts with Pi-specific Transport System to Facilitate Growth of Brevundimonas diminuta Using OP Insecticide as Source of Phosphate.The Journal of biological chemistry · 2016Article
- Common errors in mass spectrometry-based analysis of post-translational modifications.Proteomics · 2016Review
- Shotgun Proteomics of Tomato Fruits: Evaluation, Optimization and Validation of Sample Preparation Methods and Mass Spectrometric Parameters.Frontiers in plant science · 2016Article
- Heterogeneity of pancreatic cancer metastases in a single patient revealed by quantitative proteomics.Molecular & cellular proteomics : MCP · 2014Article
- Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers.Journal of proteome research · 2013Article
- Multifactorial Understanding of Ion Abundance in Tandem Mass Spectrometry Experiments.Journal of proteomics & bioinformatics · 2013Article
- Article
- Regulation of lipid metabolism by Dicer revealed through SILAC mice.Journal of proteome research · 2012Article
- Learning from decoys to improve the sensitivity and specificity of proteomics database search results.PloS one · 2012Article
- Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides.Proteomics · 2011Article
- Monoclonal antibody cocktail as an enrichment tool for acetylome analysis.Analytical chemistry · 2011Article
- Improving proteome coverage on a LTQ-Orbitrap using design of experiments.Journal of the American Society for Mass Spectrometry · 2011Article
- Sample preparation techniques for the untargeted LC-MS-based discovery of peptides in complex biological matrices.Journal of biomedicine & biotechnology · 2011Review
- Optimization of parameters for coverage of low molecular weight proteins.Analytical and bioanalytical chemistry · 2010Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Shotgun proteomics has been used extensively for characterization of a number of proteomes. High-resolution Fourier transform mass spectrometry (FTMS) has emerged as a powerful tool owing to its high mass accuracy and resolving power. One of its major limitations, however, is that the confidence level of peptide identification and sensitivity cannot be maximized simultaneously. Although it is generally assumed that higher resolution is better for peptide identifications, the precise effect of varying resolution as a parameter on peptide identification has not yet been systematically evaluated. We used the Escherichia coli proteome and a standard 48 protein mix to study the effect of different resolution parameters on peptide identifications in the setting of a shotgun proteomics experiment on an LTQ-Orbitrap mass spectrometer. We observed a higher number of peptide-spectrum matches (PSMs) whenever the MS scan was carried out by FT and the MS/MS in the ion-trap (IT) with the maximum PSMs obtained at an MS resolution of 30,000. In contrast, when samples were analyzed by FT for both MS and MS/MS, the number of PSMs was significantly lower (approximately 40% compared with FT-IT experiments) with the maximum PSMs obtained when both the MS and MS/MS resolution were set to 15,000. Thus, a 15K-15K resolution setting may provide the best compromise for studies where both speed and accuracy such as high-throughput post-translational analysis and de novo sequencing are important. We hope that our study will allow researchers to choose between different resolution parameters to achieve their desired results from proteomic analyses.
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