ArticleJournal of proteome research2011
Examining troughs in the mass distribution of all theoretically possible tryptic peptides.
Article in Journal of proteome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
13 citing papers in PubMed.
- MALDI MSI Protocol for Spatial Bottom-Up Proteomics at Single-Cell Resolution.Journal of proteome research · 2024Article
- Evaluation of Serum Proteome Sample Preparation Methods to Support Clinical Proteomics Applications.Journal of the American Society for Mass Spectrometry · 2024Article
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- Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries.Molecular & cellular proteomics : MCP · 2020Article
- Advanced Multidimensional Separations in Mass Spectrometry: Navigating the Big Data Deluge.Annual review of analytical chemistry (Palo Alto, Calif.) · 2016Article
- A deeper look into Comet--implementation and features.Journal of the American Society for Mass Spectrometry · 2015Article
- Using SEQUEST with theoretically complete sequence databases.Journal of the American Society for Mass Spectrometry · 2015Article
- Use of singular value decomposition analysis to differentiate phosphorylated precursors in strong cation exchange fractions.Electrophoresis · 2014Article
- A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information.BMC bioinformatics · 2013Article
- Use of theoretical peptide distributions in phosphoproteome analysis.Journal of proteome research · 2013Article
- De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics.Journal of the American Society for Mass Spectrometry · 2012Article
- Improved mass defect model for theoretical tryptic peptides.Analytical chemistry · 2012Article
- A parallel method for enumerating amino acid compositions and masses of all theoretical peptides.BMC bioinformatics · 2011Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
This work describes the mass distribution of all theoretically possibly tryptic peptides made of 20 amino acids, up to the mass of 3 kDa, with resolution of 0.001 Da. We characterize regions between the peaks of the distribution, including gaps (forbidden zones) and low-populated areas (quiet zones). We show how the gaps shrink over the mass range and when they completely disappear. We demonstrate that peptide compositions in quiet zones are less diverse than those in the peaks of the distribution and that by eliminating certain types of unrealistic compositions the gaps in the distribution may be increased. The mass distribution is generated using a parallel implementation of a recursive procedure that enumerates all amino acid compositions. It allows us to enumerate all compositions of tryptic peptides below 3 kDa in 48 min using a computer cluster with 12 Intel Xeon X5650 CPUs (72 cores). The results of this work can be used to facilitate protein identification and mass defect labeling in mass spectrometry-based proteomics experiments.
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