ArticleAnalytical chemistry2013
Neutron encoded labeling for peptide identification.
Article in Analytical chemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Review
- 21-plex DiLeu Isobaric Tags for High-Throughput Quantitative Proteomics.Analytical chemistry · 2020Article
- Sample Multiplexing Strategies in Quantitative Proteomics.Analytical chemistry · 2019Review
- Mass Defect-Based Dimethyl Pyrimidinyl Ornithine (DiPyrO) Tags for Multiplex Quantitative Proteomics.Analytical chemistry · 2017Article
- Review
- New-generation mass spectrometry expands the toolbox of cell and developmental biology.Genesis (New York, N.Y. : 2000) · 2017Review
- NeuCode Proteomics Reveals Bap1 Regulation of Metabolism.Cell reports · 2016Article
- Neucode Labels for Multiplexed, Absolute Protein Quantification.Analytical chemistry · 2016Article
- Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling.Analytical chemistry · 2016Review
- NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans.Molecular & cellular proteomics : MCP · 2015Article
- Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data.Molecular & cellular proteomics : MCP · 2015Article
- Development and characterization of novel 8-plex DiLeu isobaric labels for quantitative proteomics and peptidomics.Rapid communications in mass spectrometry : RCM · 2015Article
- High-resolution enabled 12-plex DiLeu isobaric tags for quantitative proteomics.Analytical chemistry · 2015Article
- Isobaric labeling-based relative quantification in shotgun proteomics.Journal of proteome research · 2014Review
- Peptide dimethylation: fragmentation control via distancing the dimethylamino group.Journal of the American Society for Mass Spectrometry · 2014Article
- Evaluation of a method for nitrotyrosine site identification and relative quantitation using a stable isotope-labeled nitrated spike-in standard and high resolution fourier transform MS and MS/MS analysis.International journal of molecular sciences · 2014Article
- 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
- Interference-free proteome quantification with MS/MS-based isobaric isotopologue detection.Journal of proteome research · 2014Article
- Neutron-encoded mass signatures for quantitative top-down proteomics.Analytical chemistry · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Metabolic labeling of cells using heavy amino acids is most commonly used for relative quantitation; however, partner mass shifts also detail the number of heavy amino acids contained within the precursor species. Here, we use a recently developed metabolic labeling technique, NeuCode (neutron encoding) stable isotope labeling with amino acids in cell culture (SILAC), which produces precursor partners spaced ~40 mDa apart to enable amino acid counting. We implement large scale counting of amino acids through a program, "Amino Acid Counter", which determines the most likely combination of amino acids within a precursor based on NeuCode SILAC partner spacing and filters candidate peptide sequences during a database search using this information. Counting the number of lysine residues for precursors selected for MS/MS decreases the median number of candidate sequences from 44 to 14 as compared to an accurate mass search alone (20 ppm). Furthermore, the ability to co-isolate and fragment NeuCode SILAC partners enables counting of lysines in product ions, and when the information is used, the median number of candidates is reduced to 7. We then demonstrate counting leucine in addition to lysine results in a 6-fold decrease in search space, 43 to 7, when compared to an accurate mass search. We use this scheme to analyze a nanoLC-MS/MS experiment and demonstrate that accurate mass plus lysine and leucine counting reduces the number of candidate sequences to one for ~20% of all precursors selected, demonstrating an ability to identify precursors without MS/MS analysis.
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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.