ArticleJournal of proteome research2014
Comparing SILAC- and stable isotope dimethyl-labeling approaches for quantitative proteomics.
Article in Journal of proteome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 106 citations in OpenAlex.
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- Oncogenic Proteomics Approaches for Translational Research and HIV-Associated Malignancy Mechanisms.Proteomes · 2023Review
- THRONCAT: metabolic labeling of newly synthesized proteins using a bioorthogonal threonine analog.Nature communications · 2023Article
- TGF-β Type I Receptor Signaling in Melanoma Liver Metastases Increases Metastatic Outgrowth.International journal of molecular sciences · 2023Article
- Mathematical modeling and biochemical analysis support partially ordered calmodulin-myosin light chain kinase binding.iScience · 2023Article
- Finding a vocation for validation: taking proteomics beyond association and location.RSC chemical biology · 2023Review
- Multiomics of Colorectal Cancer Organoids Reveals Putative Mediators of Cancer Progression Resulting from SMAD4 Inactivation.Journal of proteome research · 2023Article
- Advances in stable isotope labeling: dynamic labeling for spatial and temporal proteomic analysis.Molecular omics · 2022Review
- Recent Developments and Applications of Quantitative Proteomics Strategies for High-Throughput Biomolecular Analyses in Cancer Research.RSC chemical biology · 2021Article
- A clostripain-like protease plays a major role in generating the secretome of enterotoxigenic Bacteroides fragilis.Molecular microbiology · 2021Article
- Quantitative Proteomics Revealed the Pharmacodynamic Network of Bugu Shengsui Decoction Promoting Osteoblast Proliferation.Frontiers in endocrinology · 2021Article
- The Herbal Compound Thymol Targets MultipleFrontiers in pharmacology · 2021Article
- Analyzing Ribosome Remodeling in Health and Disease.Proteomics · 2020Review
- A-kinase-anchoring protein 1 (dAKAP1)-based signaling complexes coordinate local protein synthesis at the mitochondrial surface.The Journal of biological chemistry · 2020Article
- Target identification of natural medicine with chemical proteomics approach: probe synthesis, target fishing and protein identification.Signal transduction and targeted therapy · 2020Review
- Simultaneous, Quantitative Characterization of Protein ADP-Ribosylation and Protein Phosphorylation in Macrophages.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Site-specific N-glycosylation of HeLa cell glycoproteins.Scientific reports · 2019Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Stable isotope labeling is widely used to encode and quantify proteins in mass-spectrometry-based proteomics. We compared metabolic labeling with stable isotope labeling by amino acids in cell culture (SILAC) and chemical labeling by stable isotope dimethyl labeling and find that they have comparable accuracy and quantitative dynamic range in unfractionated proteome analyses and affinity pull-down experiments. Analyzing SILAC- and dimethyl-labeled samples together in single liquid chromatography-mass spectrometric analyses minimizes differences under analytical conditions, allowing comparisons of quantitative errors introduced during sample processing. We find that SILAC is more reproducible than dimethyl labeling. Because proteins from metabolically labeled populations can be combined before proteolytic digestion, SILAC is particularly suited to studies with extensive sample processing, such as fractionation and enrichment of peptides with post-translational modifications. We compared both methods in pull-down experiments using a kinase inhibitor, dasatinib, and tagged GRB2-SH2 protein as affinity baits. We describe a StageTip dimethyl-labeling protocol that we applied to in-solution and in-gel protein digests. Comparing the impact of post-digest isotopic labeling on quantitative accuracy, we demonstrate how specific experimental designs can benefit most from metabolic labeling approaches like SILAC and situations where chemical labeling by stable isotope-dimethyl labeling can be a practical alternative.
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Registered trials
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.