ArticleJournal of proteomics2012
Effective correction of experimental errors in quantitative proteomics using stable isotope labeling by amino acids in cell culture (SILAC).
Article in Journal of proteomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 59 citations in OpenAlex.
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- Maximized quantitative phosphoproteomics allows high confidence dissection of the DNA damage signaling network.Scientific reports · 2020Article
- Proteomic Analysis of Quercetin-Treated K562 Cells.International journal of molecular sciences · 2019Article
- The RXFP3 receptor is functionally associated with cellular responses to oxidative stress and DNA damage.Aging · 2019Article
- What is Normalization? The Strategies Employed in Top-Down and Bottom-Up Proteome Analysis Workflows.Proteomes · 2019Review
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- Identification of alcohol-binding site(s) in proteins using diazirine-based photoaffinity labeling and mass spectrometry.Chemical biology & drug design · 2019Article
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- Inferring Protein-Protein Interaction Networks From Mass Spectrometry-Based Proteomic Approaches: A Mini-Review.Computational and structural biotechnology journal · 2019Review
- Complete Native Stable Isotope Labeling by Amino Acids of Saccharomyces cerevisiae for Global Proteomic Analysis.Analytical chemistry · 2018Article
- Time-resolved proteomics of adenovirus infected cells.PloS one · 2018Article
- Allele-specific quantitative proteomics unravels molecular mechanisms modulated by cis-regulatory PPARG locus variation.Nucleic acids research · 2017Article
- Generation and quantitative proteomics analysis of CK2α/α'Scientific reports · 2017Article
- Proteomics dedicated to biofilmology: What have we learned from a decade of research?Medical microbiology and immunology · 2016Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Accurate and reliable quantitative proteomics in cell culture has been considerably facilitated by the introduction of the stable isotope labeling by amino acids in cell culture (SILAC), combined with high resolution mass spectrometry. There are however several major sources of quantification errors that commonly occur with SILAC techniques, i.e. incomplete incorporation of isotopic amino acids, arginine-to-proline conversion, and experimental errors in final sample mixing. Dataset normalization is a widely adopted solution to such errors, however this may not completely prevent introducing incorrect expression ratios. Here we demonstrate that a label-swap replication of SILAC experiments was able to effectively correct experimental errors by averaging ratios measured in individual replicates using quantitative proteomics and phosphoproteomics of ligand treatment of neural cell cultures. Furthermore, this strategy was successfully applied to a SILAC triplet experiment, which presents a much more complicated experimental matrix, affected by both incomplete labeling and arginine-to-proline conversion. Based on our results, we suggest that SILAC experiments should be designed to incorporate label-swap replications for enhanced reliability in expression ratios.
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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.