ArticleJournal of proteome research2009
Evaluation of the variation in sample preparation for comparative proteomics using stable isotope labeling by amino acids in cell culture.
Article in Journal of proteome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 51 citations in OpenAlex.
- Mass Spectrometry for Proteomics-Based Investigation.Advances in experimental medicine and biology · 2026Review
- Designing a Comparative Proteomics Experiment: Retention-Time Alignment and Imputation Algorithms Affect Statistical Comparisons between Samples.Journal of proteome research · 2025Article
- Bacterial Pyocyanin Inducible Keratin 6A Accelerates Closure of Epithelial Defect under Conditions of Mitochondrial Dysfunction.The Journal of investigative dermatology · 2023Article
- Comparison of SPEED, S-Trap, and In-Solution-Based Sample Preparation Methods for Mass Spectrometry in Kidney Tissue and Plasma.International journal of molecular sciences · 2023Article
- Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice.Proteomes · 2023Review
- Profound changes in cerebrospinal fluid proteome and metabolic profile are associated with congenital hydrocephalus.Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism · 2021Article
- Noise Exposures Causing Hearing Loss Generate Proteotoxic Stress and Activate the Proteostasis Network.Cell reports · 2020Article
- Minimal deuterium isotope effects in quantitation of dimethyl-labeled complex proteomes analyzed with capillary zone electrophoresis/mass spectrometry.Electrophoresis · 2020Article
- The effects of IFITM1 and IFITM3 gene deletion on IFNγ stimulated protein synthesis.Cellular signalling · 2019Article
- Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications?Expert review of proteomics · 2018Review
- Deducing the presence of proteins and proteoforms in quantitative proteomics.Nature communications · 2018Article
- Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics.Journal of proteome research · 2018Article
- Deep Coverage of Global Protein Expression and Phosphorylation in Breast Tumor Cell Lines Using TMT 10-plex Isobaric Labeling.Journal of proteome research · 2017Article
- Sensing Small Changes in Protein Abundance: Stimulation of Caco-2 Cells by Human Whey Proteins.Journal of proteome research · 2016Article
- Application of quantitative proteomics to the integrated analysis of the ubiquitylated and global proteomes of xenograft tumor tissues.Clinical proteomics · 2015Article
- Comparing SILAC- and stable isotope dimethyl-labeling approaches for quantitative proteomics.Journal of proteome research · 2014Article
- Protein quantitation using mass spectrometry.Methods in molecular biology (Clifton, N.J.) · 2010Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
In comparative proteomic studies, it is important to know the variability associated with sample preparation. In this study, we report the strategy of using SILAC (stable isotope labeling by amino acids in cell culture) to evaluate the effect of the variation in sample preparation for quantitative proteomics. Variability can be measured when equal amounts of light and heavy SILAC samples undergo the same sample preparation procedures in parallel, and the two samples are mixed for relative protein quantitation by mass spectrometry. The high quantitative accuracy of SILAC allows for characterization of small variations. First, the reproducibility of immunoprecipitation (IP) and in-gel digestion was evaluated, and the impact of replicate number on quantitative accuracy was characterized. Second, we evaluated the overall variation in a comparative workflow involving three sequential sample preparation steps: IP, SDS-PAGE fractionation, and in-gel digestion. The evaluation of individual sample preparation steps was very valuable for experimental design: the optimal number of replicates for each step could be readily determined and the overall variation of the workflow could be predicted from the variation of the individual steps involved. By using informed experimental design, we demonstrated that the error associated with multiple steps of sample preparation in a comparative experiment can be limited to a reasonably low level.
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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.