ArticleMethods in molecular biology (Clifton, N.J.)2018
Quantitative Proteomics of Xenopus Embryos I, Sample Preparation.
Article in Methods in molecular biology (Clifton, N.J.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Glycogen-dependent demixing of frog egg cytoplasm at increased crowding.Biophysical journal · 2026Article
- Lipid accumulation in nitrogen and phosphorus-limited yeast is caused by less growth-related dilution.Metabolic engineering · 2026Article
- Expanding Targeted Instrumentation for Discovery Applications: Complement Reporter Ion Quantification with a Quadrupole-Ion Trap Instrument.Journal of proteome research · 2025Article
- Transitions in the proteome and phospho-proteome during Xenopus laevis development.Developmental biology · 2025Article
- Dynamic Proteome Landscape During Preimplantation Human Embryo Development and Trophectoderm Stem Cell-Differentiation.Proteomics · 2025Article
- Synergistic Arg-C Ultra and Lys-C Digestion for Quantitative Proteomics.bioRxiv : the preprint server for biology · 2025Article
- ERK synchronizes embryonic cleavages in Drosophila.Developmental cell · 2024Article
- Mitochondrial ATP generation is more proteome efficient than glycolysis.Nature chemical biology · 2024Article
- Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation.Nature communications · 2024Article
- Robustness of mitochondrial biogenesis and respiration explain aerobic glycolysis.bioRxiv : the preprint server for biology · 2024Article
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- Evidence for widespread cytoplasmic structuring into mesoscale condensates.Nature cell biology · 2024Article
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- Identification of Deubiquitinase Substrates in Xenopus Egg Extract.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Differential nuclear import sets the timing of protein access to the embryonic genome.Nature communications · 2022Article
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- Article
- Cell-Lineage Guided Mass Spectrometry Proteomics in the Developing (Frog) Embryo.Journal of visualized experiments : JoVE · 2022Article
- GCN2 adapts protein synthesis to scavenging-dependent growth.Cell systems · 2022Article
- Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation.Nature chemical biology · 2021Article
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5 authors.
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Abstract
Xenopus oocytes and embryos are model systems optimally suited for quantitative proteomics. This is due to the availability of large amount of protein material and the ease of physical manipulation. Furthermore, facile in vitro fertilization provides superbly synchronized embryos for cell cycle and developmental stages. Here, we detail protocols developed over the last few years for sample preparation of multiplexed proteomics with TMT-tags followed by quantitative mass spectrometry analysis using the MultiNotch MS3 approach. In this approach, each condition is barcoded with an isobaric tag at the peptide level. After barcoding, samples are combined and the relative abundance of ~100,000 peptides is quantified on a mass spectrometer. High reproducibility of the sample preparation process prior to peptides being tagged and combined is of upmost importance for obtaining unbiased data. Otherwise, differences in sample handling can inadvertently appear as biological changes. We detail and exemplify the application of our sample workflow on an embryonic time-series of ten developmental stages of Xenopus laevis embryos ranging from the egg to stage 35 (just before hatching). Our accompanying paper (Chapter 14 ) details a bioinformatics pipeline to analyze the quality of the given sample preparation and strategies to convert spectra of X. laevis peptides into biologically interpretable data.
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