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Cell-Lineage Guided Mass Spectrometry Proteomics in the Developing (Frog) Embryo.
Baxi AB
,
Pade LR
,
Nemes P
.
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Characterization of molecular events as cells give rise to tissues and organs raises a potential to better understand normal development and design efficient remedies for diseases. Technologies enabling accurate identification and quantification of diverse types and large numbers of proteins would provide still missing information on molecular mechanisms orchestrating tissue and organism development in space and time. Here, we present a mass spectrometry-based protocol that enables the measurement of thousands of proteins in identified cell lineages in Xenopus laevis (frog) embryos. The approach builds on reproducible cell-fate maps and established methods to identify, fluorescently label, track, and sample cells and their progeny (clones) from this model of vertebrate development. After collecting cellular contents using microsampling or isolating cells by dissection or fluorescence-activated cell sorting, proteins are extracted and processed for bottom-up proteomic analysis. Liquid chromatography and capillary electrophoresis are used to provide scalable separation for protein detection and quantification with high-resolution mass spectrometry (HRMS). Representative examples are provided for the proteomic characterization of neural-tissue fated cells. Cell-lineage-guided HRMS proteomics is adaptable to different tissues and organisms. It is sufficiently sensitive, specific, and quantitative to peer into the spatio-temporal dynamics of the proteome during vertebrate development.
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35532271
???displayArticle.pmcLink???PMC9513837 ???displayArticle.link???J Vis Exp ???displayArticle.grants???[+]
Baxi,
Proteomic Characterization of the Neural Ectoderm Fated Cell Clones in the Xenopus laevis Embryo by High-Resolution Mass Spectrometry.
2018, Pubmed,
Xenbase
Baxi,
Proteomic Characterization of the Neural Ectoderm Fated Cell Clones in the Xenopus laevis Embryo by High-Resolution Mass Spectrometry.
2018,
Pubmed
,
Xenbase
Briggs,
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.
2018,
Pubmed
,
Xenbase
Budnik,
SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation.
2018,
Pubmed
Chen,
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis.
2020,
Pubmed
Choi,
Tapered-Tip Capillary Electrophoresis Nano-Electrospray Ionization Mass Spectrometry for Ultrasensitive Proteomics: the Mouse Cortex.
2017,
Pubmed
Christian,
Morphogen gradients in development: from form to function.
2012,
Pubmed
,
Xenbase
Cox,
Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ.
2014,
Pubmed
Dale,
Fate map for the 32-cell stage of Xenopus laevis.
1987,
Pubmed
,
Xenbase
DeLaney,
Recent Advances and New Perspectives in Capillary Electrophoresis-Mass Spectrometry for Single Cell "Omics".
2018,
Pubmed
Deutsch,
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.
2015,
Pubmed
Drouin,
Capillary Electrophoresis-Mass Spectrometry at Trial by Metabo-Ring: Effective Electrophoretic Mobility for Reproducible and Robust Compound Annotation.
2020,
Pubmed
GURDON,
Sexually mature individuals of Xenopus laevis from the transplantation of single somatic nuclei.
1958,
Pubmed
,
Xenbase
Garcia,
What does the future hold for Top Down mass spectrometry?
2010,
Pubmed
Gupta,
Quantitative Proteomics of Xenopus Embryos I, Sample Preparation.
2018,
Pubmed
,
Xenbase
Gygi,
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.
1999,
Pubmed
Harland,
Xenopus research: metamorphosed by genetics and genomics.
2011,
Pubmed
,
Xenbase
Hildonen,
Why less is more when generating tryptic peptides in bottom-up proteomics.
2014,
Pubmed
Hornbeck,
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.
2015,
Pubmed
Hughes,
Single-pot, solid-phase-enhanced sample preparation for proteomics experiments.
2019,
Pubmed
Jensen,
STRING 8--a global view on proteins and their functional interactions in 630 organisms.
2009,
Pubmed
Jiang,
Comparison of protein precipitation methods for sample preparation prior to proteomic analysis.
2004,
Pubmed
Kakebeen,
Tissue disaggregation and isolation of specific cell types from transgenic Xenopus appendages for transcriptional analysis by FACS.
2021,
Pubmed
,
Xenbase
Karimi,
Xenbase: a genomic, epigenomic and transcriptomic model organism database.
2018,
Pubmed
,
Xenbase
Klein,
The first cleavage furrow demarcates the dorsal-ventral axis in Xenopus embryos.
1987,
Pubmed
,
Xenbase
Letunic,
SMART: recent updates, new developments and status in 2020.
2021,
Pubmed
Lombard-Banek,
Single-Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16-Cell Frog (Xenopus) Embryo.
2016,
Pubmed
,
Xenbase
Lombard-Banek,
Single-cell proteomics in complex tissues using microprobe capillary electrophoresis mass spectrometry.
2019,
Pubmed
,
Xenbase
Lombard-Banek,
High-Sensitivity Mass Spectrometry for Probing Gene Translation in Single Embryonic Cells in the Early Frog (Xenopus) Embryo.
2016,
Pubmed
,
Xenbase
Lombard-Banek,
Microsampling Capillary Electrophoresis Mass Spectrometry Enables Single-Cell Proteomics in Complex Tissues: Developing Cell Clones in Live Xenopus laevis and Zebrafish Embryos.
2019,
Pubmed
,
Xenbase
Lombard-Banek,
In Vivo Subcellular Mass Spectrometry Enables Proteo-Metabolomic Single-Cell Systems Biology in a Chordate Embryo Developing to a Normally Behaving Tadpole (X. laevis)*.
2021,
Pubmed
,
Xenbase
Lombard-Banek,
Label-free Quantification of Proteins in Single Embryonic Cells with Neural Fate in the Cleavage-Stage Frog (Xenopus laevis) Embryo using Capillary Electrophoresis Electrospray Ionization High-Resolution Mass Spectrometry (CE-ESI-HRMS).
2016,
Pubmed
,
Xenbase
Mi,
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API.
2021,
Pubmed
Moody,
Fates of the blastomeres of the 16-cell stage Xenopus embryo.
1987,
Pubmed
,
Xenbase
Moody,
Fates of the blastomeres of the 32-cell-stage Xenopus embryo.
1987,
Pubmed
,
Xenbase
Moody,
Cell lineage analysis in Xenopus embryos.
2000,
Pubmed
,
Xenbase
Nemes,
Qualitative and quantitative metabolomic investigation of single neurons by capillary electrophoresis electrospray ionization mass spectrometry.
2013,
Pubmed
,
Xenbase
Oberg,
Statistical design of quantitative mass spectrometry-based proteomic experiments.
2009,
Pubmed
Onjiko,
Microprobe Capillary Electrophoresis Mass Spectrometry for Single-cell Metabolomics in Live Frog (Xenopus laevis) Embryos.
2017,
Pubmed
,
Xenbase
Onjiko,
In Situ Microprobe Single-Cell Capillary Electrophoresis Mass Spectrometry: Metabolic Reorganization in Single Differentiating Cells in the Live Vertebrate (Xenopus laevis) Embryo.
2017,
Pubmed
,
Xenbase
Perez-Riverol,
The PRIDE database and related tools and resources in 2019: improving support for quantification data.
2019,
Pubmed
Peshkin,
On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development.
2015,
Pubmed
,
Xenbase
Pino,
Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications.
2020,
Pubmed
Saha-Shah,
Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis.
2019,
Pubmed
,
Xenbase
Sater,
Using Xenopus to understand human disease and developmental disorders.
2017,
Pubmed
,
Xenbase
Schweppe,
BioPlex Display: An Interactive Suite for Large-Scale AP-MS Protein-Protein Interaction Data.
2018,
Pubmed
Shoemaker,
Neural Stem Cells (NSCs) and Proteomics.
2016,
Pubmed
Sun,
Single Cell Proteomics Using Frog (Xenopus laevis) Blastomeres Isolated from Early Stage Embryos, Which Form a Geometric Progression in Protein Content.
2016,
Pubmed
,
Xenbase
Sun,
Third-generation electrokinetically pumped sheath-flow nanospray interface with improved stability and sensitivity for automated capillary zone electrophoresis-mass spectrometry analysis of complex proteome digests.
2015,
Pubmed
,
Xenbase
Thompson,
Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS.
2003,
Pubmed
Toby,
Progress in Top-Down Proteomics and the Analysis of Proteoforms.
2016,
Pubmed
Tyanova,
The Perseus computational platform for comprehensive analysis of (prote)omics data.
2016,
Pubmed
Wessel,
A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids.
1984,
Pubmed
Wiśniewski,
Filter-Aided Sample Preparation for Proteome Analysis.
2018,
Pubmed
Zhang,
Protein analysis by shotgun/bottom-up proteomics.
2013,
Pubmed
Zhang,
Miniaturized Filter-Aided Sample Preparation (MICRO-FASP) Method for High Throughput, Ultrasensitive Proteomics Sample Preparation Reveals Proteome Asymmetry in Xenopus laevis Embryos.
2020,
Pubmed
,
Xenbase
Zhu,
Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells.
2018,
Pubmed
Červenka,
Proteomic Characterization of Human Neural Stem Cells and Their Secretome During in vitro Differentiation.
2020,
Pubmed
