Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
???displayArticle.abstract???
Abundant proteins challenge deep mass spectrometry (MS) analysis of the proteome. Yolk, the source of food in many developing vertebrate embryos, complicates chemical separation and interferes with detection. We report here a strategy that enhances bottom-up proteomics in yolk-laden specimens by diluting the interferences using a yolk-depleted carrier (YODEC) proteome via isobaric multiplexing quantification. This method was tested on embryos of the South African Clawed Frog (Xenopus laevis), where a >90% yolk proteome content challenges deep proteomics. As a proof of concept, we isolated neural and epidermal fated cell clones from the embryo by dissection or fluorescence-activated cell sorting. Compared with the standard multiplexing carrier approach, YODEC more than doubled the detectable X. laevis proteome, identifying 5,218 proteins from D11 cell clones dissected from the embryo. Ca. ∼80% of the proteins were quantified without dropouts in any of the analytical channels. YODEC with high-pH fractionation quantified 3,133 proteins from ∼8,000 V11 cells that were sorted from ca. 2 embryos (1.5 μg total, or 150 ng yolk-free proteome), marking a 15-fold improvement in proteome coverage vs the standard proteomics approach. About 60% of these proteins were only quantifiable by YODEC, including molecular adaptors, transporters, translation, and transcription factors. While this study was tailored to limited populations of Xenopus cells, we anticipate the approach of "dilute to enrich" using a depleted carrier proteome to be adaptable to other biological models in which abundant proteins challenge deep MS proteomics.
???displayArticle.pubmedLink???
37994825 ???displayArticle.pmcLink???PMC10872351 ???displayArticle.link???J Proteome Res ???displayArticle.grants???[+]
Baldwin,
Global analysis of cell behavior and protein dynamics reveals region-specific roles for Shroom3 and N-cadherin during neural tube closure.
2022, Pubmed,
Xenbase
Baldwin,
Global analysis of cell behavior and protein dynamics reveals region-specific roles for Shroom3 and N-cadherin during neural tube closure.
2022,
Pubmed
,
Xenbase Baxi,
Cell-Lineage Guided Mass Spectrometry Proteomics in the Developing (Frog) Embryo.
2022,
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 Cao,
Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of Plasma.
2021,
Pubmed Carotenuto,
Xenopus laevis (Daudin, 1802) as a Model Organism for Bioscience: A Historic Review and Perspective.
2023,
Pubmed
,
Xenbase Choi,
Data-Dependent Acquisition Ladder for Capillary Electrophoresis Mass Spectrometry-Based Ultrasensitive (Neuro)Proteomics.
2021,
Pubmed Davey,
The chicken as a model for embryonic development.
2007,
Pubmed Federspiel,
Conservation and divergence of protein pathways in the vertebrate heart.
2019,
Pubmed
,
Xenbase Fonslow,
Digestion and depletion of abundant proteins improves proteomic coverage.
2013,
Pubmed Fonslow,
Addendum: Digestion and depletion of abundant proteins improves proteomic coverage.
2014,
Pubmed Gao,
Novel strategy of high-abundance protein depletion using multidimensional liquid chromatography.
2006,
Pubmed Gong,
Different immunoaffinity fractionation strategies to characterize the human plasma proteome.
2006,
Pubmed Hashimoto,
Mechanical Force Induces Phosphorylation-Mediated Signaling that Underlies Tissue Response and Robustness in Xenopus Embryos.
2019,
Pubmed
,
Xenbase Haudenschild,
High abundant protein removal from rodent blood for biomarker discovery.
2014,
Pubmed Hodge,
Cleaning up the masses: exclusion lists to reduce contamination with HPLC-MS/MS.
2013,
Pubmed
,
Xenbase Jorgensen,
The mechanism and pattern of yolk consumption provide insight into embryonic nutrition in Xenopus.
2009,
Pubmed
,
Xenbase Joshi,
TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells.
2019,
Pubmed Karimi,
Xenbase: a genomic, epigenomic and transcriptomic model organism database.
2018,
Pubmed
,
Xenbase Kostiuk,
Xenopus as a platform for discovery of genes relevant to human disease.
2021,
Pubmed
,
Xenbase Kreimer,
Advanced Precursor Ion Selection Algorithms for Increased Depth of Bottom-Up Proteomic Profiling.
2016,
Pubmed Lundberg,
Spatial proteomics: a powerful discovery tool for cell biology.
2019,
Pubmed Maccarrone,
Mining the human cerebrospinal fluid proteome by immunodepletion and shotgun mass spectrometry.
2004,
Pubmed Macklin,
Recent advances in mass spectrometry based clinical proteomics: applications to cancer research.
2020,
Pubmed McAlister,
MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes.
2014,
Pubmed McLaughlin,
Subcellular proteomics combined with bioenergetic phenotyping reveals protein biomarkers of respiratory insufficiency in the setting of proofreading-deficient mitochondrial polymerase.
2020,
Pubmed 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 Motoyama,
Multidimensional LC separations in shotgun proteomics.
2008,
Pubmed Nemes,
Mass spectrometry comes of age for subcellular organelles.
2021,
Pubmed Onjiko,
Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo.
2015,
Pubmed
,
Xenbase Pade,
Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles.
2024,
Pubmed Perez-Riverol,
The PRIDE database and related tools and resources in 2019: improving support for quantification data.
2019,
Pubmed Pernemalm,
In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta.
2019,
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 Schmid,
Integrative analysis of multimodal mass spectrometry data in MZmine 3.
2023,
Pubmed Slavov,
Scaling Up Single-Cell Proteomics.
2022,
Pubmed Specht,
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2.
2021,
Pubmed Sun,
An analysis of protein abundance suppression in data dependent liquid chromatography and tandem mass spectrometry with tryptic peptide mixtures of five known proteins.
2005,
Pubmed Truong,
Data-Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics.
2023,
Pubmed Tu,
Depletion of abundant plasma proteins and limitations of plasma proteomics.
2010,
Pubmed Veldman,
Zebrafish as a developmental model organism for pediatric research.
2008,
Pubmed Viode,
A simple, time- and cost-effective, high-throughput depletion strategy for deep plasma proteomics.
2023,
Pubmed Weke,
MicroPOTS Analysis of Barrett's Esophageal Cell Line Models Identifies Proteomic Changes after Physiologic and Radiation Stress.
2021,
Pubmed Wiley,
The structure of vitellogenin. Multiple vitellogenins in Xenopus laevis give rise to multiple forms of the yolk proteins.
1981,
Pubmed
,
Xenbase Wiśniewski,
Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome.
2009,
Pubmed Woo,
High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip.
2021,
Pubmed Wühr,
Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database.
2014,
Pubmed
,
Xenbase Xu,
Benchtop-compatible sample processing workflow for proteome profiling of < 100 mammalian cells.
2019,
Pubmed Zhu,
Single chain variable fragment displaying M13 phage library functionalized magnetic microsphere-based protein equalizer for human serum protein analysis.
2012,
Pubmed
