Mass spectrometry based proteomics for developmental neurobiology in the amphibian Xenopus laevis
Tài liệu tham khảo
Aebersold, 2013, Western blots versus selected reaction monitoring assays: Time to turn the tables?, Molecular & Cellular Proteomics, 12, 2381, 10.1074/mcp.E113.031658
Arth, 2017, Inpatient hospitalization costs associated with birth defects among persons of all ages—United States, 2013, MMWR. Morbidity and Mortality Weekly Report, 66, 41, 10.15585/mmwr.mm6602a1
Baxi, 2018, Proteomic characterization of the neural ectoderm fated cell clones in the Xenopus laevis embryo by high-resolution mass spectrometry, ACS Chemical Neuroscience, 9, 2064, 10.1021/acschemneuro.7b00525
Baxi, 2020, NanoLC-MS based discovery proteomic analysis of the frog inner ear
Baxi, 2021, Proteo-metabolomic study of the spemann's organizer in the vertebrate (frog) embryo
Blum, 2018, Xenopus: An undervalued model organism to study and model human genetic disease, Cells, Tissues, Organs, 205, 303, 10.1159/000490898
Borodinsky, 2017, Xenopus laevis as a model organism for the study of spinal cord formation, development, function and regeneration, Frontiers in Neural Circuits, 11, 1, 10.3389/fncir.2017.00090
Bradbury, 2015, Standardize antibodies used in research, Nature, 518, 27, 10.1038/518027a
Cagnetta, 2018, Rapid cue-specific remodeling of the nascent axonal proteome, Neuron, 99, 29, 10.1016/j.neuron.2018.06.004
Chen, 2020, Bioinformatics methods for mass spectrometry-based proteomics data analysis, International Journal of Molecular Sciences, 21, 25
Chu, 2015, Proposed nomenclature for peptide ion fragmentation, International Journal of Mass Spectrometry, 390, 24, 10.1016/j.ijms.2015.07.021
Cox, 2014, Accurate proteome-wide label-free quantification delayed normalization and maximal peptide ratio extraction, termed MaxLFQ, Molecular & Cellular Proteomics, 13, 2513, 10.1074/mcp.M113.031591
Dale, 1987, Fate map for the 32-cell stage of Xenopus laevis, Development, 99, 527, 10.1242/dev.99.4.527
DeLaney, 2021, Mass spectrometry quantification, localization, and discovery of feeding-related neuropeptides in cancer borealis, ACS Chemical Neuroscience, 12, 782, 10.1021/acschemneuro.1c00007
DeLaney, 2019, Recent advances and new perspectives in capillary electrophoresis-mass spectrometry for single cell "omics", Molecules, 24, 1
Demircan, 2020, Proteome data to explore the axolotl limb regeneration capacity at neotenic and metamorphic stages, Data in Brief, 29, 1, 10.1016/j.dib.2020.105179
Drew, 2020, A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery, Developmental Biology, 467, 108, 10.1016/j.ydbio.2020.08.008
Duan, 2015, The roles of post-translational modifications in the context of protein interaction networks, PLoS Computational Biology, 11, 1, 10.1371/journal.pcbi.1004049
Duncan, 2016, Xenopus as a model organism for birth defects—Congenital heart disease and heterotaxy, Seminars in Cell & Developmental Biology, 51, 73, 10.1016/j.semcdb.2016.02.022
Federspiel, 2019, Conservation and divergence of protein pathways in the vertebrate heart, PLoS Biology, 17, 1, 10.1371/journal.pbio.3000437
Fonslow, 2009, Capillary electrophoresis applied to proteomic analysis, Journal of Separation Science, 32, 1175, 10.1002/jssc.200800592
Geng, 2019, Proteomic analysis of eleven tissues in the Chinese giant salamander (Andrias davidianus), Scientific Reports, 9, 1, 10.1038/s41598-019-50909-3
Han, 2008, Mass spectrometry for proteomics, Current Opinion in Chemical Biology, 12, 483, 10.1016/j.cbpa.2008.07.024
Harland, 2011, Xenopus research: Metamorphosed by genetics and genomics, Trends in Genetics, 27, 507, 10.1016/j.tig.2011.08.003
Hashimoto, 2019, Contribution of mass spectrometry-based proteomics to discoveries in developmental biology, 143
Huang, 2009, Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists, Nucleic Acids Research, 37, 1, 10.1093/nar/gkn923
Hwang, 2019, Xenopus: Driving the discovery of novel genes in patient disease and their underlying pathological mechanisms relevant for organogenesis, Frontiers in Physiology, 10, 1, 10.3389/fphys.2019.00953
Issaq, 2001, The role of separation science in proteomics research, Electrophoresis, 22, 3629, 10.1002/1522-2683(200109)22:17<3629::AID-ELPS3629>3.0.CO;2-O
Jensen, 2004, Modification-specific proteomics: Characterization of post-translational modifications by mass spectrometry, Current Opinion in Chemical Biology, 8, 33, 10.1016/j.cbpa.2003.12.009
Jensen, 2009, STRING 8—A global view on proteins and their functional interactions in 630 organisms, Nucleic Acids Research, 37, D412, 10.1093/nar/gkn760
Kong, 2017, MSFragger: Ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics, Nature Methods, 14, 513, 10.1038/nmeth.4256
Lee-Liu, 2018, Quantitative proteomics after spinal cord injury (SCI) in a regenerative and a nonregenerative stage in the frog Xenopus laevis, Molecular & Cellular Proteomics, 17, 592, 10.1074/mcp.RA117.000215
Lindemann, 2017, Strategies in relative and absolute quantitative mass spectrometry based proteomics, Biological Chemistry, 398, 687, 10.1515/hsz-2017-0104
Lombard-Banek, 2021, In vivo subcellular mass spectrometry enables proteo-metabolomic single-cell systems biology in a chordate embryo developing to a normally behaving tadpole (X. laevis), Angewandte Chemie, International Edition
Lombard-Banek, 2019, Microsampling capillary electrophoresis mass spectrometry enables single-cell proteomics in complex tissues: Developing cell clones in live Xenopus laevis and zebrafish embryos, Analytical Chemistry, 91, 4797, 10.1021/acs.analchem.9b00345
Lombard-Banek, 2016, Single-cell mass spectrometry for discovery proteomics: Quantifying translational cell heterogeneity in the 16-cell frog (Xenopus) embryo, Angewandte Chemie, International Edition, 55, 2454, 10.1002/anie.201510411
Lombard-Banek, 2017, New-generation mass spectrometry expands the toolbox of cell and developmental biology, Genesis, 55, 1, 10.1002/dvg.23012
Lombard-Banek, 2016, 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), Molecular & Cellular Proteomics, 15, 2756, 10.1074/mcp.M115.057760
Moody, 1987, Fates of the blastomeres of the 16-cell stage Xenopus embryo, Developmental Biology, 119, 560, 10.1016/0012-1606(87)90059-5
Moody, 1987, Fates of the blastomeres of the 32-cell-stage Xenopus embryo, Developmental Biology, 122, 300, 10.1016/0012-1606(87)90296-X
Nakayama, 2014, Cas9-based genome editing in Xenopus tropicalis, 355
O'Connell, 2018, Proteome-wide evaluation of two common protein quantification methods, Journal of Proteome Research, 17, 1934, 10.1021/acs.jproteome.8b00016
Ong, 2002, Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics, Molecular & Cellular Proteomics, 1, 376, 10.1074/mcp.M200025-MCP200
Onjiko, 2015, Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo, Proceedings of the National Academy of Sciences of the United States of America, 112, 6545, 10.1073/pnas.1423682112
Onjiko, 2017, Metabolic comparison of dorsal versus ventral cells directly in the live 8-cell frog embryo by microprobe single-cell CE-ESI-MS, Analytical Methods, 9, 4964, 10.1039/C7AY00834A
Onjiko, 2017, In situ microprobe single-cell capillary electrophoresis mass spectrometry: Metabolic reorganization in single differentiating cells in the live vertebrate (Xenopus laevis) embryo, Analytical Chemistry, 89, 7069, 10.1021/acs.analchem.7b00880
Onjiko, 2017, Microprobe capillary electrophoresis mass spectrometry for single-cell metabolomics in live frog (Xenopus laevis) embryos, Journal of Visualized Experiments, 1
Peshkin, 2015, On the relationship of protein and mRNA dynamics in vertebrate embryonic development, Developmental Cell, 35, 383, 10.1016/j.devcel.2015.10.010
Peuchen, 2016, Optimization and comparison of bottom-up proteomic sample preparation for early-stage Xenopus laevis embryos, Analytical and Bioanalytical Chemistry, 408, 4743, 10.1007/s00216-016-9564-2
Pino, 2020, Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications, Biochemical Society Transactions, 48, 1953, 10.1042/BST20191091
Pino, 2020, The skyline ecosystem: Informatics for quantitative mass spectrometry proteomics, Mass Spectrometry Reviews, 39, 229, 10.1002/mas.21540
Portero, 2019, Dual cationic-anionic profiling of metabolites in a single identified cell in a live Xenopus laevis embryo by microprobe CE-ESI-MS, Analyst, 144, 892, 10.1039/C8AN01999A
Pratt, 2013, Modeling human neurodevelopmental disorders in the Xenopus tadpole: From mechanisms to therapeutic targets, Disease Models & Mechanisms, 6, 1057
Presler, 2017, Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg, Proceedings of the National Academy of Sciences of the United States of America, 114, E10838
Quach, 2019, Proteomic characterization of the spemann organizer in Xenopus laevis (frog) embryos
Sater, 2017, Using Xenopus to understand human diseases and developmental disorders, Genesis, 55, 1, 10.1002/dvg.22997
Schiapparelli, 2019, The retinal ganglion cell transportome identifies proteins transported to axons and presynaptic compartments in the visual system in vivo, Cell Reports, 28, 1935, 10.1016/j.celrep.2019.07.037
Session, 2016, Genome evolution in the allotetraploid frog Xenopus laevis, Nature, 538, 336, 10.1038/nature19840
Smits, 2014, Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs, Nucleic Acids Research, 42, 9880, 10.1093/nar/gku661
Sun, 2014, Quantitative proteomics of Xenopus laevis embryos: Expression kinetics of nearly 4000 proteins during early development, Scientific Reports, 4, 1
Sun, 2016, Single cell proteomics using frog (Xenopus laevis) blastomeres isolated from early stage embryos, which form a geometric progression in protein content, Analytical Chemistry, 88, 6653, 10.1021/acs.analchem.6b01921
Tyanova, 2016, The maxquant computational platform for mass spectrometry-based shotgun proteomics, Nature Protocols, 11, 2301, 10.1038/nprot.2016.136
Virag, 2020, Current trends in the analysis of post-translational modifications, Chromatographia, 83, 1, 10.1007/s10337-019-03796-9
Walther, 2010, Mass spectrometry-based proteomics in cell biology, The Journal of Cell Biology, 190, 491, 10.1083/jcb.201004052
Wang, 2019, MALDI-imaging of early stage Xenopus laevis embryos, Talanta, 204, 138, 10.1016/j.talanta.2019.05.060
Wang, 2010, Cellular retinol binding protein 1 modulates photoreceptor outer segment folding in the isolated eye, Developmental Neurobiology, 70, 623, 10.1002/dneu.20798
Waterston, 2002, Initial sequencing and comparative analysis of the mouse genome, Nature, 420, 520, 10.1038/nature01262
Wuehr, 2014, Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database, Current Biology, 24, 1467, 10.1016/j.cub.2014.05.044
Xenopus Community, 2020
Zhang, 2013, Protein analysis by shotgun/bottom-up proteomics, Chemical Reviews, 113, 2343, 10.1021/cr3003533