GPMDB00263OtherMario Looso, Thilo Borchardt, Marcus Krueger, and Thomas BraunInstrumentNot AvailableNot availableStropicalis Ncbi, Xlaevis Ncbi, Caudatathomas.braun@mpi-bn.mpg.de20139370http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000780http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000776http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000787http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000777http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000788http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000766http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000785http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000774http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000775http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000783http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000772http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000784http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000773http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000770http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000781http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000771http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000782http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000769http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000767http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000778http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000768http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000779Max-Planck-Institute for heart and lung research, Bad Nauheim, Hessen 61231Not availableGPMDBDespite progress in the characterization of their genomes, proteomes of several model organisms are often only poorly characterized. This problem is aggravated by the presence of large numbers of expressed sequence tag clones that lack homologues in other species, which makes it difficult to identify new proteins irrespective of whether such molecules are involved in species-specific biological processes. We have used a pulsed stable isotope labeling with amino acids in cell culture (SILAC)-based mass spectrometry method, which is based on the detection of paired peptides after [(13)C(6)]lysine incorporation into proteins in vivo, to greatly increase the confidence of protein identification in cross-species database searches. The method was applied to identify nearly 3000 proteins in regenerating tails of the urodele amphibian Notophthalmus viridescens, which possesses outstanding capabilities in the regeneration of complex tissues. We reason that pulsed in vivo SILAC represents a versatile tool to identify new proteins in species for which only limited sequence information exists.Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry.Looso Mario M,Borchardt Thilo T,Krüger Marcus M,Braun Thomas T,Looso Mario M, Borchardt Thilo T, Krüger Marcus M, Braun Thomas TProtein Gene Products, Gene Proteins, polypeptide, advanced, Identification, Protein, Proteomes., precocious, Gene Products, Proteins, Identifications (Psychology), Gene, proteins, earlyBru, data, Newts, Raw, Procedures, Lysine Hydrochloride, mol, Proteins, Taricha, Gene, Spectrum Analyses, Procedure, Spectrum Analysis, uroptérygie, Spectroscopy, polypeptide, dynamic SILAC, Polypeptides, method, Lysine Acetate, Method, Acetate, method used in an experiment, Protein, Mass, Studies, Gene Products, 2, Cell., Del(8)44H, Lysine, Analysis, L-Lysine, Mass Spectrum Analyses, Mass Spectroscopy, Data Base, L Lysine, Mass Spectrum Analysis, Svc, Mass Spectrum, Tarichas, Col4a-1, tail fin, Analyses, Identification, cell, caudal subdivision, Tails, Newt, nageoire caudale, Spectrometry, epsilon-diaminocaproic acid, Identifications (Psychology), proteins, Methodological, alpha, pulse SILAC, C6H14N2O2, uroptère, Methodological Study, plan specification, Protein Gene Products, Study, Gene Proteins, tail, Methodological Studies, Lysin, pulsed SILAC, species, 6-diaminohexanoic acid, EnisylMass Spectrum Analysis, Mass Spectrum, advanced, Identification, Analyses, Proteins, Spectrometry, Identifications (Psychology), Gene, proteins, Isotope Labeling, Spectrum Analyses, Isotope-Coded Affinity, Affinity Tagging, Isotopically-Coded, Labeling, Spectrum Analysis, early, Protein Gene Products, Spectroscopy, Gene Proteins, polypeptide, Isotope, Stable, Stable Isotope, Protein, Isotope-Coded Affinity Tagging, precocious, Gene Products, Mass, Mass., Isotope-Coded, Analysis, Isotopically-Coded Affinity, Tagging, Proteomes, Stable Isotope Labeling, Isotope Coded Affinity Tagging, Mass Spectrum Analyses, Isotopically-Coded Affinity Tagging, Mass Spectroscopyprojections, big, Procedures, Lysine Hydrochloride, lamellae, Aminosaeure, number, Aminocarbonsaeure, Gene, Spectrum Analyses, Isotope-Coded Affinity, presence, process of organ, protrusion, red-spotted newt, lamella, Polypeptides, large, method, Lysine Acetate, Method, method used in an experiment, Gene Products, Mass, Studies, Red Spotted, 2, Triturus viridescens, Lysine, Analysis, Isotopically-Coded Affinity, Isotopically-Coded Affinity Tagging, Mass Spectroscopy, L Lysine, Red-Spotted Newt, Mass Spectrum Analysis, amino acids, Genomes, Analyses, Identification, Tissue, epsilon-diaminocaproic acid, proteins, ridges, C6H14N2O2, Notophthalmus viridiscens, Red-Spotted Newts, Study, Methodological Studies, Stable, papilla, Lysin, great, Isotope-Coded Affinity Tagging, species, Tagging, laminae, Stable Isotope Labeling, Newts, anatomical protrusion, anatomical process, Aminokarbonsaeure, Proteins, lamina, flanges, Procedure, Labeling, Spectrum Analysis, Spectroscopy, polypeptide, Isotope, count in organism, count, Diemictylus viridescens, Stable Isotope, Acetate, Protein, shelf, sequence, Notopthalmus viridescens, L-Lysine, flange, Isotope Coded Affinity Tagging, Mass Spectrum Analyses, organ process, Data Base, Mass Spectrum, Regenerations, shelves, Tails, Newt, expanded, Spectrometry, Identifications (Psychology), Methodological, alpha, Isotope Labeling, Amino, projection, Affinity Tagging, Methodological Study, ridge, Isotopically-Coded, primary structure of sequence macromolecule, Protein Gene Products, plan specification, Gene Proteins, process, processes, enlarged, spine, Isotope-Coded, processus, primary structure of sequence macromolecule., Acids, Red-Spotted, quantitative, eastern newt, 6-diaminohexanoic acid, Proteomes, Enisyl, presence or absence in organism2603http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32300000779dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0embl-pathogen~0project~0human_diseases~0geo_datasets~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0varsite~00.00.00.0080197409006785930.001.0falseAdvanced identification of proteins in uncharacterized proteomes by pulsed in vivo SILACTRANCHE KEY: EfXsK8WKQKnCiGubVrXxCmmygO9Wbb8TYBBFZgdSBwla6M3AjwhqeHpWgNp8DijuGCbKH49+jBc625dSmgLPaNuv0JgAAAAAAAAB0w== Newt Tail Raw Data 12. A pulsed SILAC-based mass spectrometry method was used , which is based on the detection of paired peptides after 13C6-lysine incorporation into proteins in vivo, to greatly increase the confidence of protein identification in cross-species database searches. Data from Mol Cell Proteomics. 2010 Feb 5 .2010-02-19GPM3230000077920139370