MassIVEapplication/xmlftp://massive-ftp.ucsd.edu/v01/MSV000079263/primary200OK3000ProteomicsAngus LamondQ ExactiveCaenorhabditis Elegans (ncbitaxon:6239)https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=744e0aa8584f4c06b60e7f0a2e002b4bMassIVE486MS:1002864 - No post-translational-modifications are included in the identified peptides of this datasetEffective network analysis of protein data requires high-quality proteomic datasets. Here, we report a near doubling in coverage of the C. elegans adult proteome, identifying >11,000 proteins in total with ∼9,400 proteins reproducibly detected in three biological replicates. Using quantitative mass spectrometry, we identify proteins whose abundances vary with age, revealing a concerted downregulation of proteins involved in specific metabolic pathways and upregulation of cellular stress responses with advancing age. Among these are ∼30 peroxisomal proteins, including the PRX-5/PEX5 import protein. Functional experiments confirm that protein import into the peroxisome is compromised in vivo in old animals. We also studied the behavior of the set of age-variant proteins in chronologically age-matched, long-lived daf-2 insulin/IGF-1-pathway mutants. Unexpectedly, the levels of many of these age-variant proteins did not scale with extended lifespan. This indicates that, despite their youthful appearance and extended lifespans, not all aspects of aging are reset in these long-lived mutants.Deep Proteome Analysis Identifies Age-Related Processes in C. elegans.Narayan Vikram V, Ly Tony T, Pourkarimi Ehsan E, Murillo Alejandro Brenes AB, Gartner Anton A, Lamond Angus I AI, Kenyon Cynthia Cprojections, determination, RnBP, lamellae, shelves, lamina, total expressed protein, GlcNAc 2-epimerase, flanges, ridges, organ process., projection, process of organ, ridge, AGE, lamella, processes, N-acetyl-D-glucosamine 2-epimerase, papilla, RENBP, chemical analysis, shelf, renin-binding protein, assay, laminae, Proteomes, flangeMetabolic Networks, Networks, Pxr1, Soluble, PXR1, IPP2A2, Insulin B Chain, scale tissue, Product, adult stage, X83306, metazoans, insuline humaine, protein, Progress Reports, MXK23_3, Aging, peroxisome targeting signal-1 receptor, Downregulation, CG11121, 5730420M11Rik, Insulin Like Growth Factor I, Insulin-Like 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Acceptance Processes, Regular Insulin, Spectroscopy, Acceptance Process, insulin (recombinant), Investigative Report, Receptor Down-Regulation, IGF-1, Biopharmaceuticals, RENBP, IGF-I-SmC, Biologic Product, Igf-1, Adults, Soluble Insulin, HLA-DR-associated protein II, DI-2, Biological Medicines, Upregulation, Biological Drug, I-2Dm, life, Field, Spectrometry, insulina humana, Biologics, CG4299, AGE, I-2PP1, PBD2B, Report, PBD2A, TAF-IBETA, DmelPex5, TAF-Ibeta, i2pp2a, Proteomes, lifespan, Biologic Pharmaceuticals, Processes, peltate hair, Gene, Network, Insulin B, Spectrum Analyses, AW212715, protein-containing complex, peroxisome targeting signal-1 binding, animals, PHAPII, Investigative, polypeptide chain, DmelCG11121, Insulin, Gene Products, Mass, Animal, Mass Spectroscopy, Biologicals, Drugs, CG14815, Chain, network topology analysis, somda, PTS1-BP, Receptor Up-Regulation, entire lifespan, Up Regulation, ipp2a2, Natural Product, 2pp2a, igf-1, CG10574, Biological., Iletin, 2PP2A, Insulin recombinant, taf-ibeta, dSET, dSet, Investigative Reports, Behaviors, protein uptake, Biologic, Lifespan, Pharmaceuticals, Drl, Products, Life Spans, protein complex, Biologic Medicines, RnBP, Proteins, igaad, total expressed protein, GlcNAc 2-epimerase, Down Regulation, Mdu, group, N-acetyl-D-glucosamine 2-epimerase, MS, Down-Regulation, native protein, Sodium Insulin, natural protein, I-2PP2A, mda, Down-Regulation (Physiology), Protein, Research Reports, Metazoa, Dm I-2, Biopharmaceutical, I2PP2A, Insulin A Chain, Sodium, peroxisomal targeting signal 1 (PTS1) binding, Novolin, PEX5, scales, Mass Spectrum Analyses, Metabolic Pathways, ARABIDOPSIS PEROXIN 5, ami, Mass Spectrum, Acceptance, Exubera, scale, Metabolic, ensemble, med, PTS1R, Protein Gene Products, Drug, multicellular animals, Gene Proteins, dSET/TAF-Ibeta, 2610030F17Rik, Reports, renin-binding protein, Natural Products, Metabolic Pathway, Receptor, ATPEX5, Summary, AA407739, Field ReportNemata, RnBP, protein complex, Proteins, GlcNAc 2-epimerase, Gene, proteins, protein, protein-containing complex, AGE, Protein Gene Products, Gene Proteins, roundworm, nematode, protein polypeptide chains, N-acetyl-D-glucosamine 2-epimerase, native protein, natural protein, polypeptide chain, RENBP, Protein, nematodes, Gene Products, renin-binding protein, roundworms., protein aggregatepyridoxine-dependent, Saturated Fatty, acido graso, Esterified Fatty Acids, acidos grasos, CG 1618, Peptidomics, pyridoxine dependency with seizures, Aminosaeure, number, Aminocarbonsaeure, metazoans, Comt, dNSF, Amino acid, Gene, NSF1, protein, Progress Reports, Spectrum Analyses, Aging, alpha-amino acid, protein-containing complex, animals, presence, Downregulation, NSF, Nsf, peptide, Polypeptides, protein polypeptide chains, CG1618, peptido, Investigative, DmNSF, polypeptide chain, acides gras, Biological, Summary Report, Metabolism, single-organism carbohydrate metabolic process, Mass, Gene Products, dNSF1, AGE., dNsf1, Saturated Fatty Acids, Esterified Fatty Acid, Analysis, Animal, protein aggregate, Peroxisome, Summary Reports, peroxisomal, Mass Spectroscopy, Esterified, Mass Spectrum Analysis, Animalia, Senescence, Fatty Acids, network topology analysis, multicellular organismal carbohydrate metabolic process, amino acids, peptides, Analyses, Progress Report, Esterified Fatty, Aliphatic, proteins, Progress, Biological Aging, Aliphatic Acids, Field Reports, ATQ1, peroxisome vesicle, DmelCG1618, peptidos, Investigative Reports, com, epilepsy, Saturated, protein complex, RnBP, Aminokarbonsaeure, Proteins, total expressed protein, GlcNAc 2-epimerase, alpha-amino acids, function, Fettsaeuren, Spectrum Analysis, Peptide, alpha-amino carboxylic acids, Down Regulation, Spectroscopy, polypeptide, Fettsaeure, count in organism, N-acetyl-D-glucosamine 2-epimerase, MS, Down-Regulation, native protein, natural protein, Investigative Report, Receptor Down-Regulation, Down-Regulation (Physiology), RENBP, Protein, Research Reports, Metazoa, dNSF-1, Mass Spectrum Analyses, dnsf1, Mass Spectrum, Acid, Amino Acid, Fatty Acid, carbohydrate metabolism, Saturated Fatty Acid, Amino acids, PDE, Field, Spectrometry, AASA dehydrogenase deficiency, Aliphatic Acid, acide gras, Amino, Carbohydrate, Protein Gene Products, multicellular animals, Gene Proteins, fatty acids, Report, Reports, pyridoxine dependency, pyridoxine-dependent epilepsy, renin-binding protein, Peptid, NSF-1, Acids, Polypeptide, Receptor, EPD, Epd, Summary, Proteomes, Field Report3PXD004584trueAge-related changes in protein abundance in nematodesUsing quantitative mass spectrometry together with protein and peptide-level fractionation, we can now report a major increase in coverage of the C. elegans proteome, identifying over 9,300 proteins in three biological replicates. The resulting data have been assembled into a searchable, online resource with a user-friendly graphical interface to provide convenient and open access to the community (https://www.peptracker.com/epd/). By quantifying these proteins in fertile, post-reproductive and aging animals, we show that there is a striking change in abundance of ~8% of the proteome during the course of aging. Network analysis of our proteomics data reveals a concerted down-regulation of proteins involved in fatty acid, amino acid and carbohydrate metabolism, as well as peroxisome function, with increasing age.Fri Aug 21 13:37:00 BST 2015MSV00007926327453442