{"database":"PAXDB","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["10090"],"full_dataset_link":["https://pax-db.org/dataset/10090/1762132932"],"submitter_email":["mering@imls.uzh.ch"],"submitter_affiliation":["University of Zurich"],"sample_protocol":[""],"repository":["PAXDB"],"data_protocol":["For the rescaling, the\ndatasets are first parsed or processed such that the data reflect\nproportional abundances of whole protein molecules\n(i.e. proportionality to counts of complete, individual protein\nmolecules, not to molecular weights, protein volumes, or digested\npeptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up\nto one million; this means the abundance of each protein of\ninterest is finally expressed in (parts per million,) relative to\nall other proteins in a sample. \nFor a given protein abundance dataset, we then compute\nthe absolute log abundance ratios of all pairs of proteins\nannotated to be functionally linked. The median of these absolute\nlog abundance ratios represents an indirect quality\nmetric: the closer it is to zero, the better (i.e. the more there\nis consistency between abundance values and functional annotations\nsuch as protein complexes or pathways). We then\ncompute a background expectation for this metric, by permuting\nthe abundance values in a given dataset randomly,\nand recomputing the median log abundance ratios. The permutation\nis repeated several times, yielding a distribution of\nmedians. The actually observed median is then expressed as a\nZ-score distance to the random distribution ofmedians—this\ndistance is termed the interaction consistency score."],"pubmed_abstract":["Skeletal muscle constitutes 40% of individual body mass and plays vital roles in locomotion and whole-body metabolism. Proteomics of skeletal muscle is challenging because of highly abundant contractile proteins that interfere with detection of regulatory proteins. Using a state-of-the art MS workflow and a strategy to map identifications from the C2C12 cell line model to tissues, we identified a total of 10,218 proteins, including skeletal muscle specific transcription factors like myod1 and myogenin and circadian clock proteins. We obtain absolute abundances for proteins expressed in a muscle cell line and skeletal muscle, which should serve as a valuable resource. Quantitation of protein isoforms of glucose uptake signaling pathways and in glucose and lipid metabolic pathways provides a detailed metabolic map of the cell line compared with tissue. This revealed unexpectedly complex regulation of AMP-activated protein kinase and insulin signaling in muscle tissue at the level of enzyme isoforms."],"pubmed_title":["Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors."],"pubmed_authors":["Deshmukh Atul S AS, Murgia Marta M, Nagaraj Nagarjuna N, Treebak Jonas T JT, Cox Jürgen J, Mann Matthias M"],"data_synonyms":["Add, DmelCG43443, ADD, ADD-87, Hts-RC, data, AU023367, Data Set, protein complex, supply, Proteins, Ovhts, Gene, HtsRC, CG9325, protein, neutral molecular compounds, protein-containing complex, Dmel_CG9325, Xt, Peptide, 1B1, add, Polypeptides, anon-EST:Posey9, protein polypeptide chains, native protein, peptido, htsRC, GLI3-190, natural protein, polypeptide chain, Add-hts, Protein, CG43443, Gene Products, l(2)k14523, Dmel_CG34197, l(2)00634, median, Ovhts-RC, background, supply and distribution, protein aggregate, all_pairs, molecule, Bph, molecula, Random selection by shearing, oligonucleotide random primer, proportion, HTS-R1, HTS, Hts, molecules, peptides, l(2)k06121, adducin, GLI3FL, distribution, AI854843, proportionality, add-like, HTS-RC, rate, proteins, Molekuel, Pdn, sample population, introduction, Protein Gene Products, Gene Proteins, Adducin, RANDOM, 10^[-6], ppm, sample, supply., quotient, Peptid, peptidos, Polypeptide, Attention Deficit Hyperactivity Disorder, l(2)01103, EST D, CG34197, HtsF, ratio"],"pubmed_title_synonyms":["Metabolic Networks, Networks, Plantaris, Gastrocnemius Muscle, Pathway, Anterior, Peptidomics, Laboratory, Skeletal, Mus domesticus, Anterior Tibial Muscle, mouse, Splice Variants, Network, Factor, Metabolic Network, Isoform, Muscle, Protein Splice, House Mouse, skeletal muscle, mice C57BL/6xCBA/CaJ hybrid, Mus muscaris, Soleus, somatic muscle, House, Mus, Voluntary Muscle, Voluntary, Protein, Voluntary Muscles, Variant, Mus musculus domesticus, Isoforms, Mice, Metabolic Pathways, Splice Variant, Mus musculus, Transcription, Protein Splice Variant, Factors, Soleus Muscle, Metabolic, Swiss, Tibial Muscle, mice, Swiss Mouse, Pathways, House Mice, Swiss Mice, Protein Splice Variants, Protein Isoform, Skeletal Muscles, domesticus, Laboratory Mice, Skeletal Muscle, Plantaris Muscle, Muscles, Variants, Metabolic Pathway, Mouse, house mouse, Anterior Tibial, Gastrocnemius, Laboratory Mouse, Transcription Factor., striated muscle, skeletal muscle system"],"name_synonyms":["Line, Cell Lines, Cell., muscle, musculus, Cell, muscle element, Lines"],"pubmed_abstract_synonyms":["biochemical pathways, Metabolic Networks, Networks, Soluble, Insulin B Chain, Plantaris, Metabolic Process, Adenosine 5' Phosphate, Anterior, dAmph, Activity, methionine aminopeptidase activity, APRTD, Adenylic Acid, Skeletal, Glukose, Myocyte, Anterior Tibial Muscle, Metabolic Concepts, Monohydrate, Splice Variants, insuline humaine, (DL)-Isomer, 5'-Adenosine monophosphate, PAdo, CG3629, Protein Splice, Social Controls, 6-(D-(2-amino-2-phenylacetamido))-3, portion of muscle tissue, damph, human insulin, Dextrose, ampicillin acid, AP, Line, Adenosine-5'-monophosphoric acid, Concepts, 2, aminobenzylpenicillin, Kinase, Metabolism Concept, Work Flow, animal, Phenomenon, Muscle Cell, Formal Social Controls, WMS, peptidase M activity, adenomas, AI661365, Art, portion of tissue, ART, rabGAPLP, insulin, L-methionine aminopeptidase activity, ampicillin anhydrous, Muscle Tissues, Protein Splice Variant, 3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID, Myod-1, catabolism, Tissue, RabGAP-5, Pathways, metabolic process resulting in cell growth, proteins, Protein Isoform, adenosine phosphate, DL-glucose, 5'-Adenylic acid, phosphate d'adenosine, Ba, Social, insulin human, Muscles, ampicilina, RUSC3, Mature Muscle Cell, signaling process, biotransformation, GPHYSD2, Gastrocnemius, Catabolism, SGS, single organism signaling, Anhydrous ampicillin, insulinum humanum, bHLHc1, Pathway, Regular, dl, 2'-Adenosine Monophosphate, Adenosine 3'-Phosphate, (2S, Process, Adenosine Phosphate Dipotassium, metabolism resulting in cell growth, Arts, MYH-associated polyposis, autosomal recessive familial adenomatous polyposis, Maps, Metabolic Network, Isoform, 2'-Adenylic Acid, ACMICD, Adenosine 3' Phosphate, Regular Insulin, l(2)01092, organism, insulin (recombinant), Workflows, MYOD, MyoD, 3-dimethyl-7-oxo-4-thia-1-azabicyclo(3.2.0)heptane-2-carboxylic acid, BHLHC3, Voluntary Muscle, Voluntary, DmelCG3629, glucose import, Lipid, Voluntary Muscles, 2'-Adenylic, BcDNA:LP01770, tissue portion, fosfato de adenosina, 3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid, secretion, simple tissue, IVF, (alpha-D)-Isomer, D-(-)-6-(alpha-aminophenylacetamido)penicillanic acid, Soluble Insulin, 5R, autosomal recessive, Lines, D-Glucose, Acid, RUTBC3, DLL, Factors, whole organism, Control, insulina humana, Adenosine 5'-Phosphate, Biocatalyst., Phosphaden, 6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3, MASS, Controls, Mature, 5'-O-phosphonoadenosine, E(Arp), En(Arp), ampicillinum, RABGAP5, Activities, Contractile Protein, CLOCK Protein, Adenosine, SNF1-RELATED PROTEIN KINASE 2-2, dll, myocyte, PUM, D Glucose, SNF1-related protein kinase 2.2, Koerper, multiple colorectal, spindle cells, AGRT, Monophosphate, Glucose Monohydrate, Regulation, Protein Kinase, adenosini phosphas, Work Flows, DAMP, Regulations, lipids, DmelCG8604, biological signaling, Gastrocnemius Muscle, multi-cellular organism, amph, Phosphate Disodium, Peptidomics, Myocytes, Glucose, Processes, Biocatalysts, Adenosine 2' Phosphate, FBN, Gene, 9930121L06Rik, Network, Insulin B, Metabolic Processes, adenosine 5'-(dihydrogen phosphate), Transcription Factor, skeletal muscle, Locomotor, Damp, l(2)387, ECTOL1, Metabolism, Insulin, Gene Products, Variant, Isoforms, 5'-Adenylic, Metabolism Phenomena, 6R)-6-{[(2R)-2-amino-2-phenylacetyl]amino}-3, familial adenomatous polyposis, MAP, Splice Variant, Chain, 5'-AMP, Transcription, 2' Adenosine Monophosphate, Adenylate, Tibial Muscle, Circadian Locomotor Output Cycles Kaput Proteins, Tissues, familial adenomatous polyposis 2, Metabolic Concept, Protein Splice Variants, Locomotor Activity, Skeletal Muscles, Muscle Cells, ATP-protein phosphotransferase, OCTD, autosomal recessive multiple colorectal adenomas, Skeletal Muscle, Iletin, Enzyme, ampicilline, SNRK2-2, Plantaris Muscle, Insulin recombinant, Ado5'P, 5'-Phosphate, glucose uptake, textus muscularis, Anterior Tibial, 2.7, Anhydrous, MYF3, MYF4, striated muscle, 2'-AMP, ADENOSINE MONOPHOSPHATE, MUTYH-Associated Polyposis, (beta-D)-Isomer, degradation, Formal Social Control, body, Proteins, Cell Lines, whole body, 5' Adenylic Acid, Factor, Muscle, 2'-Adenosine, Cell, muscle cell, Concept, Metabolic Phenomena, Soleus, Mature Muscle Cells, Metabolism Concepts, ampicillin, somatic muscle, AMP, Amp, muscle fiber, SRK2D, native protein, Sodium Insulin, Social Control, Protein, Phenomena, 5'-Adenylic Acid, Insulin A Chain, CG8604, MFS1, Adenosine Phosphate, Sodium, Novolin, D-(-)-ampicillin, metabolism, Metabolic Pathways, WMS2, AI503393, Adenosine 5'-phosphate, Metabolic Phenomenon, muscular tissue, 6R)-6-{[(2R)-2-amino-2-phenylethanoyl]amino}-3, multicellular organism metabolic process, Exubera, SPK-2-2, Phosphate Dipotassium, Soleus Muscle, biodegradation, Metabolic, ABPC, Kinases, Locomotor Activities, adenosine-5'P, pA, Disodium, MYH-Associated Polyposis, Adenosine 2'-Phosphate, signalling, Anhydrous Dextrose, Protein Gene Products, Gene Proteins, Adenosine Phosphate Disodium, single-organism metabolic process, Dipotassium, Contractile, Snm1l, signalling process, SSKS, Variants, Metabolic Pathway, MAP syndrome, regulation, 2' Adenylic Acid, PROTEIN KINASE, Muscle Tissue, Adenylic acid, FAP2, skeletal muscle system, Anabolism, colorectal adenomatous polyposis, Glc"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"M.musculus - Cell line, SC (Deshmukhetal,molcellproteomics2015)","description":"abundance based on Spectral counting, Interaction consistency score: 20.2, Coverage: 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