PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering10090https://pax-db.org/dataset/10090/3153802780mering@imls.uzh.chUniversity of ZurichPAXDBFor the rescaling, the datasets are first parsed or processed such that the data reflect proportional abundances of whole protein molecules (i.e. proportionality to counts of complete, individual protein molecules, not to molecular weights, protein volumes, or digested peptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up to one million; this means the abundance of each protein of interest is finally expressed in (parts per million,) relative to all other proteins in a sample. For a given protein abundance dataset, we then compute the absolute log abundance ratios of all pairs of proteins annotated to be functionally linked. The median of these absolute log abundance ratios represents an indirect quality metric: the closer it is to zero, the better (i.e. the more there is consistency between abundance values and functional annotations such as protein complexes or pathways). We then compute a background expectation for this metric, by permuting the abundance values in a given dataset randomly, and recomputing the median log abundance ratios. The permutation is repeated several times, yielding a distribution of medians. The actually observed median is then expressed as a Z-score distance to the random distribution ofmedians—this distance is termed the interaction consistency score.Mammalian skeletal muscles are composed of multinucleated cells termed slow or fast fibers according to their contractile and metabolic properties. Here, we developed a high-sensitivity workflow to characterize the proteome of single fibers. Analysis of segments of the same fiber by traditional and unbiased proteomics methods yielded the same subtype assignment. We discovered novel subtype-specific features, most prominently mitochondrial specialization of fiber types in substrate utilization. The fiber type-resolved proteomes can be applied to a variety of physiological and pathological conditions and illustrate the utility of single cell type analysis for dissecting proteomic heterogeneity.Single muscle fiber proteomics reveals unexpected mitochondrial specialization.Murgia Marta M, Nagaraj Nagarjuna N, Deshmukh Atul S AS, Zeiler Marlis M, Cancellara Pasqua P, Moretti Irene I, Reggiani Carlo C, Schiaffino Stefano S, Mann Matthias MAdd, 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, ratioSpecialists, Mitochondrial, contractile fibre, muscle fiber, myocyte, Specialist, Specialism., muscle fibre, ATP synthase D chain, Peptidomics, mitochondrial, muscle cellTissue, Muscle Tissues, muscle, Muscle., Muscle, Muscle Tissue, Tissues, musculus, muscle elementSpecialist, muscle system, Procedures, heterogeneity., determination, musculi, Peptidomics, set of muscles, Feature, musculature system, STK10, muscles, set of skeletal muscles, total expressed protein, A4, Muskelsystem, FASTK, compositionality, Procedure, Muscle, composed of, mitochondrial, Specialism, Cell, TYPE, LGMD2C, DAGA4, Techniques, Workflows, Characteristic, ATP synthase D chain, sensitive, Method, chemical analysis, Studies, Specialists, slow, techniques, Work Flow, MAM, SCG3, sensitivity, Technique, slow speed, Mitochondrial, Muscle Tissues, muscles set, DMDA1, Tissues, content, motor system, Tissue, Specificity, composition, Methodological, procedures, Features, Methodological Study, cell_type, Fast, muscule system, allergic reaction, Study, DMDA, Methodological Studies, Specificity and Sensitivity, ATP:Fas-activated serine/threonine protein phosphotransferase activity, structure, SCARMD2, musculature, Sensitivity, assay, Characteristics, Muscle Tissue, Proteomes, FAST, Work Flows, muscle group, methodology0falseM.musculus - Muscle, SC (Murgiaetal.,emborep2015)abundance based on Spectral counting, Interaction consistency score: 6.9, Coverage: 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