PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering10090https://pax-db.org/dataset/10090/3996841450mering@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.Examination of multiple proteomics datasets within or between species increases the reliability of protein identification. We report here proteomes of inner-ear hair bundles from three species (chick, mouse, and rat), which were collected on LTQ or LTQ Velos ion-trap mass spectrometers; the constituent proteins were quantified using MS2 intensities, which are the summed intensities of all peptide fragmentation spectra matched to a protein. The data are available via ProteomeXchange with identifiers PXD002410 (chick LTQ), PXD002414 (chick Velos), PXD002415 (mouse Velos), and PXD002416 (rat LTQ). The two chick bundle datasets compared favourably to a third, already-described chick bundle dataset, which was quantified using MS1 peak intensities, the summed intensities of peptides identified by high-resolution mass spectrometry (PXD000104; updated analysis in PXD002445). The mouse bundle dataset described here was comparable to a different mouse bundle dataset quantified using MS1 intensities (PXD002167). These six datasets will be useful for identifying the core proteome of vestibular hair bundles.Hair-bundle proteomes of avian and mammalian inner-ear utricles.Wilmarth Phillip A PA, Krey Jocelyn F JF, Shin Jung-Bum JB, Choi Dongseok D, David Larry L LL, Barr-Gillespie Peter G PGAdd, 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, ratioaverage, Stars, Ionen, ion, Ion, MS1, Ms1, MALE STERILITY 1 PROTEIN, male sterility 1, MS/MS, iones, MS2, Striated muscle activator of Rho-dependent signaling, E430039A18Rik, CD156., T6G21.3, STARS, ions, CD156a, tandem MSOtolithic Organ, fur, setulae, Saccules, ENL/AF9, Fetal Hairs, whisker, Utricle and Saccule, auditory apparatus, Fetal Hair, Otolithic., birds, coat/ hair, System, avian, vibrissa, hair, Vestibulocochlear System, Hairs, Rnase3, Vestibulocochlear, Utricles, Apparatus, microchaeta, Ears, CG4913, R1, Hair, ENL/AF-9, auditory system, auris, R7, dENL/AF9, DmelCG4913, quill, Fetal, Otolithic Organs, Vestibulocochlear Apparatus, Saccule, ECP, Ear, EAR, coat hair, Proteomes, Utricle, Lanugo, OrganOtolithic Organ, average, Saccules, Utricle and Saccule, Stars, ion, MS1, MALE STERILITY 1 PROTEIN, MS/MS, iones, MS2, Striated muscle activator of Rho-dependent signaling, E430039A18Rik, Otolithic, muscle, CD156., Utricles, T6G21.3, ions, CD156a, muscle element, Ionen, Ion, Otolithic Organs, Ms1, male sterility 1, musculus, Saccule, utriculus, STARS, tandem MS, Utricle, Organsetulae, Rat, ion, determination, Laboratory, Mus domesticus, Norway Rat, protein, Progress Reports, House Mouse, Norway Rats, RP11-508D10.1, Hair, peptide, Tnfsf5, Polypeptides, protein polypeptide chains, rat, peptido, Summary Report, Mammals, Norway rat, Analysis, protein aggregate, Summary Reports, WMS, T-BAM, Mass Spectrum Analysis, type 5 acid phosphatase, Fetal Hairs, tartrate-resistant acid ATPase, peptides, Progress Report, Analyses, vibrissa, E430039A18Rik, Swiss Mice, proteins, T6G21.3, Laboratory Rat, Progress, TRAP3, T-cell antigen Gp39, Tudor repeat associator with PCTAIRE-2, Field Reports, Fetal, TNFSF5, house mouse, T5ap, MGC - 45012, GPHYSD2, SGS, CD40L, Stars, Data Set, Tnfrsf5, mouse, Cd40l, Hairs, Rattus, Spectrum Analysis, mice C57BL/6xCBA/CaJ hybrid, hCD40L, ACMICD, Spectroscopy, Mus norvegicus, Rattus norwegicus, Investigative Report, Ionen, IMD3, TNF-related activation protein, Ly-62, Mus musculus, whisker, MS/MS, mice, Field, Swiss Mouse, NKTL, Spectrometry, AW743063, MASS, AI326936, rats, domesticus, Report, TrATPase, IGM, CD40LG, Mouse, Polypeptide, Fetal., STARS, Proteomes, norvegicus, TRAP, p50, Peptidomics, Ly62, TAPK, nucleocapsid, FBN, Gene, Spectrum Analyses, protein-containing complex, TR-AP, Rattus sp. strain Wistar, Investigative, Rats, polypeptide chain, House, Ms1, ECTOL1, GP39, Gene Products, Mass, Mus musculus domesticus, Rattus rattiscus, CD40-L, Mice, Mass Spectroscopy, Lanugo, gp39, brown rat, CD154, Rattus norvegicus, Fetal Hair, CATC4, GKLP, MS1, Swiss, iones, MS2, coat/ hair, ions, CD156, OCTD, PCTAIRE2-binding protein, MGC:45012, TEIF, Trap, quill, male sterility 1, HIGM1, peptidos, species, Investigative Reports, C78062, Rattus norvegicus8, fur, P105, NTKL, data, protein complex, PCTAIRE2BP, Proteins, total expressed protein, Bp50, ACP5, SPENCDI, Peptide, Mus muscaris, polypeptide, MS, native protein, natural protein, Mus, Laboratory Rats, Protein, Research Reports, chemical analysis, core, MFS1, tandem MS, Mass Spectrum Analyses, WMS2, Mass Spectrum, MALE STERILITY 1 PROTEIN, Striated muscle activator of Rho-dependent signaling, hair, House Mice, CD156a, microchaeta, Laboratory Mice, Protein Gene Products, Gene Proteins, ear hair, Reports, Ion, SSKS, Peptid, Norway, TRACP, assay, coat hair, Summary, Laboratory Mouse, Field Report, Gunn rats0falseM.musculus - Utricle epithelia, average of 2 measurements, MS1 extracted ion chromatogram and sum of MS2 intensity (Wilmarthetal.,scidata,2015)abundance based on average of 2 measurements, MS1 extracted ion chromatogram and sum of MS2 intensity, Interaction consistency score: 9.2, Coverage: 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