PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering8355https://pax-db.org/dataset/8355/913028949mering@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.<h4>Background</h4>Mass spectrometry-based proteomics enables the global identification and quantification of proteins and their posttranslational modifications in complex biological samples. However, proteomic analysis requires a complete and accurate reference set of proteins and is therefore largely restricted to model organisms with sequenced genomes.<h4>Results</h4>Here, we demonstrate the feasibility of deep genome-free proteomics by using a reference proteome derived from heterogeneous mRNA data. We identify more than 11,000 proteins with 99% confidence from the unfertilized Xenopus laevis egg and estimate protein abundance with approximately 2-fold precision. Our reference database outperforms the provisional gene models based on genomic DNA sequencing and references generated by other methods. Surprisingly, we find that many proteins in the egg lack mRNA support and that many of these proteins are found in blood or liver, suggesting that they are taken up from the blood plasma, together with yolk, during oocyte growth and maturation, potentially contributing to early embryogenesis.<h4>Conclusion</h4>To facilitate proteomics in nonmodel organisms, we make our platform available as an online resource that converts heterogeneous mRNA data into a protein reference set. Thus, we demonstrate the feasibility and power of genome-free proteomics while shedding new light on embryogenesis in vertebrates.Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database.Wühr Martin M, Freeman Robert M RM, Presler Marc M, Horb Marko E ME, Peshkin Leonid L, Gygi Steven S, Kirschner Marc W MWAdd, 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, ratiodSetdb1, egg, RNA, Peptidomics, Polyadenylated, Unfertilized Egg, African clawed frog, Eggs, X. laevis, Messenger RNA, common platanna, SetDB1, clawed frog <Xenopus laevis>, Data Base., Unfertilized Eggs, Dmel_CG30422, AAM70794, Messenger, 1802), Poly(A)+ mRNA, Dmel_CG30426, INSDC_feature:mRNA, Bufo laevis, Xenopus leavis, clawed frog, Polyadenylated RNA, AAF47268 Dm, Ova, Non Polyadenylated, Polyadenylated Messenger RNA, Unfertilized, dEset, dsetdb1, Poly(A)+ RNA, Non Polyadenylated mRNA, protein_coding_transcript, BcDNA:AT13877, mRNA, Poly(A) Tail, Polyadenylated Messenger, dSETDB1, Non-Polyadenylated, messenger RNA, CG30426, CG12196, CG30422, Non-Polyadenylated mRNA, Dmsetdb1, Egg, DmSetdb1, SETDB1, template RNA, Xenopus laevis (Daudin, DmelCG12196, platanna, X. laevi, Polyadenylated mRNA, Platanna, Poly(A) RNA, Dm-setdb1, Platannasegg cell, mature oocyte, ovum.dSetdb1, IPP2A2, egg, Postnidation Embryo, Materials, Pre-implantation Embryo Development, Unfertilized Egg, Ass-1, Sequence Determination, Blood, Post-implantation, Visible Light, protein, Pre implantation Embryo Development, Embryonic Programming, 5730420M11Rik, protein polypeptide chains, Techniques, Embryo Development, Personal, DSmurf, Method, 1802), AA408052, hnu, fold, Analysis, protein aggregate, Fs(3)Hor, Non Polyadenylated, foton, Mass Spectrum Analysis, Psychological, SET, Fresh Frozen Plasmas, Fresh Frozen, DmelCG2684, Analyses, Genomes, TAF-I, Determination, Polyadenylated Messenger, iecur, proteins, procedures, CG30426, NTef2, Sequence Determinations, free, CG30422, Preimplantation Embryo Development, DmelCG4299, Social, ASS, DNA Sequence Analysis, IGAAD, set, Dmsetdb1, SETDB1, TNFSF14, Xenopus laevis (Daudin, Methodological Studies, DmelCG10574, Smurf, DmelCG12196, Social Power, plasma, CG4943, Power, gamma, D-smurf, phapii, Frozen Plasma, embryonal development, Radiation, Polyadenylated, UNQ391/PRO726, African clawed frog, StF-IT-1, common platanna, SetDB1, Light, clawed frog <Xenopus laevis>, Psychological Powers, Procedure, Lack, Plasmas, Spectrum Analysis, results, Determinations, Fs(3)Sz11, Spectroscopy, Dmel_CG30422, LIGHT, Dmel_CG30426, DNA Sequence Determinations, Genetic Materials, embryo Ce, DNA Sequence, Genetic Material, DNA sequencing, Polyadenylated Messenger RNA, Visible Radiations, dsetdb1, portion of blood plasma, Visible Radiation, Non Polyadenylated mRNA, HLA-DR-associated protein II, protein_coding_transcript, HVEML, DI-2, DmelCG4943, I-2Dm, dSETDB1, Spectrometry, INSDC_feature:gene, CG4299, whole genome, Methodological, Methodological Study, Non-Polyadenylated mRNA, early, I-2PP1, DmSetdb1, blood plasm, light quantum, TAF-IBETA, Material, Horka, CG2684, Fs(3)Horka, Cistron, TAF-Ibeta, DNA, Powers, i2pp2a, Proteomes, Poly(A) RNA, Postimplantation, Embryonic Programmings, Dm-setdb1, Platannas, Fresh, Psychological Power, Procedures, Fresh Frozen Plasma, Peptidomics, Professional Power, Eggs, dSmurf1, embryogenesis, Gene, Spectrum Analyses, Development, protein-containing complex, PHAPII, jecur, Ly113, Unfertilized Eggs, Prenidation Embryo Development, AAM70794, polypeptide chain, Messenger, yolk, Embryonic Developments, Mass, Gene Products, Studies, clawed frog, DmF2, Animal, AAF47268 Dm, Ova, Technique, Mass Spectroscopy, portion of blood, lod, Unfertilized, Postnidation, Blood Plasma, Genetic, BcDNA:AT13877, Lichtquant, ipp2a2, Postnidation Embryo Development, 2pp2a, messenger RNA, Pre-implantation, Visible, CG12196, CG10574, Sequencing, Study, template RNA, 2PP2A, d-smurf, embryogenesis and morphogenesis, taf-ibeta, Blood Plasmas, dSET, dSet, photon, TR2, Sequence Analyses, RNA, data, whole blood, protein complex, vertebrate blood, X. laevis, Proteins, igaad, Post implantation Embryo Development, total expressed protein, Messenger RNA, Post-implantation Embryo Development, Preimplantation, Dsmurf, Cistrons, CD258, group, dSmurf, Frozen Plasmas, MS, native protein, natural protein, I-2PP2A, Poly(A)+ mRNA, DNA Sequencing, Smurf ubiquitin ligase, Protein, Dm I-2, proteomic analysis, I2PP2A, INSDC_feature:mRNA, Bufo laevis, Vertebrata, Xenopus leavis, Professional, background, Polyadenylated RNA, techniques, Vertebrate, Mass Spectrum Analyses, Postimplantation Embryo Development, Data Base, embryonic stage, Embryonic, Radiations, Plasma, Mass Spectrum, Embryo, dEset, Poly(A)+ RNA, ensemble, mRNA, Poly(A) Tail, HVEM-L, Photoradiation, Non-Polyadenylated, Embryogenesis, portion of plasma, Lds, introduction, DNA Sequence Determination, LTg, Protein Gene Products, Gene Proteins, Livers, dSET/TAF-Ibeta, Egg, Personal Power, 2610030F17Rik, DNA Sequence Analyses, Photoradiations, vertebrates., Power (Psychology), platanna, AA407739, Polyadenylated mRNA, X. laevi, Platanna, methodology0falseXlaevis - Egg cell, SC (Wuehretal,currbiol,2014)abundance based on Spectral counting, Interaction consistency score: 1.9, Coverage: 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