PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering9606https://pax-db.org/dataset/9606/2334528786mering@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.Here, we present a method for in-depth human plasma proteome analysis based on high-resolution isoelectric focusing HiRIEF LC-MS/MS, demonstrating high proteome coverage, reproducibility and the potential for liquid biopsy protein profiling. By integrating genomic sequence information to the MS-based plasma proteome analysis, we enable detection of single amino acid variants and for the first time demonstrate transfer of multiple protein variants between mother and fetus across the placenta. We further show that our method has the ability to detect both low abundance tissue-annotated proteins and phosphorylated proteins in plasma, as well as quantitate differences in plasma proteomes between the mother and the newborn as well as changes related to pregnancy.In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta.Pernemalm Maria M, Sandberg AnnSofi A, Zhu Yafeng Y, Boekel Jorrit J, Tamburro Davide D, Schwenk Jochen M JM, Björk Albin A, Wahren-Herlenius Marie M, Åmark Hanna H, Östenson Claes-Göran CG, Westgren Magnus M, Lehtiö Janne JAdd, 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, ratioFresh, Frozen Plasma, placentas (exact, human being, Fresh Frozen Plasma, determination, protein complex, Blood, plural), Modern, Proteins, placenta (Spanish, total expressed protein, Gene, protein, protein-containing complex, Plasmas, Human, Frozen Plasmas, protein polypeptide chains, native protein, placentae (exact, exact), Homo sapiens, natural protein, polypeptide chain, chemical analysis, Protein, Gene Products, tissue portion, simple tissue, protein aggregate, placenta, Man, Plasma, portion of tissue, Fresh Frozen Plasmas, Fresh Frozen, portion of blood plasma, Blood Plasma, Man (Taxonomy), allantoic placenta, Tissue, portion of plasma, proteins, man, human, Protein Gene Products, 胎座 (Japanese, Gene Proteins, portion of placenta tissue (exact), blood plasm, Placentas., Normal, Modern Man, Blood Plasmas, Placentomes, Placentome, assay, Proteomes, eutherian placenta, plasma, PlacentomaPlasma, Fresh, Frozen Plasmas, Fresh Frozen Plasmas, Fresh Frozen, blood plasm, portion of blood plasma, Blood Plasma, Frozen Plasma, Fresh Frozen Plasma, Blood Plasmas, Blood, portion of plasma, Plasmas, plasma.liquid chromatography tandem mass spectroscopy, Fresh, Neonates, fetus stage, human being, Procedures, Fresh Frozen Plasma, determination, Effects, embryo late stage, Blood, Aminosaeure, Aminocarbonsaeure, placenta (Spanish, Amino acid, Neonate, Gene, protein, Pregnancies., alpha-amino acid, protein-containing complex, Long Term, LC-MS-MS, Human, Liquid Biopsies, method, Techniques, protein polypeptide chains, Fetuses, PREGN, exact), Homo sapiens, polypeptide chain, Method, method used in an experiment, LC-MSMS, Studies, Gene Products, Low, protein aggregate, placenta, Effect, Technique, Man, fetus, portion of tissue, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, me75, LCMSMS, amino acids, Man (Taxonomy), Biopsies, Longterm, Tissues, Tissue, Mother, proteins, Long-Term, Isoelectric, Structures, man, Structure, D17Mit170, T1, Mummified, 胎座 (Japanese, Study, portion of placenta tissue (exact), Abilities, Methodological Studies, Fetal, Normal, Blood Plasmas, Long-Term Effect, Fetal Structure, Biopsy, Long-Term Effects, eutherian placenta, plasma, LC-MS2, Newborn Infants, NEWBORN (0-27 DAYS), Neonatal, Frozen Plasma, placentas (exact, cou, Infants, protein complex, Aminokarbonsaeure, plural), Modern, Placentas, Proteins, LC-MS/MS, Aptitudes, Longterm Effect, total expressed protein, alpha-amino acids, Procedure, Tl3, Plasmas, Tl2, alpha-amino carboxylic acids, embryo late growth stage, Ability, Frozen Plasmas, LC/MS/MS, Lr, native protein, placentae (exact, natural protein, chemical analysis, Protein, Long Term Effects, sequence, tissue portion, Newborn Infant, simple tissue, Fetal Structures, Mummified Fetus, Plasma, Amino Acid, Acid, portion of blood plasma, Amino acids, Electrofocusing, Gestation, allantoic placenta, Newborns, portion of plasma, Talents, Focusing, Methodological, Amino, Fetus, Methodological Study, Fetal Tissue, human, primary structure of sequence macromolecule, Longterm Effects, plan specification, Protein Gene Products, Gene Proteins, Retained Fetus, blood plasm, Fetal Tissues, liquid chromatography-tandem mass spectroscopy, Talent, Modern Man, fetal stage, Placentomes, Bra, Liquid, Placentome, liquid chromatography tandem mass spectrometry, Newborn, Acids, Retained, assay, Proteomes, Placentoma0falseH.sapiens - Plasma, iBAQ (Pernemalmetal,elife.2019)abundance based on iBAQ, Interaction consistency score: 4.2, Coverage: 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