PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering10090https://pax-db.org/dataset/10090/2383348395mering@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.The current study used three different proteomic strategies, which differed by their extent of intact protein separation, to examine the proteome of a pluripotent mouse embryonic stem cell line, R1. Proteins from whole-cell lysates were subjected either to 2-D-LC, or 1-DE, or were unfractionated prior to enzymatic digestion and subsequent analysis by MS. The results yielded 1895 identified non-redundant proteins and, for 128 of these, the specific isoform could be determined based on detection of an isoform-specific peptide. When compared with two previously published proteomic studies that used the same cell line, the current study reveals 612 new proteins.Expanding the mouse embryonic stem cell proteome: combining three proteomic approaches.Gundry Rebekah L RL, Tchernyshyov Irina I, Sheng Shijun S, Tarasova Yelena Y, Raginski Kimberly K, Boheler Kenneth R KR, Van Eyk Jennifer E JEAdd, 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, rationear to, close to, Mouse Embryonic, mESCs, approaches, Cells, Stem Cells, vicinity of., Mouse Embryonic Stem, total expressed protein, mESC, Proteomes, Mouse Embryonic Stem Cellsaliva atomaris, saliva molecularis, Peptidomics., Salivas, sailva normalis, muscle, musculus, muscle elementextent, dTAF[[II]]230, TAF[[II]]250, d230, determination, completeness, mESCs, protein complex, Proteins, Stem Cells, TAF200, Cell Lines, total expressed protein, Gene, l(3)84Ab, dTAFII250, protein, BG:DS00004.13, TAFII-250, protein-containing complex, TAF250/230, EfW1, Mouse Embryonic Stem Cell, Cell, results, Peptide, dTAF230, dmTAF[[II]]230, polypeptide, peptide, Polypeptides, protein polypeptide chains, Mouse Embryonic, TAFII250, native protein, peptido, natural protein, polypeptide chain, dmTAF1, Taf230, p230, Protein, chemical analysis, Gene Products, Line, TAF[[II]]250/230, TFIID, protein aggregate, Separated, TAF250, Lines, Taf[[II]]250, study, Separation, Taf200, Divorced, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, peptides, cel, Protein., cell, Separations, Taf1p, proteins, Divorces, TAF[II]250, CG17603, TAF[[II]], Protein Gene Products, Gene Proteins, dTAF250, DmelCG17603, Taf250, SR3-5, Isolation of Nuclei TAgged in specific Cell Types, Cells, Mouse Embryonic Stem, Peptid, peptidos, assay, Polypeptide, TAF, mESC, Proteomes, TAF230, TAF10falseM.musculus - Saliva, SC (Gundry,proteomics,2010)abundance based on Spectral counting, Interaction consistency score: 11.1, Coverage: 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