PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering547559https://pax-db.org/dataset/547559/113269583mering@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 dynamic changes that take place along the phases of microbial growth (lag, exponential, stationary, and death) have been widely studied in bacteria at the molecular and cellular levels, but little is known for archaea. In this study, a high-throughput approach was used to analyze and compare the proteomes of two haloarchaea during exponential and stationary growth: the neutrophilic Haloferax volcanii and the alkaliphilic Natrialba magadii. Almost 2000 proteins were identified in each species (≈50% of the predicted proteome). Among them, 532 and 432 were found to be differential between growth phases in H. volcanii and N. magadii, respectively. Changes upon entrance into stationary phase included an overall increase in proteins involved in the transport of small molecules and ions, stress response, and fatty acid catabolism. Proteins related to genetic processes and cell division showed a notorious decrease in amount. The data reported in this study not only contributes to our understanding of the exponential-stationary growth phase transition in extremophilic archaea but also provides the first comprehensive analysis of the proteome composition of N. magadii. The MS proteomics data have been deposited in the ProteomeXchange Consortium with the dataset identifier JPST000395.Proteomic Study of the Exponential-Stationary Growth Phase Transition in the Haloarchaea Natrialba magadii and Haloferax volcanii.Cerletti Micaela M, Giménez María Ines MI, Tröetschel Christian C, D' Alessandro Celeste C, Poetsch Ansgar A, De Castro Rosana Ester RE, Paggi Roberto A RA, Paggi Roberto A RAAdd, 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, ratioGas-Liquid-Solid Phase Transitions, study, development, Sol-Gel Phase Transition, Transitions, Natronobacterium magadii, Sol-Gel Phase, Phase Transitions, Gas Liquid Solid Phase Transitions, Sol-Gel, growth pattern, Sol-Gel Phase Transitions, Halobacterium volcanii., non-developmental growth, Phase Transition, Gas-Liquid-Solid Phase Transition, postnatal development, postnatal growth, growth and development, Transition, Gas-Liquid-Solid, growth, Sol Gel Phase Transition, Gas-Liquid-Solid PhaseKoerper., organism, whole body, multi-cellular organism, whole organism, animal, bodyGas-Liquid-Solid Phase Transitions, PP17, deceased, Ghrfr, Transitions, ion, determination, Peptidomics, PP19, Phase Transition, postnatal development, Phases, Gene, growth and development, eubacteria, Cardiac Death, neutral molecular compounds, End-Of-Life, Divisions, Mendosicutes, protrusion, solute:solute exchange, Readability, Cardiac, reduced, fatty acid catabolism, responsivity, Gene Products, SMN, Smn, 1110025J15Rik, Bacteriobiota, tiny, Gas-Liquid-Solid, molecule, Gas-Liquid-Solid Phase, C1orf215, molecula, study, reactivity, 19k, Eubacteria, molecules, M Phases, Sol-Gel, Cell Division Phase, Metabacteria, dSTRAD, iones, M, hypoplasia, End Of Life, proteins, Cell Division, Molekuel, DmelCG7693, fatty acid degradation, ions, Division, 4624, Monera, Pp17, Bacteria Woese et al. 2024, genetic, Pp18, Bacteria (ex Cavalier-Smith 1987), Division Phase, Bacteria <bacteria>, Prokaryotae, Pp19, Pig, Lag, LAG, Procaryotae, fungi, species, P18, l(3)07551, Archaebiota, Transition, P19, constitutitional genetic, Sol Gel Phase Transition, small, Data Set., bacteria, data, Archaebacteria, Archaeobacteria, anatomical protrusion, Sol-Gel Phase Transitions, Proteins, familial, cell cycle quiescence, lag, total expressed protein, RCB2758, lit, Cell Divisions, Cell, predicted, development, native protein, Halobacterium volcanii, Ionen, single-organism transport, Protein, chemical analysis, LAP18, post-mortem, Near-Death Experience, prokaryotes, STE20-like/SPAK, Death, M Phase, Archebacteria, Lap18, little, dOSR1, Phase, Sol-Gel Phase Transition, Pr22, death, Natronobacterium magadii, Sol-Gel Phase, Phase Transitions, Gas Liquid Solid Phase Transitions, growth pattern, CG7693, underdeveloped, Determination of Death, non-developmental growth, Op18, not Bacteria Haeckel 1894, archaea, postnatal growth, Understanding, Protein Gene Products, Gene Proteins, stationary phase, PR22, Ion, spine, prokaryote, OP18, Gas-Liquid-Solid Phase Transition, Archaeon, small molecule transport, inherited genetic, assay, response, fatty acid breakdown, growth, hereditary, Proteomes, Prokaryota0falseNmagadii ATCC43099 - Whole organism, calculated iBAQ (Cerlettietal,proteomics2018)abundance based on calculated iBAQ, Interaction consistency score: 1.9, Coverage: 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