PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering1140https://pax-db.org/dataset/1140/4072311492mering@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.Circadian rhythms are self-sustained and adjustable cycles, typically entrained with light/dark and/or temperature cycles. These rhythms are present in animals, plants, fungi, and several bacteria. The central mechanism behind these "pacemakers" and the connection to the circadian regulated pathways are still poorly understood. The circadian rhythm of the cyanobacterium Synechococcus elongatus PCC 7942 (S. elongatus) is highly robust and controlled by only three proteins, KaiA, KaiB, and KaiC. This central clock system has been extensively studied functionally and structurally and can be reconstituted in vitro. These characteristics, together with a relatively small genome (2.7 Mbp), make S. elongatus an ideal model system for the study of circadian rhythms. Different approaches have been used to reveal the influence of the central S. elongatus clock on rhythmic gene expression, rhythmic mRNA abundance, rhythmic DNA topology changes, and cell division. However, a global analysis of its proteome dynamics has not been reported yet. To uncover the variation in protein abundances during 48 h under light and dark cycles (12:12 h), we used quantitative proteomics, with TMT 6-plex isobaric labeling. We queried the S. elongatus proteome at 10 different time points spanning a single 24-h period, leading to 20 time points over the full 48-h period. Employing multidimensional separation and high-resolution mass spectrometry, we were able to find evidence for a total of 82% of the S. elongatus proteome. Of the 1537 proteins quantified over the time course of the experiment, only 77 underwent significant cyclic variations. Interestingly, our data provide evidence for in- and out-of-phase correlation between mRNA and protein levels for a set of specific genes and proteins. As a range of cyclic proteins are functionally not well annotated, this work provides a resource for further studies to explore the role of these proteins in the cyanobacterial circadian rhythm.Daily rhythms in the cyanobacterium synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins.Guerreiro Ana C L AC, Benevento Marco M, Lehmann Robert R, van Breukelen Bas B, Post Harm H, Giansanti Piero P, Maarten Altelaar A F AF, Axmann Ilka M IM, Heck Albert J R AJAdd, 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, ratiosmall, phapii, IPP2A2, Peptidomics, Proteins, igaad, StF-IT-1, Gene, Spectrum Analyses, Spectrum Analysis, PHAPII, group, Spectroscopy, 5730420M11Rik, MS, native protein, reduced, I-2PP2A, Dm I-2, Protein, I2PP2A, Mass, Gene Products, Analysis, tiny, Mass Spectrum Analyses, Mass Spectroscopy, Mass Spectrum Analysis, Mass Spectrum, SET, HLA-DR-associated protein II, Analyses, underdeveloped, ensemble, DI-2, TAF-I, Protein., I-2Dm, ipp2a2, Spectrometry, hypoplasia, 2pp2a, proteins, CG4299, CG10574, DmelCG4299, I-2PP1, Protein Gene Products, Gene Proteins, IGAAD, set, dSET/TAF-Ibeta, 2610030F17Rik, TAF-IBETA, 2PP2A, DmelCG10574, taf-ibeta, dSET, dSet, TAF-Ibeta, AA407739, i2pp2aKoerper., organism, whole body, multi-cellular organism, whole organism, animal, bodyMaterials, MBP-C, Phases, Visible Light, Nycthemeral Rhythms, Apaf-1, CG3629, Divisions, Long Term, 5730420M11Rik, DmelCG11081, protein polypeptide chains, T22F8_160, ATGPR7, DPlexA, hnu, circadian response, GRP8, GRP7, Analysis, Non Polyadenylated, Animalia, Eosinophil granule major basic protein, SET, thymus nucleic acid, Divorced, M Phases, hac-1, Genomes, Analyses, M, KAT13D, proteins, Divorces, Myelin membrane encephalitogenic protein, CG17245, Ba, Bacteria Woese et al. 2024, DmelCG4299, set, Bacteria <bacteria>, Prokaryotae, Rhythms, Role Concepts, Procaryotae, close to, Synechococcus PCC 7942, Radiation, Molds, dl, Polyadenylated, UNQ391/PRO726, land plants, anon-53Fa, Longterm Effect, l(2)SH0173, Light, XClock, Cell Divisions, Spectrum Analysis, l(2)01092, TPSG1, LIGHT, Role Concept, Role, prokaryotes, shi, desoxyribose nucleic acid, CG6829, BcDNA:GM05237, dark/hac-1/dapaf-1, GLYCINE-RICH PROTEIN 8, Polyadenylated Messenger RNA, DLL, Non Polyadenylated mRNA, HVEML, protein_coding_transcript, HLA-DR-associated protein II, DI-2, I-2Dm, Spectrometry, whole genome, E(Arp), Non-Polyadenylated mRNA, I-2PP1, higher plants, dll, light quantum, TAF-IBETA, F2G1.4, Material, Synechococcus 7942, ds DNA, PRSS31, response to circadian rhythm, TAF-Ibeta, Anacystis nidulans R2-SPc', DNA, Anacystis nidulans, TMT, Poly(A) RNA, Prokaryota, DNS, (Deoxyribonucleotide)n, Peptidomics, Effects, R75289, Twenty-Four Hour Rhythm, number, 5330400M04Rik, protein-containing complex, animals, body system, Synechococcus sp. (strain PCC 7942), and RNA binding 1, Ly113, clk, l(2)387, Deoxyribonucleic Acid, Twenty-Four Hour Rhythms, Diurnal, Gene Products, Synechococcus sp. (PCC 7942), system, Pilz, Filamentous Fungi, Diurnal Rhythms, anatomical systems, Nycthemeral Rhythm, Cell Division Phase, Longterm, Lichtquant, plex A, plex B, messenger RNA, Double Stranded, 2pp2a, Proteoglycan 2, MBL, Deoxyribonucleic acid, Filamentous Fungus, Long-Term, MBP, Division, Expressions, Anacystis nidulans R2, CG10574, DmelCG17245, Bacteria (ex Cavalier-Smith 1987), template RNA, 2PP2A, Rhythm, ATGRP7, ATGRP8, photon, dSET, dSet, TR2, Expression, (Deoxyribonucleotide)m, Nycthemeral, 2.7, dark/dapaf-1/hac-1, bacteria, RNA, dApaf-1, DNAn+1, Proteins, Fungus, Messenger RNA, Mycota, CD258, Cell, Concept, near to, APAF1, MS, Experiment, Temperatures, native protein, Hac-1, I-2PP2A, Synechococcus sp. PCC 7942, Poly(A)+ mRNA, chemical analysis, Long Term Effects, Dm I-2, INSDC_feature:mRNA, MBL2D, Mass Spectrum Analyses, Phase, Twenty-Four Hour, underdeveloped, mRNA, ensemble, HVEM-L, Separations, GR-RBP7, GR-RBP8, Dark/Dapaf-1/HAC1, Synechococcus sp. PCC7942, Longterm Effects, multicellular animals, Gene Proteins, Xclk, Photoradiations, prokaryote, vicinity of, Desoxyribonukleinsaeure, twenty-four hour rhythm, Polyadenylated mRNA, Hac-1/Dark, IPP2A2, T22F8.160, determination, and rna binding 2, Synechocystis sp. PCC 7942, Feature, DmelCG6829, metazoans, MBP1, protein, Roles, Concepts, Apaf1, protein aggregate, ARK, Effect, foton, Circadian, Mass Spectrum Analysis, HSMBPC, Art, Eubacteria, Gene Expressions, reference sample, TAF-I, Polyadenylated Messenger, hypoplasia, arc, plants, mKIAA0334, ark, T1, Division Phase, IGAAD, TNFSF14, DmelCG10574, GLYCINE RICH PROTEIN 7, MBPD, Pregnancy-associated major basic protein, Double-Stranded DNA, dApaf1, deoxyribonucleic acids, DNAn, glycine-rich RNA-binding protein 8, Long-Term Effects, gamma, phapii, D-Apaf-1, Fungi, StF-IT-1, Double-Stranded, Mold, Nyctohemeral, (Deoxyribonucleotide)n+m, Spectroscopy, Syncchococcus PCC7942, Menstruation, mld, S-adenosyl-L-methionine:thiol S-methyltransferase activity, DmelCG3629, C76307, Synechococcus leopoliensis strain PCC 7942, BcDNA:LP01770, Genetic Materials, Hmbpr, PlexA1, Genetic Material, Visible Radiations, Visible Radiation, cold, PlexB, Circadian Rhythms, PlexA, Diurnal Rhythm, Plant, EMBP, hac1, CG4299, Features, Plex1, En(Arp), Synechococcus sp. IAM M-200, organ system, dapaf-1S, apaf-1, dapaf-1L, Filamentous, Cistron, Myelin A1 protein, diurnal rhythm, PLEXB, i2pp2a, Proteomes, protein levels, Synechococcus leopoliensis UTEX 2434, Dapaf-1/HAC-1, Gene, CG11081, eubacteria, circadian rhythm, Spectrum Analyses, presence, Deoxyribonucleic acids, PHAPII, Dark/Hac-1/dApaf1, COLEC1, Hac1, Dark/Hac-1/dApaf-1, reduced, polypeptide chain, Messenger, Mass, D-Plex A, Animal, Bacteriobiota, tiny, Separated, Mass Spectroscopy, bHLHe8, study, Genetic, ipp2a2, dapaf-1, dapaf, Cell Division, labeling, Visible, dark, Monera, DARK, taf-ibeta, Long-Term Effect, fungi, Characteristics, dArk, Dapaf-1, thiol methyltransferase activity, Controlled, small, Controlling, data, protein complex, Nyctohemeral Rhythms, igaad, total expressed protein, apaf1, plex, Cistrons, BMPG, group, Twenty Four Hour Rhythm, count in organism, Characteristic, natural protein, Period, Metazoa, Protein, I2PP2A, Dark, GLYCINE-RICH RNA-BINDING PROTEIN 7, Polyadenylated RNA, connected anatomical system, ds-DNA, M Phase, Dark/Apaf-I, Radiations, Mass Spectrum, Separation, Poly(A)+ RNA, Synechococcus PCC7942, Poly(A) Tail, not Bacteria Haeckel 1894, Nyctohemeral Rhythm., Photoradiation, Non-Polyadenylated, fungus, golli-mbp, dApaf-1/DARK/HAC-1, LTg, Protein Gene Products, dSET/TAF-Ibeta, 2610030F17Rik, approaches, assay, AA407739, Nyctohemeral Rhythm, dAPAF-10falseSelongatus PCC7942 - Whole organism, SC (Guerreiroetal,molcellproteomics2014)abundance based on Spectral counting, Interaction consistency score: 9.2, Coverage: 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