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AfzalMass SpectrometryShotgun proteomicsNot availableHsaxHumanNb4Cell cycleFasphttp://www.ebi.ac.uk/pride/archive/projects/PXD000678Single Shot Analysis (PepTracker submissions 483, 581, 561). For protein extraction, NB4 cells were pelleted, washed twice with cold PBS and then lysed in 0.3 – 1.0 ml HES lysis buffer (2% SDS, 10 mM HEPES pH 7.4, 1 mM EDTA, 250 mM sucrose, Roche protease inhibitors, Roche PhosStop). Lysates were heated to 95 °C for 10 min and homogenized using Qiashredder (Qiagen). 200 μg of the lysate was further processed for LC-MS/MS analysis using a modification of the FASP protocol. Briefly, lysates were loaded onto pre-equilibrated 30 kD-cutoff spin columns (Sartorius) and washed twice using denaturing urea buffer (8 M urea, 10 mM Tris, pH 7.4). Proteins were reduced with TCEP (25 mM in denaturing urea buffer), for 15 min at room temperature and alkylated with iodoacetamide (55 mM in denaturing urea buffer), in the dark for 45 min at room temperature. Lysates were then buffer-exchanged into 0.1 M triethylammonium bicarbonate, pH 8.5 (TEAB, Sigma) and digested with trypsin (1:50, Promega) overnight at 37 °C. Digestion efficiency was checked by SDS-PAGE analysis and protein staining with SimplyBlue SafeStain (Life Technologies). After collecting the first peptide flow-through, the spin column was washed twice with 0.1 M TEAB, then twice with 0.5 M NaCl. The flow-through and washes were combined and desalted using SepPak-C18 SPE cartridges (Waters). Peptides were then dried and resuspended in 5% formic acid for LC-MS/MS analysis. hSAX Analysis (PepTracker submissions 2441 and 2441). For protein extraction, NB4 cells were pelleted, washed twice with cold PBS and then lysed in 0.3 – 1.0 ml urea lysis buffer (8 M urea, 100 mM Tris pH 7.4, Roche protease inhibitors, Roche PhosStop). Lysates were vigorously mixed for 30 min at room temperature and homogenized using a Branson Digital Sonifier (30% power, 30 s). Lysates were diluted with digest buffer (100 mM Tris pH 8.0 + 1 mM CaCl2) to reach 4 M urea, and then digested with 1:50 Lys-C (Wako Chemicals) overnight at 37 °C. The digest was then split into two fractions. The first was retained as the Lys-C digest. The second was diluted with digest buffer to reach 0.8 M urea and double-digested with trypsin (1:50, Promega). Digest efficiencies were checked by SDS-PAGE analysis and protein staining. The digests were then desalted using SepPak-C18 SPE cartridges, dried, and resuspended in 50 mM borate, pH 9.3. Peptides were separated onto a Dionex Ultimate 3000 HPLC system equipped with an AS24 strong anion exchange column, using hSAX chromatography. Peptides were chromatographed using a borate buffer system, namely 10 mM sodium borate, pH 9.3 (Buffer A) and 10 mM sodium borate, pH 9.3 + 0.5 M sodium chloride (Buffer B) and eluted using an exponential elution gradient into 12 x 750 μl fractions. The peptide fractions were desalted using SepPak-C18 SPE plates and then resuspended in 5% formic acid for LC-MS/MS analysis.PrideNot availablemethylated lysineoxidized residuephosphorylated residueAcetylmethylated arginineN-acylated residuedeamidated residue2-pyrrolidone-5-carboxylic acid (Gln)The RAW data files produced by the mass spectrometer were analysed using the quantitative proteomics software MaxQuant, version 1.3.0.5 with an integrated search engine, Andromeda. The database supplied to the search engine was a UniProt human protein database (Human Reference Proteome retrieved on August 19, 2012) combined with a commonly observed contaminants list. The initial mass tolerance was set to 7 p.p.m. and MS/MS mass tolerance was 0.5 Da. Enzyme was set to trypsin/P with up to 2 missed cleavages. Deamidation, oxidation of methionine and Gln->pyro-Glu were searched as variable modifications. Identification was set to a false discovery rate of 1%. To achieve reliable identifications, all proteins were accepted based on the criteria that the number of forward hits in the database was at least 100-fold higher than the number of reverse database hits, thus resulting in a false discovery rate of less than 1%. Protein isoforms and proteins that cannot be distinguished based on the peptides identified are grouped by MaxQuant and displayed on a single line with multiple UniProt identifiers. The label free quantitation (LFQ) algorithm in MaxQuant was used for protein quantitation. The algorithm has been previously described (Luber, Cox et al. 2010). The MaxQuant data analysis was repeated with searches for the following post-translational modifications: Phospho(STY), Methyl/Di-Methyl (KR), and Acetyl (K). Protein quantitation was performed on unmodified peptides and peptides that have modifications that are known to occur during sample processing (pyro-Glu, deamidation). All resulting MS data were integrated and managed using PepTracker (http://www.PepTracker.com). The downstream data interpretation (protein and RNA data) of cell cycle stages in this study was performed primarily using the R language (version 0.95.262). An initial cleaning step was performed to improve the quality and value of the dataset. This step involved removing proteins with less than 2 peptide identifications, those labeled as either contaminants, or reverse hits and those where data was missing in any of the fractions. Proteins were further filtered using a procedure analogous to a Œchecksum function in computing. An algorithm was constructed to assess the self-consistency of the quantitation based on known relationships between the elutriated fractions. The intensities measured in the asynchronous NB4 cell population can thus be modeled as a linear combination of the intensities originating from the six elutriated fractions that have been normalized by the measured cell count in each elutriated fraction. For each protein, the theoretical linear combination of elutriated fraction intensities (scaled by cell number) should match the protein intensity measured experimentally in the asynchronous population. Similar factors were calculated between adjacent fractions (for example, F1 versus F2), using cell number and the proportions of cells in each phase, as determined by flow cytometry. These stringent criteria left a subset of the total proteins detected with very high data coverage across the 6 elutriated cell cycle fractions and high self-consistency in quantitation. Absolute protein abundances were estimated using the iBAQ algorithm, as previously described (Schwanhausser, Busse et al. 2011).ProteomicsProf Angus LamondLTQ Orbitrap VelosQ ExactiveCollege of Life Sciences, University of DundeePARTIALHomo Sapiens (human)v.z.afzal@dundee.ac.uk24596151 Ly T, Ahmad Y, Shlien A, Soroka D, Mills A, Emanuele MJ, Stratton MR, Lamond AI. A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells. Elife. 2014 Jan 1;3:e01630 10.7554/eLife.01630BiologicalSchool of Life SciencesTechnological advances have enabled the analysis of cellular protein and RNA levels with unprecedented depth and sensitivity, allowing for an unbiased re-evaluation of gene regulation during fundamental biological processes. Here, we have chronicled the dynamics of protein and mRNA expression levels across a minimally perturbed cell cycle in human myeloid leukemia cells using centrifugal elutriation combined with mass spectrometry-based proteomics and RNA-Seq, avoiding artificial synchronization procedures. We identify myeloid-specific gene expression and variations in protein abundance, isoform expression and phosphorylation at different cell cycle stages. We dissect the relationship between protein and mRNA levels for both bulk gene expression and for over ∼6000 genes individually across the cell cycle, revealing complex, gene-specific patterns. This data set, one of the deepest surveys to date of gene expression in human cells, is presented in an online, searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/). DOI: http://dx.doi.org/10.7554/eLife.01630.001.A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells.Ly Tony T, Ahmad Yasmeen Y, Shlien Adam A, Soroka Dominique D, Mills Allie A, Emanuele Michael J MJ, Stratton Michael R MR, Lamond Angus I AIl(2)k04204, sodium salt, CPD photolyase activity, ammonium formate, 13C-labeled, cadmium salt, PhrB photolyase activity, Ethylenediaminetetraacetic acid, chronic obstructive pulmonary disease (COPD), l(3)96Fd, SDH, Basodexan, magnesium formate, eosinophilia, Apaf-1, zinc salt, (ethylenedinitrilo)tetraacetic acid, l(2)k09905, dmTAF[[II]]230, SDS, Polypeptides, protein polypeptide chains, T22F8_160, cobalt(II) formate dihydrate, Loeffler Endocarditis, Protease Inhibitor, ATGPR7, B1, Chronic irreversible airway obstruction, Urea, GRP8, 2, GRP7, 3, HLHm8, NUP96, outer pigmented layer of retina, epithelium, Borate, DmelCG8428, strong, Idiopathic Hypereosinophilic Syndrome, Spin, Divorced, sodium meta borate, TFIID TAF250, sarcoma of breast, hac-1, cel, N, Salt, Su(Mir)1, (24)NaCl, chemical analysis., CAFL - Chronic airflow limitation, proteins, CaCl2, Divorces, HPLC, SUPPRESSOR OF AUXIN RESISTANCE 3, AI047805, salt, SPIN, pigment epithelium of retina, Peptidohydrolase Inhibitor, decreased, disease (COPD), BTKAP1, D1, pigmented retina epithelium, s, autolysin activity, Prx3, GTFII-I, acidum edeticum, Histological Labeling, nickel salt, Calcium chloride anhydrous, LC-MS2, 6030441I21Rik, spnE, dTAF[[II]]230, chronic obstructive lung disease [Ambiguous], subdivided, BZRP, ES|130, cobalt (+2) salt, Trypsin/K, fs(1)hls, anon-53Fa, TAF200, 2'', l(2)SH0173, breast sarcoma, BAP135, PBS, PBR, CHRONIC OBSTRUCTIVE AIRWAY DIS, common salt, sodium (4:1:1) salt, Dm1, magnesium salt, Hydrolase Inhibitor, dipyrimidine photolyase (photosensitive), BAP-135, Airflow Obstruction, CG6829, forked, dark/hac-1/dapaf-1, GLYCINE-RICH PROTEIN 8, Chronic Obstructive Airways Disease, Chronic obstructive lung disease, divided, Grv, Antagonists, alpha-D-Glucopyranoside, disodium salt, formate, hypereosinophilic syndrome, spn-E/hls, cromium (+3), N'-1, GtfII-I, lysed material, study protocol, septate, beta Trypsin, Painful bladder syndrome, E(spl)bHLH, l(2)W5, F2G1.4, Taf250, grv, OBSTRUCTIVE PULMONARY DISEASE (COPD), liquid chromatography-tandem mass spectroscopy, bacteriolytic toxin activity, ammonium (4:1) salt, Endopeptidase, Peptide Peptidohydrolase Inhibitor, lead (+2) salt, 42/4, TAF230, BPBS, NB4, F10B6_15, Sucrose, OG12X, lifespan, DmelCG3158, nickel formate dihydrate, lead formate, sarcoma of the breast, Endopeptidase Inhibitors, fractured, aluminum salt, CAO - Chronic airflow obstruction, ES130, beta-D-Fruf-(2<->1)-alpha-D-Glcp, Carbamide, CHRONIC OBSTRUCTIVE PULM DIS, Chronic obstructive pulmonary disease NOS, protein-containing complex, hypereosinophilic disease, body system, and RNA binding 1, F10B6.15, EDTA tetraanion, CG7826, deoxyribodipyrimidine photolyase activity, stratum pigmentosum retinae, l(2)k05821, Chronic obstructive pulmonary disease finding, PULMONARY DISEASE (COPD), l(2)k15606, tough, LC-MSMS, CG7835, Gene Products, CG42273, system, Peptide Hydrolase, Carmol, ji, anatomical systems, dTAF[[II]]250, 2'''-(ethane-1, 2-Ethane diylbis-(N-(carboxymethyl)glycine), thallium (+1) salt, cell, ethylenediamine tetraacetic acid tetraanion, (22)Na, isolated cases, Monosodium Salt, beta-Trypsin, rubidium salt, F23A5.3, 4733401P19Rik, pk18, methanoic acid, Antagonist, MBR, dTAF250, ATGRP7, Protease Antagonists, ATGRP8, m8, NEC, Kochsalz, PTBR, Chronic, Peptide Peptidohydrolase Inhibitors, peptidos, En(spl), sodium diborate, BB077577, SUCROSE, Chromatographies, 4-(2-hydroxyethyl)-, PTHB1, WBSCR6, dark/dapaf-1/hac-1, monosodium metaborate, Komex, chronic obstructive airways disease NOS, M8, dApaf-1, COAD, Proteins, CG18076, split, BG:DS00004.13, Stainings, potassium formate, copper (+2) salt, COLD - Chronic obstructive lung disease, buffer, Cell, chronic, bnch, dTAF230, l(2)k02511, polypeptide, APAF1, native protein, Temperatures, sacarosa, Natriumchlorid, carbonyldiamide, Hac-1, C18, cupric formate, chemical analysis, CG3158, hemorrhaged, TAF[[II]]250/230, bHLHb36, (COPD), chronic airway obstruction, NaCl, chronic obstructive, aluminum formate, CAL - Chronic airflow limitation, Taf[[II]]250, AU020952, torn, RPE, lithium formate, holin, underdeveloped, Separations, GR-RBP7, GR-RBP8, kak, SWDS, Dark/Dapaf-1/HAC1, Peptidohydrolase Inhibitors, mDRC, retinal pigment epithelium, OG12, ME-IV, p. pigmentosa retinae, plan specification, Gene Proteins, Peptidase, homeless, Antiprotease, chronic obstructive lung disease (disorder), liquid chromatography tandem mass spectrometry, deoxyribonucleate pyrimidine dimer lyase (photosensitive), Peptide Hydrolase Inhibitors, Og12x, e(spl), chronic obstructive pulmonary disease, ethylenediaminetetraacetate tetraanion, liquid chromatography tandem mass spectroscopy, DIWS, Hac-1/Dark, Endopeptidase Inhibitor, T22F8.160, determination, and rna binding 2, Chronic Airflow Obstructions, DmelCG6829, Peptide Hydrolase Inhibitor, zinc formate, HEPES Monosodium Salt, lead salt, 6330543G17Rik, protein, lysis, pigmented epithelium, clefted, Productivity, peptide, halite, ammonium tetraformate, ClvPrd, peptido, chronic obstructive airways disease NOS (disorder), RRp, Inhibitors, Min, Williams-Beuren syndrome chromosomal region 6 protein, 2', Apaf1, Chronic Obstructive Pulmonary Disease (COPD), protein aggregate, Hydrolase Inhibitors, present in fewer numbers in organism, ARK, DmelCG42273, Edetic acid, HEPES Monosodium, 2-diyldinitrilo)tetraacetate, COLD (chronic obstructive lung disease), LCMSMS, ion(4-), peptides, NEC in ICD9CM_2006, entire life cycle, E927b, pigmented retina, hypoplasia, min, arc, CLAC, mAPC, IBP, copper, ark, DNA cyclobutane dipyrimidine photolyase activity, T1, NB.4, Chronic airflow limitation, cloruro sodico, BNIP-H, lithium salt, SOLO DANCERS, 1-Piperazineethanesulfonic acid, GLYCINE RICH PROTEIN 7, monohydrate, Diws1t, disodium borate, l(2)CA4, idiopathic, necrosis, dApaf1, TEAB, (ethane-1, Bladder pain syndrome, glycine-rich RNA-binding protein 8, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, ammonium (2:1) salt, somatic mutation, NB-4, CHRONIC, PRE, ethylenediaminetetraacetate, obstructive lung disease, rock salt, Peptidase Inhibitor, D-Apaf-1, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, LC-MS/MS, Dmel_CG7826, AI836084, {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID, Labeling and Staining, TAFII-250, pigmented retinal epithelium, TAF250/230, Peptide Peptidohydrolase, beta-D-fructofuranosyl, fragmented, Airflow Obstructions, ur, shortstop/kakapo, pulmonary disease (COPD), carbamide, TAFII250, retinal pigment, Su(H)[[m8]], low temperature, DmelCG18076, CHRONIC OBSTRUCTIVE, chronic obstructive pulmonary disease and allied conditions, SRF-Phox1-interacting protein, Chronic airway disease, resistant to imatinib, bacteriocin activity, NOS, boric acid (H2B4O7), Loeffler's Endocarditis, nickel (+2) salt, retinal pigment layer, Dmel_CG7835, COPD NOS, CHRONIC OBSTRUCTIVE LUNG DIS, Mnb, MNB, Chronic airway obstruction, l(2R)W5, ammonium salt, calcium chloride, Painful Bladder Syndrome, table sugar, eosinophilic leukocytosis, cold, 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside, retinal pigmented epithelium, life, 3322401A10Rik, cracked, cobaltous formate, hac1, AW124434, CG17603, natrii chloridum, TAF[[II]], SHOT, organ system, dapaf-1S, Chronic Airflow Obstruction, phr A photolyase activity, H2NC(O)NH2, apaf-1, lysin activity, Peptidase Inhibitors, dapaf-1L, DNA-photoreactivating enzyme, Labelings, anon-EST:Liang-1.71, WBS, SR3-5, COPD - Chronic obstructive pulmonary disease, Acetamide, copper salt, chronic obstructive airways disease, Antiproteases, CG8428, sodium borate (NaBO2), Polypeptide, obstructive pulmonary disease (COPD), HEPES, HES, Hes, Inhibitor, COLD, chronic obstructive lung disease, 1728, Bladder Pain Syndrome, d230, CG8365, Dapaf-1/HAC-1, En(spl)-C, ES/130, DISEASE (COPD), Histological Labelings, cesium salt, Gene, dTAFII250, Protease, circadian rhythm, hes, hES, ethylenediaminetetraacetic acid, photoreactivating enzyme activity, EfW1, TFII-I, spn E, LC-MS-MS, Buffer, Bruton tyrosine kinase-associated protein 135, formic acid, Dark/Hac-1/dApaf1, Karbamid, Cold, method, Hac1, potassium salt, Dark/Hac-1/dApaf-1, Pulmonary Disease, polypeptide chain, reduced, resilient, dmTAF1, Taf230, subnumerary, 14C-labeled, Acide ethylenediaminetetracetique, method used in an experiment, Harnstoff, Sacharose, IB291, Histological, Protease Antagonist, stratum pigmentosa retinae, tiny, AA673430, Separated, acide edetique, Shot, Pro-Mega, TAF250, E(spl) m8, calcium dichloride, Taf200, Cold Temperatures, MOS3, l(2)k10821, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, Staining, Saccharose, PRECOCIOUS, entire lifespan, dapaf-1, chlorure de sodium, sodium metaborate, Taf1p, dapaf, dark, decreased number, calcium formate, Chronic Obstructive, calcium chloride anhydrous, Sodium Chloride, edta, E(Spl), 2-diyldinitrilo)tetraacetic acid, lysate, sodium tetraborate, DARK, Espl, EDTA, N-2-Hydroxyethylpiperazine-N'-2'-ethanesulfonic Acid, cromium (+3) salt, E(spl), BTK-associated protein 135, AA553322, TAF, dArk, Dapaf-1, F23A5_3, 2-iodo-, sodium formate, TCEP, COPD, small, COAD - Chronic obstructive airways disease, DYRK1, TAF[[II]]250, heptahydrate, nickel formate, DBI, protein complex, kop, not elsewhere classified, E(spl)-C, clone 1.71, strontium formate, l(3)84Ab, apaf1, CG18637, DmelCG8365, strontium salt, Labeling, PULM DIS CHRONIC OBSTRUCTIVE, Peptide, acido edetico, Chronic obstructive pulmonary disease finding (finding), stratum pigmentosum (retina), LC/MS/MS, MODIFIER OF SNC1, natural protein, PKBS, p230, sucrose, Protein, deoxyribonucleic photolyase activity, TFIID, table salt, Dyrk1, 25/11, GLYCINE-RICH RNA-BINDING PROTEIN 7, Dark, connected anatomical system, Dark/Apaf-I, SPN-E, chronic obstructive airway disease, Temperature, l(2)k05434, Separation, TAF[[II]]230, E(spl)m8, photolyase activity, uree, l(2)k03010, Dops, Spn-E, urea, CC1, H4edta, Sodium chloride (NaCl), Tripcellim, N 2 Hydroxyethylpiperazine N' 2' ethanesulfonic Acid, TAF[II]250, CGI-97, beta-D-fructofuranosyl alpha-D-glucopyranoside, dApaf-1/DARK/HAC-1, chromic formate, UREA, l(2)10403, Protein Gene Products, spin-E, Trypure, DmelCG17603, Cane sugar, E(spl)-m8, E(spl)M8, hls, [CaCl2], calcium salt, cold (chronic obstructive lung disease), Peptid, edetic acid, assay, Chronic Obstructive Lung Disease, hypereosinophilic disorder, fs(3)hls, White sugar, dAPAF-1, TAF1, sodium chlorideleukemia, dTAF[[II]]230, TAF[[II]]250, d230, leukemia granulocytic, human being, leukemia myelogenous, malignant, myelocytic leukaemia, TAF200, Gene, l(3)84Ab, dTAFII250, BG:DS00004.13, TAFII-250, TAF250/230, EfW1, Cell, Division Cycles, dTAF230, dmTAF[[II]]230, non-lymphocytic leukemia, TAFII250, dmTAF1, Taf230, p230, Cycle, leukemia myeloid, TAF[[II]]250/230, TFIID, non-lymphoblastic leukemia, myeloid granulocytic leukemia, TAF250, myeloid leukemia, Cell Division Cycles, Cycles, Taf[[II]]250, Taf200, myelogenous leukaemia, dTAF[[II]]250, TAF[[II]]230, Gene Expressions, TFIID TAF250, Division Cycle, myeloid leukaemia, leukaemia granulocytic, cel, cell, Cell Division Cycle, non-lymphoblastic leukaemia, cell-division cycle, granulocytic, Taf1p, Cell Division, TAF[II]250, myeloid granulocytic leukaemia, CG17603, Expressions, man, leukaemia myelogenous, TAF[[II]], human, myelocytic leukemia, dTAF250, DmelCG17603, TAF1., non-lymphocytic leukaemia, Taf250, leukaemia myeloid, SR3-5, Cell Cycles, Expression, myelogenous leukemia, Non-Lymphocytic Leukemia, TAF, TAF230DmGluClalpha, Thiofaco M-50, Ribonucleic, cox4, Raw, Ethanol Absolute, Ass-1, SMC4, Glu, GLU, l(3)61Ea, Splice Variants, P150, Protein Splice, Silent Spirit, glc, 5730420M11Rik, dmTAF[[II]]230, Polypeptides, protein polypeptide chains, NB4 cell, Drug Tolerance, 2-Aminoglutaric acid, DmGluT1, DmelCG1921, 80%, GRP1, Grp1, p150, glu, fold, Software Engineering, Analysis, Cell Numbers, Cell Sortings, Non Polyadenylated, WMS, Cell Division Cycles, SET, E, F, InChIKey=LFQSCWFLJHTTHZ-UHFFFAOYAB, TFIID TAF250, Analyses, Densities, cel, COXIV, M, phosphatase 2A inhibitor I2PP2A, PTPSTEP, DmGLUT1, Aminoethanol, proteins, Protein Isoform, DrosGluCl, number of, Denatured Ethanol, COXA_DROME, SURGICAL AND MEDICAL PROCEDURES, DmelCG4299, set, Dehydrated ethanol, Beta-Ethanolamine, Cox4, Ethyl Alcohol & Water, 70%, sample, 1.3.3.3, GLUCL, COX-VA, drug tolerance, SGS, GPH, spiritus vini, GluCl, Cell Sorting, Beta-Hydroxyethylamine, dTAF[[II]]230, 95%, Data Set, Beta-Aminoethanol, immune system tolerance, CG13908, TAF200, Ethanol Absolute Bp, Procedure, 2H2, Software Tools, ACMICD, Absolute Alcohol, 0074/12, Computer Applications, 96%, Algorithm, AL024441, Computer Applications Software, Methionin, Ribonucleic acids, methionine, Hmet, [OEtH], DmelCG7535, Acid, Software Applications, HLA-DR-associated protein II, Dm-GluCl, DmelCG43946, DI-2, CG11628, Coprogen oxidase, Source Software, Cell Densities, I-2Dm, proportionality, Number, rate, Striatum-enriched protein-tyrosine phosphatase, inhibitor of granzyme A-activated DNase, Ethyl Hydroxide, Ethylol, Fluorescence-Activated Cell, Methylcarbinol, alcohol etilico, 1H3, human, I-2PP1, Denatured Alcohol Sd-1, Applications, Self Tolerance, TAF-IBETA, Taf250, 50%, Denatured Alcohol Cd-10, TAF-Ibeta, School-Age Population, Liquimeth, TAF230, Computer Software Applications, glutamic acid, CLK, 2-amino-4-(methylsulfanyl)butanoic acid, GRP1/cytohesin 1, p150/glued, Peptidomics, False, Denatured Alcohol, etanol, number, protein-containing complex, Ethanol 200 Proof, CG11633, Fluorescence-Activated, CG10664, Fluorescence-Activated Cell Sortings, Microfluorometry, 40%, DmSMC4/gluon, IV, Gene Products, Variant, Tecsol C, DmGlu, Application, Cytofluorometry, Glutamic acid, Cycles, Open Source Softwares, School-Age Populations, proportion, dTAF[[II]]250, Tecsol, interventionDescription, Flow Cytofluorometries, cell, Software Application, spry, Cell Division Cycle, cell-division cycle, Open Source Software, Argos, 2pp2a, Cell Density, Protein Splice Variants, CG4531, Population, man, CG10574, Alcool Etilico, Computer Software Application, dTAF250, C2H5OH, Anhydrol, 2PP2A, 2-amino-4-(methylthio)butanoic acid, Tools, 30%, COX, Flow, dSET, dSet, Flow Microfluorometries, Cytometry, CT23049, ETA, peptidos, 426, metionina, Anhydrous, rlt, Absolute Ethanol, Sortings, CS3-3, DrosGluCl-alpha1, RNA, BcDNA:LD20207, Proteins, Denatured Alcohol Sd-3a, CG1086, stepk, RNS, function, BG:DS00004.13, Flow Cytometries, L-Isomer, Cell, Engine, Tool, Dmel_CG13908, dTAF230, Glycinol, polypeptide, CLK/STY, Spry, p150[Glued], Denatured Alcohol Cd-5a, 20%, Immune Tolerance, native protein, I-2PP2A, Glutamate, Dm I-2, alcool ethylique, TAF[[II]]250/230, MFS1, C2H6O, GluCla, Flow Microfluorometry, Beta-Aminoethyl Alcohol, Glutaminsaeure, l(3)05959, Ethyl Hydrate, Met, Intervention, Taf[[II]]250, Counts, DL-Glutaminic acid, Col4a-1, Denatured Alcohol Sd-28, Denatured, Caswell No, Numbers, Ribonucleic Acid, Sry, School Age Populations, l(3)05845, DmelCG11628, Computer Programs, DmelCG4531, Gene Proteins, Aos, 10%, CG14724, Applications Softwares, Denatured Alcohol Sd-17, l(3)rJ472, quotient, Variants, Ethylolamine, Gluon, l(3)L1H, quantitative, Data Analyses, Immunological Tolerance, Pyro, Bru, IPP2A2, Languages, Dmel_CG1086, protein, Diluted, STY, Sty, 1-hydroxyethane, peptide, Glt1, School-Age, L-Isomer Methionine, Ethanol, Methionine, peptido, ClvPrd, AA408052, Alkohol, Flow Microfluorimetry, DmelCG10664, protein aggregate, sty, Computer Program, t1, RNA Gene Products, dGluCl-alpha, Svc, PPG, Protein Splice Variant, BcDNA:HL07853, peptides, Fluorescence Activated Cell Sorting, TAF-I, Open, human protein, CLK|STY, Computer Programs and Programming, Jaysol S, arg, Aethanol, Estimated, [CH2Me(OH)], free, Thanol, dSPRY, ASS, Dmglut1, IGAAD, DmSMC4, DmelCG10574, l(2)k08110, Cell Cycles, CG7535, Glutaminic acid, Dehydrated, GPHYSD2, Racemethionine, Flow Cytofluorometry, DrosGlu-Cl-alpha, ratio, phapii, Fluorescence-Activated Cell Sorting, Alcohol, PLATEST, ribose nucleic acid, 5%, 2-Amino-4-(methylthio)butyric acid, ribonucleic acids, StF-IT-1, Search, extra or missing physical or functional parts, Isoform, TAFII-250, TAF250/230, Source Softwares, Division Cycles, CG1921, Programs, Microfluorimetry, Program, TAFII250, VA, School Age, Ribonukleinsaeure, p150/Glued, 3.1.3.48, Computer Applications Softwares, Immunologic Tolerance, pentosenucleic acids, Softwares, COX IV, DYNA_DROME, CG11397, Populations, Cytofluorometries, HSDB 531, Dialects, Algorithm., EtOH, Division Cycle, Va, Step, Alcare Hand Degermer, COX IV-1, MASS, CG4299, Envision Conditioner Pdd 9020, CG17603, TAF[[II]], BcDNA.LD20207, GLP-1, Tolerance, STEP, SR3-5, Cell Number, Ethanol Extra Pure, anon-WO0118547.156, Polypeptide, DmelCG14724, i2pp2a, Proteomes, Denatured Alcohol Cd-5, Etanolo, P150[Glued], Platelets, Cox4a, DL-Glutamic acid, d230, human being, Count, l(3)S007412, Density, L Isomer, USAF EK-1597, FBN, CG9206, Gene, dTAFII250, Computer, EfW1, presence, PHAPII, Reagent Alcohol, Intervention or Procedure, cytohesin/GRP1, Aethylalkohol, l(3)rQ526, dSMC4, template-activating factor I, polypeptide chain, dmTAF1, ECTOL1, Taf230, Cycle, Ethyl Alcohol Anhydrous, L-Methionine, Del(8)44H, Isoforms, l(3)j5E11, Pedameth, Splice Variant, TAF250, study, Search Engines, Colamine, Taf200, Coproporphyrinogenase, DmelCG11397, Microfluorometries, ipp2a2, l(2)SH2 0323, Interventional, Taf1p, Cell Division, OCTD, Non-Polyadenylated RNA, Ethanol Anhydrous, Denatured Alcohol Sd-39b, DrosGluCl-alpha, Denatured Alcohol Sd-39c, Neural-specific protein-tyrosine phosphatase, taf-ibeta, Synasol, DmAos, has or lacks parts of type, firmness, School Age Population, TAF, Cytometries, Applications Software, Intervention Strategies, Open Source, data, TAF[[II]]250, Computer Software, DL-Methionine, protein complex, igaad, total expressed protein, l(3)84Ab, Jaysol, Alcohol Anhydrous, Peptide, mereological quality, count in organism, l(3)rJ812, Software Tool, DmelCG9206, natural protein, Denatured Alcohol Sd-13a, yeast nucleic acid, p230, p150[glued], Protein, I2PP2A, Algrain, TFIID, glut1, IV-1, Software, l(2)SH0323, Data Base, WMS2, Ethyl Alcohol, CYH1, ribonucleic acid, 2-aminopentanedioic acid, TAF[[II]]230, gil, Non Polyadenylated RNA, FCP-D, Engineering, tend, Non-Polyadenylated, TAF[II]250, InChI=1/C2H6O/c1-2-3/h3H, Dialect, l(2)k08819, sample population, Protein Gene Products, dSET/TAF-Ibeta, Cell Counts, hydroxyethane, 2610030F17Rik, CG43946, DmelCG17603, Denatured Alcohol Sd-23a, Data, Spirit, SSKS, CCO, cardinality, Sorting, alpha-amino-gamma-methylmercaptobutyric acid, Peptid, variable, AA407739, presence or absence in organism, TAF1projections, pyridoxine-dependent, Astrin, Ribonucleic, leukemia granulocytic, artificial sequence, Materials, determination, protein, phosphorylation, dmTAF[[II]]230, protein polypeptide chains, DEEPEST, Analysis, protein aggregate, Non Polyadenylated, RNA Gene Products, myeloid leukemia, Mass Spectrum Analysis, Cell Division Cycles, Gene Expressions, TFIID TAF250, Analyses, leukaemia granulocytic, cel, proteins, Dietary Fiber, D11Bhm180e, allergic reaction, MAP126, papilla, Cell Cycles, dTAF[[II]]230, anatomical protrusion, Data Set, ribose nucleic acid, vitamin B6-dependent seizures, ribonucleic acids, lamina, TAF200, flanges, RNA-seq, TAFII-250, TAF250/230, Spectrum Analysis, Division Cycles, Spectroscopy, TAFII250, AI874642, Ribonukleinsaeure, pyridoxine-dependent epilepsy caused by ALDH7A1 mutant, shelf, pentosenucleic acids, Genetic Materials, Mastrin, Ribonucleic acids, Genetic Material, myeloid granulocytic leukemia, Acid, protein_coding_transcript, Division Cycle, shelves, PDE, Spectrometry, INSDC_feature:gene, CG17603, projection, TAF[[II]], ridge, human, SYNTHETIC CONSTRUCT sequences, Taf250, spine, Material, SR3-5, hypersensitivity reaction disease, pyridoxine-dependent epilepsy, artificial, Cistron, EPD, Epd, Proteomes, TAF230, antiquitin deficiency, d230, human being, Peptidomics, lamellae, myelocytic leukaemia, Gene, Mitotic spindle-associated protein p126, dTAFII250, Spectrum Analyses, protein-containing complex, EfW1, process of organ, protrusion, lamella, non-lymphocytic leukemia, polypeptide chain, dmTAF1, sensitive, Taf230, Cycle, Gene Products, Mass, Whole Transcriptome Shotgun Sequencing, sensitivity, Mass Spectroscopy, TAF250, Cycles, Taf200, dTAF[[II]]250, hMAP126, Genetic, myeloid leukaemia, cell, Cell Division Cycle, non-lymphoblastic leukaemia, cell-division cycle, messenger RNA, granulocytic, Taf1p, Cell Division, ridges, man, leukaemia myelogenous, Expressions, Non-Polyadenylated RNA, dTAF250, template RNA, leukaemia myeloid, ATQ1, hypersensitivity reaction, myelogenous leukemia, Expression, TAF, laminae, epilepsy, leukemia, RNA, TAF[[II]]250, Encyclopedias, protein complex, leukemia myelogenous, malignant, anatomical process, Phosphorylations, total expressed protein, l(3)84Ab, artificial gene, RNS, BG:DS00004.13, synthetic DNA, Cistrons, Cell, dTAF230, native protein, natural protein, yeast nucleic acid, p230, chemical analysis, Protein, leukemia myeloid, INSDC_feature:mRNA, TAF[[II]]250/230, synthetic, TFIID, S17, flange, non-lymphoblastic leukemia, Mass Spectrum Analyses, organ process, Data Base, Deepest, Taf[[II]]250, pyridoxine dependency with seizures., ribonucleic acid, Mass Spectrum, hypersensitivity, myelogenous leukaemia, hypersensitive, TAF[[II]]230, mRNA, Non Polyadenylated RNA, Non-Polyadenylated, AASA dehydrogenase deficiency, TAF[II]250, Ribonucleic Acid, myeloid granulocytic leukaemia, synthetic constructs, myelocytic leukemia, processes, process, DmelCG17603, non-lymphocytic leukaemia, pyridoxine dependency, processus, regulation, assay, Non-Lymphocytic Leukemia, TAF1projections, pyridoxine-dependent, Astrin, Ribonucleic, leukemia granulocytic, artificial sequence, Materials, determination, protein, NK/GPI., phosphorylation, dmTAF[[II]]230, protein polypeptide chains, DEEPEST, Analysis, protein aggregate, Gpi-1, Non Polyadenylated, RNA Gene Products, myeloid leukemia, Mass Spectrum Analysis, Cell Division Cycles, Gene Expressions, TFIID TAF250, Analyses, leukaemia granulocytic, cel, Nlk, proteins, Dietary Fiber, D11Bhm180e, allergic reaction, MAP126, papilla, Cell Cycles, Gpi, dTAF[[II]]230, anatomical protrusion, Data Set, ribose nucleic acid, vitamin B6-dependent seizures, ribonucleic acids, lamina, TAF200, flanges, RNA-seq, TAFII-250, TAF250/230, Spectrum Analysis, Division Cycles, Spectroscopy, TAFII250, AI874642, mOC-X, Ribonukleinsaeure, pyridoxine-dependent epilepsy caused by ALDH7A1 mutant, shelf, pentosenucleic acids, Genetic Materials, Mastrin, Ribonucleic acids, NK|GPI, Genetic Material, myeloid granulocytic leukemia, Acid, ORG, Org, protein_coding_transcript, Division Cycle, shelves, PDE, Spectrometry, Gpi1-r, Gpi1-s, INSDC_feature:gene, CG17603, Gpi1-t, projection, TAF[[II]], ridge, human, SYNTHETIC CONSTRUCT sequences, Taf250, spine, Material, SR3-5, hypersensitivity reaction disease, pyridoxine-dependent epilepsy, artificial, Cistron, EPD, Epd, Proteomes, Bglap-rs1, TAF230, Gpi1s, antiquitin deficiency, d230, human being, Peptidomics, AI461847, lamellae, pyridoxine dependency with seizures, myelocytic leukaemia, Gene, Mitotic spindle-associated protein p126, dTAFII250, Spectrum Analyses, protein-containing complex, EfW1, process of organ, DOI, protrusion, lamella, non-lymphocytic leukemia, polypeptide chain, dmTAF1, sensitive, Taf230, Cycle, Gene Products, Mass, Whole Transcriptome Shotgun Sequencing, Pgi, sensitivity, Mass Spectroscopy, TAF250, doi, Cycles, Taf200, dTAF[[II]]250, hMAP126, Genetic, myeloid leukaemia, cell, Gpi-1r, Gpi-1s, Phi, Cell Division Cycle, non-lymphoblastic leukaemia, cell-division cycle, Gpi-1t, messenger RNA, granulocytic, Taf1p, Cell Division, ridges, man, leukaemia myelogenous, Expressions, Non-Polyadenylated RNA, dTAF250, template RNA, leukaemia myeloid, ATQ1, hypersensitivity reaction, myelogenous leukemia, Expression, TAF, laminae, epilepsy, leukemia, RNA, TAF[[II]]250, Encyclopedias, protein complex, leukemia myelogenous, malignant, anatomical process, Phosphorylations, total expressed protein, l(3)84Ab, artificial gene, RNS, BG:DS00004.13, synthetic DNA, MF, Cistrons, Amf, Cell, dTAF230, native protein, natural protein, yeast nucleic acid, p230, chemical analysis, Protein, leukemia myeloid, INSDC_feature:mRNA, TAF[[II]]250/230, synthetic, TFIID, S17, flange, non-lymphoblastic leukemia, Mass Spectrum Analyses, organ process, Data Base, NK, Deepest, Taf[[II]]250, ribonucleic acid, Mass Spectrum, hypersensitivity, myelogenous leukaemia, hypersensitive, TAF[[II]]230, mRNA, Non Polyadenylated RNA, Non-Polyadenylated, AASA dehydrogenase deficiency, TAF[II]250, Ribonucleic Acid, myeloid granulocytic leukaemia, synthetic constructs, myelocytic leukemia, processes, process, DmelCG17603, non-lymphocytic leukaemia, pyridoxine dependency, processus, regulation, assay, Non-Lymphocytic Leukemia, TAF1leukemia, dTAF[[II]]230, TAF[[II]]250, d230, leukemia granulocytic, human being, leukemia myelogenous, malignant, myelocytic leukaemia, TAF200, Gene, l(3)84Ab, dTAFII250, BG:DS00004.13, TAFII-250, TAF250/230, EfW1, Cell, Division Cycles, dTAF230, dmTAF[[II]]230, non-lymphocytic leukemia, TAFII250, dmTAF1, Taf230, p230, Cycle, leukemia myeloid, TAF[[II]]250/230, TFIID, non-lymphoblastic leukemia, myeloid granulocytic leukemia, TAF250, myeloid leukemia, Cell Division Cycles, Cycles, Taf[[II]]250, Taf200, myelogenous leukaemia, dTAF[[II]]250, TAF[[II]]230, Gene Expressions, TFIID TAF250, Division Cycle, myeloid leukaemia, leukaemia granulocytic, cel, cell, Cell Division Cycle, non-lymphoblastic leukaemia, cell-division cycle, granulocytic, Taf1p, Cell Division, TAF[II]250, myeloid granulocytic leukaemia, CG17603, Expressions, man, leukaemia myelogenous, TAF[[II]], human, myelocytic leukemia, dTAF250, DmelCG17603, TAF1., non-lymphocytic leukaemia, Taf250, leukaemia myeloid, SR3-5, Cell Cycles, Expression, myelogenous leukemia, Non-Lymphocytic Leukemia, TAF, TAF230349trueA Proteomic Chronology of Gene Expression through the Cell Cycle in Human Myeloid Leukemia Cells.Technological advances have enabled the analysis of cellular protein and RNA levels with unprecedented depth and sensitivity, allowing for an unbiased re-evaluation of gene regulation during fundamental biological processes. Here, we have chronicled the dynamics of protein and mRNA expression levels across a minimally perturbed cell cycle in human myeloid leukemia cells using centrifugal elutriation combined with mass spectrometry-based proteomics and RNA-Seq, avoiding artificial synchronization procedures. We identify myeloid-specific gene expression and variations in protein abundance, isoform expression and phosphorylation at different cell cycle stages. We dissect the relationship between protein and mRNA levels for both bulk gene expression and for over ~6,000 genes individually across the cell cycle, revealing complex, gene-specific patterns. This dataset, one of the deepest surveys to date of gene expression in human cells, is presented in an online, searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/).2014-03-122014-01-09PXD0006782806551646099180498511145422492156843544071284218327042363336351198343006636362758385696363121766668888111430155571145263145262364934613126957366649239161936413645106656889511363647627236611123294422295558326813042323122586365434607925193659106321432059712938655819125023254537111957748186619682158672256807617554373592536685862740816918045427877512010892250583674147956410039236942049433445974142001258641935293NCBITaxon:77643671567593643867716054048313152826930456271639162429204277944762376369612181003296292211376394863948840479NCBITaxon:21571315273105106712502782059687201651636840717363096989361047821483643204292941010613204913816937432773204645351111032174592161292886712886764100694569410167634102107612773511316582135843014172981746336754128735675684030135062181301941119294393671104113644591394984320253012703202214987511047594120478861347495153721109716529982790513555139803175854398012608663980813757555183201964471114155421932555211383439119318198139818102697026635311069955529NCBITaxon:47518502983354764146547798251021691572739823897648407413735186287054824153NCBITaxon:5055798446752510003643341475480210359741370811546654789835322159983810677103481985234878042253148841422286322663479461571871259399159919157295292921175271986014884063342495186912342352381523359858985988655974649987039202111072363527215987419082874394232418235024145113969293190259390719017463601237474636172262536001319722119158531058859698951105198997237989772000263419610264266722758858156899628737562690724420237172019998570724074767927459615333554319311671833554184005136861505968666211961748666134751536329NCBITaxon:176328628711033348837670580271848186536859598607575527472036105135294296110098402321000734882412336363071047005187878945556449447NCBITaxon:13356262664955419591399878168119011478281055524NCBITaxon:960613585846900813668481979153519307285930085264114090051184995262254121337591390143811139442370416744312044143708351581990119519532590841370137023943222774862615835583715371633376057267998086371137121906503714759172073127262981274575727090309031637910372814243371421044792491108239412NCBITaxon:96156588581478026926610065813735275045413566381647520375064422366950212934979054632245552536519976499081438992374537472647323760264731288705595536141691525274032716029385114978647943637552938247943722511775299120447416738721750919384413765939343271591002263767423444234546700128768959119846704146479293652803428038280351080348330779179392112621229502711311803738681911265269971028622527391076015973611432425071140981087135547743658142450722953379698204232124223321803369822347081645733185889716546759928777020382931412529550811481744888643745264999728303571830855071762997076789268370415156288765138856392456115293202086595551655181135491432137159749535026143213858781707683194963401614280053164686275110466038151845474485009747697477118051240174841855601555479204274201488711053253297261005941289093164351211604990013894382835423242331082934122058560416299131122731701879915429131267818187104931640729946714423683033373304852646383011306413992530642369923121162065261610337286129940207340115357652611114716133865431201725323712552329935316317NCBITaxon:1108499384106326787286232193348620862116079139222768119612552281495393213223233477412182753291757312994886181408434103351996313924891392488115338115339330439375569928626559933911209488624157183997586444237486435332444260665332413439097682127178637197985686399983998686553529148654104298635735825763288401986498238011191102868899958665220341632138119380625631886571303443112130886581144889198466645463NCBITaxon:11072NCBITaxon:11071142800628835374375116597145943116598854331116781077854314408043933434NCBITaxon:11082693977381382189931824431935128387145953116885311213278695berry8694100333586972443664701501114286921504751499105484204714722354025120847014649744497431170089306218644193061107632330805660396016217974825853946055396513212790568813377512981766378876017112147861050236694657349632051124501897441739412450128853183889198679488531911137910371647351660152943631631198573896939343237956026087121346334323223544314275241433611334565560291699636436802790105603140818838185733703401881274414437552196969716203871398558408172405598609183827275921274423408170275981274420127442623545513656533821176275943282474801199150956481882291690255120455148167238473848190695148498101510693731263753405203860186497405224052141856451804NCBITaxon:8134780091522754847938703338493871917226175610946161435120325812055052352594473205493864112572265121651253880376686120678112202230743220118670511867057387334869121938791868023980071868012154514683514081861508471206777691838851608611388869152167786721279010087043512317196928123929486771331548454226126219813188268241122926571632957693812471246148545132838834839294911390363120416266589077151488003694269416943694518790101508081705394206542105568731744712701532924281411194669116960145458695320101981264690550537140815769739283031238391128312821280281101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