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WuMass SpectrometryShotgun proteomicsNot availableAbiotic stress / drought tolerance / plant proteomics / rice / shotgun proteomics / clpd1 proteasehttp://www.ebi.ac.uk/pride/archive/projects/PXD004096LeafOne Nipponbare (drought sensitive) and one IAC1131 (drought tolerant) seed were sown in soil. There were 15 pots in total as there were 3 pots for each treatment. The experiments were carried out in glass-houses with temperature set to 28/22°C (day/night) and a 12-h photoperiod. Light intensity exceeded 700 µmol m-2 s-1 throughout. Plant seedlings were well watered for 40 days. Extreme drought stress was imposed by withholding water for 7 days. For the moderate drought treatment, the amount of water transpired by plants was recorded daily by measuring the weight of pots, and then the plants were watered with ½ of the water that had transpired. Severely stressed plants (47 days old) were re-watered to field capacity for three days. Thus, five group of triplicate samples were collected at 40 days (control A), 47 days (extreme and moderate drought) and 50 days (recovery and control B). Leaf tissue was immediately lyophilized.Fifty mg of freeze-dried leaf powder was extracted using trichloroacetic acid/acetone. Proteins were separated on Bio-Rad 10% Tris-HCl precast gels then followed by trypsin in-gel digestion. The tryptic digest protein extracts from 1-DE gel slices were analysed by nanoflow LC-MS/MS (nanoLC-MS/ MS) using a LTQ-XL ion-trap mass spectrometer (Thermo, CA, USA). Raw files generated from mass spectrometry were converted to mzXML format and processed through the global proteome machine (GMP) software using version 2.1.1 of the X!Tandem algorithm.PrideSpectrum countingiodoacetamide derivatized residuemonohydroxylated residueThe 30 lists of proteins obtained from triplicate analyses of two cultivars at five different time points were filtered using two criteria. A protein was retained as a valid hit in the final dataset if (i) the protein was identified in all three replicates of at least one condition, and (ii) the total number of spectral counts in triplicates of at least one condition was a minimum of six. This transforms the low-stringency protein identification data from individual replicate analyses into a single high-stringency dataset of reproducibly identified proteins present at each time point [15]. The protein FDR was then calculated using the reverse database as decoy, hence protein FDR = (#Reverse protein identified)/ (Total protein identifications) × 100; in addition the peptide FDR was calculated as Peptide FDR = 2 × (#Reverse peptide identifications)/ (Total peptide identifications) × 100. Protein abundance data were calculated using Normalized Spectral Abundance Factors (NSAF), with an addition of a spectral fraction of 0.5 to all spectral counts to compensate for null values and enable log transformation for subsequent statistical analyses. Summed NSAF values were used as a measure of relative protein abundance. A series of t-tests was performed to find the proteins changed in expression significantly between conditions; the main focus was on comparisons of all other categories with the control and extreme conditions, respectively. The two sample unpaired t-tests were performed on log-transformed NSAF data, and proteins with a t-tests p-value less than 0.05 were regarded as differentially expressed. The resulting sets of up- and down-regulated proteins were then functionally annotated. An analysis of variance was performed to identify proteins changing in abundance among those proteins present reproducibly in all five conditions. The analysis was performed on log-transformed NSAF data and proteins with a p-value less than 0.05 were considered to show a significant change between the different experimental conditions. Gene ontology (GO) annotation was extracted from the UniProt database and matched to the list of reproducibly identified proteins using PloGo. The available GO annotation was summarized for each category of interest from a list of selected GO categories, for the up-regulated, down-regulated, and unchanged proteins for each of the t-tests undertaken. The GO annotations were plotted side by side for the up-, down-regulated, and unchanged proteins. For GO categories of interest, NSAF abundance data were merged and plotted to obtain an image of overall protein abundance change over time for biological process categories.ProteomicsPaul A. HaynesLTQChemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie UniversityPARTIALOryza Sativa (rice)yunqi.wu@mq.edu.au27195813 Wu Y, Mirzaei M, Pascovici D, Chick JM, Atwell BJ, Haynes PA. Quantitative proteomic analysis of two different rice varieties reveals that drought tolerance is correlated with reduced abundance of photosynthetic machinery and increased abundance of ClpD1 protease. J Proteomics. 2016 Jun 30;143:73-82 10.1016/j.jprot.2016.05.01430656201 Wu Y, Mirzaei M, Atwell BJ, Haynes PA. Label-free and isobaric tandem mass tag (TMT) multiplexed quantitative proteomic data of two contrasting rice cultivars exposed to drought stress and recovery. Data Brief. 2019 22:697-702 10.1016/j.dib.2018.12.041Macquarie UniversityAustraliaTwo rice cultivars, IAC1131 (drought tolerant) and Nipponbare (drought sensitive), with contrasting genetic backgrounds and levels of tolerance to drought, were analysed using both label-free and tandem mass tags (TMTs) quantitative proteomics approaches, aiming to elucidate the mechanisms of drought tolerance. Four-week-old seedlings of both cultivars were grown in large soil volumes in the glasshouse under controlled conditions and then exposed to moderate and extreme drought for 7 days, followed by 3 days of re-watering period. Mature leaves were harvested from plants of each treatment for protein extraction and subsequent complementary shotgun proteomic analyses. The data from this study are related to the research article "Quantitative proteomic analysis of two different rice varieties reveals that drought tolerance is correlated with reduced abundance of photosynthetic machinery and increased abundance of ClpD1 protease" (Wu et al., 2016) [1].<h4>Unlabelled</h4>Rice is the major staple food for more than half of world's population. As global climate changes, we are observing more floods, droughts and severe heat waves. Two rice cultivars with contrasting genetic backgrounds and levels of tolerance to drought, Nipponbare and IAC1131, were used in this study. Four-week-old seedlings of both cultivars were grown in large soil volumes and then exposed to moderate and extreme drought for 7days, followed by 3days of re-watering. Mature leaves were harvested from plants from each treatment for protein extraction and subsequent shotgun proteomic analysis, with validation of selected proteins by western blotting. Gene Ontology (GO) annotations of differentially expressed proteins provide insights into the metabolic pathways that are involved in drought stress resistance. Our data indicate that IAC1131 appears to be better able to cope with stressful conditions by upregulating a suite of stress and defence response related proteins. Nipponbare, in contrast, lacks the range of stress responses shown by the more stress tolerant variety, and responds to drought stress by initiating a partial shutdown of chlorophyll biosynthesis in an apparent attempt to preserve resources.<h4>Significance</h4>In this study, two rice genotypes with contrasting drought tolerance were exposed to soil water deficits, and proteomic changes were observed in mature leaf laminae. Plants were well watered and then switched to conditions of either moderate drought or extreme drought followed by three days of recovery. Proteins were identified and quantified using both label-free and Tandem Mass Tag multiplexing approaches. Several biochemical pathways were significantly altered in response to water deficit. Most notably, the up-regulation of ClpD1 protease responded strongly in the drought-tolerant landrace; this protein is typically involved in heat and osmotic stress response. In contrast, porphyrin and chlorophyll biosynthesis pathways were down-regulated, indicating suppression of the photosynthetic machinery.Quantitative proteomic analysis of two different rice varieties reveals that drought tolerance is correlated with reduced abundance of photosynthetic machinery and increased abundance of ClpD1 protease.Label-free and isobaric tandem mass tag (TMT) multiplexed quantitative proteomic data of two contrasting rice cultivars exposed to drought stress and recovery.Wu Yunqi Y, Mirzaei Mehdi M, Atwell Brian J BJ, Haynes Paul A PAWu Yunqi Y, Mirzaei Mehdi M, Pascovici Dana D, Chick Joel M JM, Atwell Brian J BJ, Haynes Paul A PAion, Raw, rad, Visible Light, monosomy 2q32, trichloro-, RP11-508D10.1, 5730420M11Rik, 2-Propanone, protein polypeptide chains, hydrogen chloride, Gmp, GMP, hnu, Colony forming unit in culture, HCL-C, Software Engineering, Analysis, SET, Divorced, type 5 acid phosphatase, Grain, Analyses, developmental field, phosphatase 2A inhibitor I2PP2A, Tissue, Plant Embryo, proteins, Divorces, DmelCG4299, allergic reaction, set, T-cell antigen Gp39, Wasserstoffchlorid, scientific observation, Sprouted, monosomy 2q32-q33, TNFSF5, cN-II, LC-MS2, tolerant, Radiation, land plants, Tnfrsf5, ENSMUSG00000025039, Light, Oryza sativa cultivar Nipponbare, Spectrum Analysis, Software Tools, hCD40L, 種子 (Japanese, Computer Applications, Plant Sprouts, LIGHT, DmelCG42628, SATB2-associated syndrome, Computer Applications Software, Del(2)(q32), Chlorwasserstoff, IMD3, Daylight, simple tissue, Raps, leukemic reticuloendotheliosis, Nipponbare, Hydrogen Oxide, Acid, Seeds, reticulate acropigmentation of Dohi, 2q32q33 microdeletion syndrome, Software Applications, HLA-DR-associated protein II, HVEML, DI-2, Source Software, I-2Dm, NKTL, dyschromatosis symmetrica hereditaria 1, Spectrometry, Dmel_CG15720, Plant Zygote, inhibitor of granzyme A-activated DNase, beta Trypsin, 葉 (Japanese, I-2PP1, Speed, Seedling, Grains, Applications, higher plants, light quantum, TAF-IBETA, Acide, liquid chromatography-tandem mass spectroscopy, TAF-Ibeta, chlorane, Pnt5, PNT5, Computer Software Applications, Plant Sprout, Acide trichloracetique, chlorure d'hydrogene, Ly62, TAPK, dyschromatosis symmetrica hereditaria, protein-containing complex, Chalk, TR-AP, DmelCG5692, Ly113, granulocyte/monocyte progenitor, SATB2 syndrome, organ field, sensitive, Peat, LC-MSMS, GP39, Sprouted Seed, Gene Products, field, Light Cycles, trichloracetique, SPG45, Application, gp39, plantae, CD154, Cycles, Open Source Softwares, GKLP, CATC4, pins, Hydrogen chloride, Lichtquant, Software Application, beta-Trypsin, Open Source Software, 2pp2a, Zygote, ions, study assay, PINS, CG10574, Computer Software Application, PCTAIRE2-binding protein, MGC:45012, 2PP2A, Daylight Cycles, hairy cell leukemia, Tools, dSET, dSet, photon, TR2, SPG65, Drl, Light-Dark, Elaiosomes, measuring, NTKL, grupo, CG5692, Oryza sativa Nipponbare, Proteins, chloridohydrogen, DSH, DSH1, ACP5, CD258, 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number, IMAGE, Gene, protein, protein-containing complex, Gene Ontology Project, Long Term, Gene Ontology, period, peptide, Polypeptides, protein polypeptide chains, ClvPrd, peptido, polypeptide chain, diseases, Gene Products, disease or disorder, Project, diseases and disorders, Low, Analysis, protein aggregate, Effect, physiological process., human disease, me75, methods, FOCUS, peptides, reference sample, Analyses, Longterm, experimental section, ANOVA, proteins, present in organism, Long-Term, number of, D17Mit170, T1, non-neoplastic, Variance Analysis, sample, has or lacks parts of type, disorder, Homo sapiens disease, peptidos, Long-Term Effect, time point, Long-Term Effects, Controlled, data, Controlling, cou, Data Set, protein complex, T5E21.12, Proteins, disorders, Longterm Effect, single organism process, medical condition, extra or missing physical or functional parts, Tl3, Tl2, Peptide, mereological quality, polypeptide, Lr, native protein, natural protein, Protein, Long 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Grains, red rice <Oryza sativa>, higher plants, Self Tolerance, Tolerance, enr, enlarged, approaches, rice, hypersensitivity reaction disease, SSKS, vicinity of, Sprouted Seeds, quantitative, earth, time, accessory, Immunological Tolerance, presence or absence in organismsmall, increased, underdeveloped, number, Oryza sativa, response to thirst, hypoplasia, increased number., decreased number, presence, supernumerary, Rice, present in greater numbers in organism, count in organism, red rice <Oryza sativa>, decreased, response to dehydration, reduced, subnumerary, rice, Rices, proteomic analysis, red rice, response to drought, quantitative, tiny, drought tolerance, present in fewer numbers in organism, Asian cultivated rice, accessory, presence or absence in organism496trueQuantitative proteomic analysis of two different rice varieties reveals that drought tolerance is correlated with reduced abundance of photosynthetic machinery and increased abundance of ClpD1 proteaseRice is the major staple food for more than half of world's population. As global climate changes, we are observing more floods, droughts and severe heat waves. Two rice cultivars with contrasting genetic backgrounds and levels of tolerance to drought, Nipponbare and IAC1131, were used in this study. Four-week-old seedlings of both cultivars were grown in large soil volumes and then exposed to moderate and extreme drought for 7 days, followed by 3 days of re-watering. Mature leaves were harvested from plants from each treatment for protein extraction and subsequent shotgun proteomic analysis, with validation of selected proteins by western blotting. Gene Ontology (GO) annotations of differentially expressed proteins provide insights into the metabolic pathways that are involved in drought stress resistance. Our data indicate that IAC1131 appears to be better able to cope with stressful conditions by up regulating a suite of stress and defence response related proteins. Nipponbare, in contrast, lacks the range of stress responses shown by the more stress tolerant variety, and responds to drought stress by initiating a partial shutdown of chlorophyll biosynthesis in an apparent attempt to preserve resources.2016-09-152016-05-18PXD0040964466449917558258038804333029535851114512067811080612461962461972842188090320637522995811363350906836351524260275838538791187947398007186801NCBITaxon:1280572307688881114301187263555571468351452627412583649117571508472746707364113546138855821803582329031388869152167786889539978447512951398704351123294126246942229692812397713311809933995232310343043654813583334607925198183659219813143205971293818826826558194762149363295726373719222212502321979116938197912NCBITaxon:12721119577412478186613283882813955843451358672217554372949140816918045416193426683413903634530586112041623264460711210411706127443210859561496367469412831666943694559729452811320810039241065837514633087936944784475174206542208964317447127020896344597413797912838411946694006671454587932993529320101981264690410661145755121659940483392512165972165954550131528269731606212133128312821280339523218108323217825252920435315227794428112353153454349825741948147871720309498019752555536231439841356742951053948824261914548140479NCBITaxon:21571150621551531292439899037122857782996597532059687623193516309800588845586978181780817363094317956606989361604885661409859104782566416242515059071187023482118705320491381693630638632355543204663222618663312994565860688453515126232172192174592161295671713604410016023587002642036945694101676341021076127735113165821504802392547279332160428146100291358430357861746331325291118700215764180969975665457744491566667547604452467675684030191726518130194111929439633664113633672175111764510239870932025NCBITaxon:4055932582359092788396523652649821787074982163472565691569387224982116544872056973474951666905108944835525663661410NCBITaxon:4932871556891758543102459808108944475741755518100058945268087322875351908323311561263730069303911415542193255521872587268723872487298727123598755529NCBITaxon:475154762422314146547730551800664417725564843376771581419198822445299767446982510216998231174673897641041051155744689444474153NCBITaxon:5055796016776744685100036487529600NCBITaxon:58116534911822637082483341475480557841946751299114578458359741276473194439137086326547876569835566369838192011164034624136810893161001428099612NCBITaxon:548681NCBITaxon:582054641498523077479464098609958652283637379196627290587668960596061572951372218759446708756227086266596417110133548330903497412982998603878348106267566430615127936543194747033424947223598596108961588655974649987039202111072878272154078211908503757075298351170828206189257771480418985487350247158779627300251563041190252867463604614796469644375939491146247274612874601134506253256648452659197221963819155263858859652639NCBITaxon:6157505210283071105172375059576131302409720002634196105264110909469407722774694163485689961123869497515NCBITaxon:2NCBITaxon:135231703612506174767927450627249159615384005257313246432136861505962697968666299034694171344346360347515363296440421018194301086731018510976063558633149616128628724620096692729435133813216968583551865368595968912801726071018568729411009118696141633316780781186941436183NCBITaxon:6191118698840231719475932118691443906NCBITaxon:102982100071257118348824387279694836419080218787864515970384766425731055347095145122578656870861822607046183260705260707NCBITaxon:7803906NCBITaxon:1502451516658457702921158612184519307920928520131974707856100713370565295076192126385454195NCBITaxon:3055504457391538337991399878168192875NCBITaxon:10239NCBITaxon:7142829126806315327341478281309570547044830064175158592381055524159084128108228233446900815025754122810451930174830085210977970671356225833136185509924NCBITaxon:56938268830640527796179469958334240906151015151034809NCBITaxon:63124067448242813076707087613837047592723708281677285035158199011951953370249240536088817562615835583337602126719285321773572671193501846451772998086167879177437371110490563712153481724073714121532395767690147266470913170475712562745790311333550372885962859634792491308126387121203511082332648373153214693NCBITaxon:9615383235946331858626079914126220029813141313493760833344926701311111497019281239655833325283010184138569591110065812375612750454266625515197887492003750360094129349715300910766204114903524725175014012573983649908515151438992NCBITaxon:1155237453988374744544641521399274356235931179286643235983906288705158059553611945993271602938511497861603293338922853422999810894535936457428412754121536024271831627713512251179948875058NCBITaxon:10407242715502779167971816738713491306274158955210103065027802915954126291586600255158493765327159570210022633889423451287689135588675512930945146479203124216413328038280351928434369093581539858089462108034817939211825902878892950274560990690174934681927256322732189038292867572279011247190400727NCBITaxon:57965374571143112335235621140206411981087135547714245072295337969835552222129163470871410457751262161154293157546139622421392139077020206032818573231143193382935508332923074112922114816402784896160106772526499975744727580240550717629925122968335366581926832140535762294128160783957632066724005402965432823122737777298184318322465962057554992295757575928459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