Data independent acquisition (DIA) has emerged as a promising mass spectrometry based approach, combining the advantages of shotgun and targeted proteomics. Here we applied a DIA approach (termed SWATH) to monitor the dynamics of the Drosophila melanogaster embryonic proteome upon heat-shock treatment. Embryos were incubated for 0.5, 1 or 3 h at 37 °C to induce heat-shock or maintained at 25 °C. The present dataset contains SWATH files acquired on a Sciex Triple-TOF 6600. A spectral library built in-house was used to analyse these data and led to the quantification of more than 2500 proteins at every timepoint. The files presented here are permanent digital maps and can be reanalysed to search for new questions. The data have been deposited with the ProteomeXchange Consortium with the dataset identifier PRIDE: PXD004753.B.F, D.K and D.J.H.N are funded by BBSRC, United Kingdom (Ref: BB/L002817/1)

Fabre, BF

Korona, D

Lilley, KS

Nightingale, DJH

Russell, SR

Data in Brief

PubMed

AbstractData independent acquisition (DIA) has emerged as a promising mass spectrometry based approach, combining the advantages of shotgun and targeted proteomics. Here we applied a DIA approach (termed SWATH) to monitor the dynamics of the Drosophila melanogaster embryonic proteome upon heat-shock treatment. Embryos were incubated for 0.5, 1 or 3h at 37°C to induce heat-shock or maintained at 25°C. The present dataset contains SWATH files acquired on a Sciex Triple-TOF 6600. A spectral library built in-house was used to analyse these data and led to the quantification of more than 2500 proteins at every timepoint. The files presented here are permanent digital maps and can be reanalysed to search for new questions. The data have been deposited with the ProteomeXchange Consortium with the dataset identifier PRIDE: PXD004753

Fabre, Bertrand

Korona, Dagmara

Nightingale, Daniel J.H.

Russell, Steven

Lilley, Kathryn S.

Elsevier - Publisher Connector 

SWATH-MS dataset of heat-shock treated Drosophila melanogaster embryos 

Data independent acquisition (DIA) has emerged as a promising mass spectrometry based approach, combining the advantages of shotgun and targeted proteomics. Here we applied a DIA approach (termed SWATH) to monitor the dynamics of the Drosophila melanogaster embryonic proteome upon heat-shock treatment. Embryos were incubated for 0.5, 1 or 3 h at 37 °C to induce heat-shock or maintained at 25 °C. The present dataset contains SWATH files acquired on a Sciex Triple-TOF 6600. A spectral library built in-house was used to analyse these data and led to the quantification of more than 2500 proteins at every timepoint. The files presented here are permanent digital maps and can be reanalysed to search for new questions. The data have been deposited with the ProteomeXchange Consortium with the dataset identifier PRIDE: PXD004753

Nightingale, Daniel JH

Lilley, Kathryn S

Apollo (Cambridge)

Contents lists available at ScienceDirectData in BriefData in Brief 9 (2016) 991–995http://d2352-34(http://cn CorrE-m1 Thjournal homepage: www.elsevier.com/locate/dibData ArticleSWATH-MS dataset of heat-shock treatedDrosophila melanogaster embryosBertrand Fabre a,b,d,n,1, Dagmara Korona c,d,1,Daniel J.H. Nightingale a,b,d, Steven Russell c,d,Kathryn S. Lilley a,b,d,na Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, U.Kb Department of Biochemistry, University of Cambridge, Cambridge, U.Kc Department of Genetics, University of Cambridge, Cambridge, U.Kd Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.Ka r t i c l e i n f oArticle history:Received 22 August 2016Received in revised form15 October 2016Accepted 10 November 2016Available online 16 November 2016Keywords:Drosophila melanogasterHeat shockMass-spectrometrySWATHx.doi.org/10.1016/j.dib.2016.11.02809/& 2016 Published by Elsevier Inc. Thisreativecommons.org/licenses/by/4.0/).esponding authors.ail addresses: bff22@cam.ac.uk (B. Fabre), kese authors contributed equally to this woa b s t r a c tData independent acquisition (DIA) has emerged as a pro-mising mass spectrometry based approach, combining theadvantages of shotgun and targeted proteomics. Here weapplied a DIA approach (termed SWATH) to monitorthe dynamics of the Drosophila melanogaster embryonic pro-teome upon heat-shock treatment. Embryos were incubatedfor 0.5, 1 or 3 h at 37 °C to induce heat-shock or maintained at25 °C. The present dataset contains SWATH ﬁles acquired on aSciex Triple-TOF 6600. A spectral library built in-house wasused to analyse these data and led to the quantiﬁcation ofmore than 2500 proteins at every timepoint. The ﬁles pre-sented here are permanent digital maps and can be reanalysedto search for new questions. The data have been depositedwith the ProteomeXchange Consortium with the datasetidentiﬁer PRIDE: PXD004753.& 2016 Published by Elsevier Inc. This is an open access articleunder the CC BY license(http://creativecommons.org/licenses/by/4.0/).is an open access article under the CC BY license.s.lilley@bioc.cam.ac.uk (K.S. Lilley).rk.B. Fabre et al. / Data in Brief 9 (2016) 991–995992Speciﬁcations TableSMTHDEEDDubject area Biology.ore speciﬁcsubject areaProteomics, Drosophila melanogaster, Heat-shock.ype of data Table, ﬁgure.ow data wasacquiredMass spectrometry, SWATH acquisition mode on a Sciex Triple-TOF 6600.ata format Analysed.xperimentalfactorsSWATH-MS analysis of a heat-shock time course on Drosophila melanogasterembryos.xperimentalfeaturesDrosophila melanogaster embryos were subjected to heat-shock for differenttimes, collected, lysed, digested with trypsin and analysed in SWATH acquisitionmode on a Sciex Triple-TOF 6600. The data were analysed using SpectronautTM.ata sourcelocationCambridge, United Kingdom.ata accessibility SWATH data have been deposited with the ProteomeXchange Consortium via thePRIDE partner repository with the dataset identiﬁer PRIDE: PXD004753.Value of the data Heat-shock time course experiment with Drosophila melanogaster embryos useful to study thedynamics of the heat-shock response. Deep proteome coverage with more than 2500 proteins identiﬁed (FDRo0.001%) and quantiﬁed atevery time points with expected heat-shock proteins regulation useful for developing and testingSWATH-MS data analysis tools/workﬂows. SWATH permanent digital maps that can be searched with new hypotheses (using optimizedspectral library, analysis of the post-translational modiﬁcations, etc.).1. DataProtein expression levels of Drosophila melanogaster embryos were monitored by SWATH-MS [1]after heat-shock treatments. Proteins were extracted from embryos using a total lysis with a buffercontaining 4% SDS. Samples were prepared using a GeLCMS preparation method and proteins weredigested with trypsin. HRM peptides were spiked into the samples before analysis. The peptides wereanalysed using a SWATH acquisition mode on a Sciex triple-TOF 6600. The workﬂow used in thisstudy is illustrated in Fig. 1A. The dataset presented here includes all the SWATH raw ﬁles and outputﬁles from the Spectronaut analysis (Supplementary table).2. Experimental design, materials and methods2.1. Fly lines, embryo collection and protein extractionAdult ﬂies of the sequenced D. melanogaster iso-1 strain from the Bloomington Stock Centre (y1;Gr22biso-1Gr22diso-1cn1CG33964iso-1bw1sp1; LysCiso-1MstProxiso-1GstD5iso-1Rh61) were kept on standardyeast-cornmeal media in a 12-h light-dark cycle at 25 °C and 75% relative humidity. Embryos werecollected from cages on apple juice agar plates 16 h after egg laying. After collection, embryos wereincubated at 37 °C for 0.5, 1 or 3 h or retained at 25 °C for 3 h. The timepoints chosen in this studywere adapted from [2]. The embryos were then dechorionated with 50% bleach, washed with water,frozen in liquid nitrogen and kept at 80 °C. Four independent biological replicates were collected for0102030405060708090100Untreated HS 0.5h HS 1h HS 3hCoefficient of variation (%)y = 0.9545x + 0.1165 R² = 0.9378 01234560 1 2 3 4 5 6Log 10protein intensity untreated  replicate 1Log10protein intensity untreated replicate 2Peptides microflow LC-MS/MS on a Triple-TOF 6600ProteinsTrypsindigestionProteinextractionEmbryos +/- Heat-Shock(HS for 0.5, 1 or 3h)SWATHFDR 0.001% at the peptide level n=4HRM peptides2529 proteins quantified Fig. 1. A) Overall strategy to characterize the dynamics of the D. melanogaster embryonic proteome after heat-shock treatment(HS) using SWATH-MS. Embryos were collected and treated for 0.5, 1 or 3 h at 37 °C or untreated. Proteins were extracted,digested with trypsin and HRM peptides were spiked into the samples before injection. The samples were analysed usingSWATH acquisition mode on a Sciex Triple-TOF 6600. The resulting ﬁles were analysed with SpectronautTM. 2529 proteins werequantiﬁed using this workﬂow. B) Reproducibility of the protein intensity measurements between biological replicates. TheLog10 transformed protein intensities were plotted for replicates 1 and 2 of the untreated condition. C) The Coefﬁcient ofvariation (CVs) between the biological replicates were calculated for each condition.B. Fabre et al. / Data in Brief 9 (2016) 991–995 993each time point. Embryos were lysed in Tris 50 mM pH 7.5, 4% SDS, protease inhibitor (Complete,Roche) using a Dounce homogenizer (50 strokes per sample). Each sample was then heated for 5 minat 95 °C. The samples were sonicated (Bioruptor (Diagenode), position high, 30 s on, 30 s off for10 min), centrifuged at 14,000 g for 10 min and the pellets were discarded.2.2. Sample preparation for mass-spectrometry analysisIn gel digestion was used for sample preparation as described in [3]. HRM peptides (Biognosys)were added to each sample before injection on the mass spectrometer.2.3. Generation of the spectral libraryFor the generation of the SWATH assay library, a high pH reverse phase fractionation of 1 mg of aprotein sample from embryos collected over a 24 h period was performed. Peptides were loaded ontoan Acquity bridged ethyl hybrid C18 UPLC column (Waters, 2.1 mm inner diameter 150 mm, 1.7 mmparticle size), and separated with a gradient from 0 to 35% buffer B in 50 min, and 35–100% buffer B in7 min (buffer A: 20 mM NH4-formate pH10; buffer B: 20 mM NH4-formate pH10/80% ACN) at a ﬂowrate of 0.244 ml min1. Chromatographic performance was monitored by sampling the eluate with adiode array detector (Acquity UPLC, Waters) scanning between wavelengths from 210 to 400 nm.Fractions were collected at 1 min intervals. Thirty-two fractions were collected, dried with a Speed-Vac and resuspended in 3% acetonitrile/0.1% formic acid and analysed in Information DependentB. Fabre et al. / Data in Brief 9 (2016) 991–995994Acquisition (IDA) mode on a TripleTOF 6600 mass spectrometer (Sciex). Half of the peptides fromeach fraction were injected per run. To each peptide sample, HRM peptides (Biognosys) were addedbefore analysis. Mass spectrometry analyses were performed on a TripleTOF 6600 mass spectrometerﬁtted with a Duospray ion source (Sciex) and coupled to an ACQUITY UPLC System (Waters). Thesamples were injected onto a MicroLC column (150 mm longx0.3 mm inner diameter) with ChromXPC18CL, 300Âe pore size, 3 μm diameter particles (Sciex). Samples were run using a 49 min gradientfrom 3–40% solvent B (solvent A 0.1% formic acid, 5% DMSO in water; solvent B: 0.1% formic acid, 5%DMSO in acetonitrile) at a ﬂow rate of 5 ml/min. Data were acquired using an ion spray voltage of5.5 kV, curtain gas at 25 psi and nebulizer gas at 10 psi. A IDA method was set up with the MS surveyrange set between 350 and 1250 m/z (250 ms accumulation time) followed by dependent MS/MSscans with a mass range set between 100 and 2000 m/z (100 ms accumulation time) of the 20 mostintense ions in the high sensitivity mode with a 2þ to 5þ charge state. Dynamic exclusion was set fora period of 15 s and a tolerance of 50 ppm. Rolling collision energy was used.The .wiff ﬁles were analysed with MaxQuant [4] version 1.5.2.8 with the same parameters asdescribed in [6].The library was built using Spectronaut 8 from Biognosys [5], using the default settings, from theresulting combined ﬁle from the MaxQuant analysis. The library contains 40963 peptides corre-sponding to 5348 protein groups. The output ﬁles from the MaxQuant analysis have been depositedwith the ProteomeXchange Consortium via the PRIDE partner repository, along with SWATH data,under the dataset identiﬁer PXD004753.2.4. SWATH data acquisitionThe SWATH MS analysis was performed on a Triple-TOF 6600 as described in [6].2.5. SWATH data analysisSpectronaut 8 (Biognosys) was used to analyse the SWATH experiments. Default settings wereused except for the retention time prediction type that was set to dynamic iRT with a correction factorfor window of 2. A Q-value of 105 (corresponding to a FDR of 0.001% at the peptide level) was used.Proteins with at least two peptides were used for quantitative analysis. The sum of peptides intensitywas used as protein intensity. Good measurement reproducibility of intensities was observedbetween the biological replicates as illustrated in the Fig. 1B. Using our analytical workﬂow, themedian coefﬁcient of variation between the biological replicates are between 12 and 15% for thedifferent time points (Fig. 1C). Fold changes were calculated by comparing the intensities of theproteins at each time point to the untreated sample (Supplementary table).2.6. Data availabilityAll the mass spectrometry data have been deposited with the ProteomeXchange [7] Consortiumvia the PRIDE partner repository with the dataset identiﬁer PRIDE: PXD004753.The results from the SWATH analysis of the heat-shock time course experiment are provided inSupplementary Table.AcknowledgementsFunding: B.F, D.K and D.J.H.N are funded by BBSRC, United Kingdom (Ref: BB/L002817/1).B. Fabre et al. / Data in Brief 9 (2016) 991–995 995Transparency document. Supporting informationTransparency data associated with this article can be found in the online version at http://dx.doi.org/10.1016/j.dib.2016.11.028.Appendix A. Supporting informationSupplementary data associated with this article can be found in the online version at http://dx.doi.org/10.1016/j.dib.2016.11.028.References[1] L.C. Gillet, P. Navarro, S. Tate, H. Rost, N. Selevsek, L. Reiter, et al., Targeted data extraction of the MS/MS spectra generatedby data-independent acquisition: a new concept for consistent and accurate proteome analysis, Mol. Cell. Proteom.: MCP 11(O111) (2012) 016717.[2] K. Richter, M. Haslbeck, J. Buchner, The heat shock response: life on the verge of death, Mol. Cell. 40 (2010) 253–266.[3] B. Fabre, T. Lambour, L. Garrigues, F. Amalric, N. Vigneron, T. Menneteau, et al., Deciphering preferential interactions withinsupramolecular protein complexes: the proteasome case, Mol. Syst. Biol. 11 (2015) 771.[4] J. Cox, M. Mann, MaxQuant enables high peptide identiﬁcation rates, individualized p.p.b.-range mass accuracies andproteome-wide protein quantiﬁcation, Nat. Biotechnol. 26 (2008) 1367–1372.[5] R. Bruderer, O.M. Bernhardt, T. Gandhi, S.M. Miladinovic, L.Y. Cheng, S. Messner, et al., Extending the limits of quantitativeproteome proﬁling with data-independent acquisition and application to acetaminophen-treated three-dimensional livermicrotissues, Mol. Cell. Proteom.: MCP 14 (2015) 1400–1410.[6] B. Fabre, D. Korona, A. Groen, J. Vowinckel, L. Gatto, M.J. Deery, M. Ralser, S. Russell, K.S., Lilley, Analysis of Drosophilamelanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches,Proteomics 16 (2016) 2068–2080.[7] J.A. Vizcaino, E.W. Deutsch, R. Wang, A. Csordas, F. Reisinger, D. Rios, et al., ProteomeXchange provides globally coordinatedproteomics data submission and dissemination, Nat. Biotechnol. 32 (2014) 223–226.

SWATH-MS dataset of heat-shock treated Drosophila melanogaster embryos.

Bertrand Fabre

Dagmara Korona

Daniel J.H. Nightingale

Steven Russell

Kathryn S. Lilley

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SWATH-MS dataset of heat-shock treated Drosophila melanogaster embryos

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SWATH-MS dataset of heat-shock treated Drosophila melanogaster embryos

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