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PXD000069

PXD000069 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleShotgun proteomics of Ophrys orchid flowers
DescriptionProteomics data from a combind transcriptome/proteome study of three sexually deceptive orchids of the genus Ophrys. Data are from labella of mature, unpollinated flowers of (1) Ophrys exaltata subsp. archipelagi, (2) O. sphegodes, and (3) O. garganica. Proteomics data were searched against SwissProt and TAIR databases and further against organism-specific databases obtained from transcriptome sequencing (454, Sanger ESTs and Solexa data). Thirteen trypsinised gel slices per sample were subjected to electrospray ionisation-based LC-MS/MS analysis with a 2D linear ion trap Finnigan LTQ (Thermo Electron Corporation) equipped with an Ultimate Nano HPLC System (Dionex Corporation). Mass spectra were searched against SwissProt and Arabidopsis TAIR9 protein databases to identify peptides. Additionally, spectra were searched against protein databases created from the Ophrys reference transcriptome obtained in this study. Stringent criteria were used for the assignment of spectra to peptides (95% peptide identification probability) in Scaffold 3.3 (Proteome Software Inc., USA). In order to maximise the utility of proteomics data for uncovering proteins predicted by the orchid transcriptome, a minimum of one unique peptide was used for protein identification, while using two different stringency levels for the probabilistic assignment of peptides to proteins (99% for highest quality, HQ; 90% to maximise protein discovery, PD, in the absence of a fully sequenced genome). Concerning the sequencing and transcriptomics results: Three normalised cDNA libraries were constructed from three different Ophrys species, O. exaltata, O. garganica, and O. sphegodes. These libraries were 454 pyrosequenced and all the high quality reads generated in this study are available in the Sequence Read Archive (SRA) of the National Centre for Biotechnology Information (NCBI) with the accession number SRA060767. Additional sequencing of O. sphegodes flower labella yielded 1.7 Mbp of Sanger (dbEST library LIBEST_028084; dbEST IDs 77978749-77979571; GenBank accessions JZ163765-JZ164587) and 2.5 Gbp of Illumina Solexa (SRA060767) data.
HostingRepositoryPRIDE
AnnounceDate2013-08-21
AnnouncementXMLSubmission_2013-08-21_02:33:11.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD000069
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterPhilipp Schlueter
SpeciesList scientific name: Ophrys exaltata subsp. archipelagi (Orchid) (Ophrys arachnitiformis subsp. archipelagi); NCBI TaxID: 884019; scientific name: Ophrys garganica; NCBI TaxID: 145943; scientific name: Ophrys sphegodes (Early spider orchid) (Arachnites aranifera); NCBI TaxID: 145953;
ModificationListiodoacetamide derivatized residue; monohydroxylated residue; neutral loss: 63.998285
Instrumentlinear ion trap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02012-11-13 15:45:37ID requested
12013-06-24 01:28:50announced
12014-07-28 00:24:32announced
22013-08-21 02:33:11announcedAdd reference
Publication List
Sedeek KE, Qi W, Schauer MA, Gupta AK, Poveda L, Xu S, Liu ZJ, Grossniklaus U, Schiestl FP, Schl, ΓΌ, ter PM, Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive orchids. PLoS One, 8(5):e64621(2013) [pubmed]
Keyword List
submitter keyword: sexually deceptive orchids
proteomics
flower labellum
Ophrys
plant-pollinator interaction
LTQ
Contact List
Philipp Schlueter
contact affiliationInstitute of Systematic Botany, University of Zurich
contact emailphilipp.schlueter@systbot.uzh.ch
Full Dataset Link List
Dataset FTP location
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Repository Record List
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