PXD000265

PXD000265 is an original dataset announced via ProteomeXchange.

Title	Oryza sativa egg, sperm, callus, pollen and seedling proteome
Description	In angiosperms, female gamete differentiation, fertilization, and subsequent zygotic development occur in embryo sacs deeply embedded in the ovaries. Despite their importance in plant reproduction and development, how the egg cell is specialized, fuses with the sperm cell, and converts into an active zygote for early embryogenesis remains unclear. This lack of knowledge is partly attributable to the difficulty of direct analyses of gametes in angiosperms. In this study, proteins from egg and sperm cells obtained from Oryza sativa flowers were separated by one-dimensional polyacrylamide gel electrophoresis and globally identified by highly sensitive liquid chromatography coupled with tandem mass spectroscopy. Proteome analyses were also conducted for seedlings, callus, and pollen grains to compare their protein expression profiles to those of gametes. Database was searched using Mascot software (ver.2.2.1, Matrix Science, MA, USA) with the following parameters. The fixed modification was propionasmide (Cys) and variable modification parameters were pyro-Glu, acetylation (protein N-terminus), and oxidation (Met). The maximum missed cleavage was set at 3 with a peptide mass tolerance of +/– 15 ppm. Peptide charges from +2 to +4 states and MS/MS tolerances of +/– 0.8 Da were allowed.
HostingRepository	PRIDE
AnnounceDate	2013-08-14
AnnouncementXML	Submission_2013-08-14_05:27:55.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000265
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Masato Taoka
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	monohydroxylated residue; acetylated residue; neutral loss: 63.998285; S-carboxamidoethyl-L-cysteine; deaminated residue
Instrument	radial ejection linear ion trap

Revision	Datetime	Status	ChangeLog Entry
0	2013-05-23 02:35:11	ID requested
1	2013-08-02 04:42:27	announced
1	2014-07-28 00:38:42	announced
⏵ 2	2013-08-14 05:27:55	announced	Add reference

Abiko M, Furuta K, Yamauchi Y, Fujita C, Taoka M, Isobe T, Okamoto T, Identification of proteins enriched in rice egg or sperm cells by single-cell proteomics. PLoS One, 8(7):e69578(2013) [pubmed]

submitter keyword: O. sativa, egg, sperm, callus, pollen, seedling LC-MS/MS

Masato Taoka
contact affiliation	Graduate School of Science and Engineering, Tokyo Metropolitan University
contact email	mango@tmu.ac.jp

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/2013/08/PXD000265

• PRIDE
  1. 29572
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Gel25
     3. ModificationList: S-carboxamidoethyl-L-cysteine, monohydroxylated residue,
     4. Name: 110603okamoto25.mgf-ine.xls
     5. PublicationRef: PMID23936051
  2. 29560
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Gel1-2
     3. ModificationList: monohydroxylated residue, acetylated residue, neutral loss,
     4. Name: 110603okamoto12.mgf-ine.xls
     5. PublicationRef: PMID23936051
  3. 29608
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Gel5-6
     3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, deaminated residue, acetylated residue, neutral loss,
     4. Name: 120118P03.mgf-121336.xls
     5. PublicationRef: PMID23936051
  4. 29597
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Gel5-6
     3. ModificationList: monohydroxylated residue, acetylated residue, S-carboxamidoethyl-L-cysteine, deaminated residue,
     4. Name: 120306okamoto-M03.mgf-104615.xls
     5. PublicationRef: PMID23936051
  5. 29573
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Gel1-2
     3. ModificationList: deaminated residue, monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, neutral loss,
     4. Name: 120110C-01.mgf-104144.xls
     5. PublicationRef: PMID23936051
  6. 29591
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Gel15-16
     3. ModificationList: monohydroxylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, neutral loss,
     4. Name: 120112S08.mgf-102925.xls
     5. PublicationRef: PMID23936051
  7. 29609
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Gel7-8
     3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, deaminated residue, neutral loss,
     4. Name: 120118P04.mgf-121511.xls
     5. PublicationRef: PMID23936051
  8. 29562
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Gel5-6
     3. ModificationList: monohydroxylated residue, acetylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine,
     4. Name: 110603okamoto56.mgf-ine.xls
     5. PublicationRef: PMID23936051
  9. 29596
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Gel3-4
     3. ModificationList: monohydroxylated residue, acetylated residue, S-carboxamidoethyl-L-cysteine,
     4. Name: 120306okamoto-M02.mgf-104535.xls
     5. PublicationRef: PMID23936051
  10. 29604
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel19-20
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, deaminated residue, neutral loss,
      4. Name: 120306okamoto-M10.mgf-105434.xls
      5. PublicationRef: PMID23936051
  11. 29574
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel3-4
      3. ModificationList: deaminated residue, monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, neutral loss,
      4. Name: 120110C-02.mgf-104412.xls
      5. PublicationRef: PMID23936051
  12. 29603
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel17-18
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, deaminated residue,
      4. Name: 120306okamoto-M09.mgf-105329.xls
      5. PublicationRef: PMID23936051
  13. 29583
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel21-22
      3. ModificationList: deaminated residue, monohydroxylated residue, acetylated residue, S-carboxamidoethyl-L-cysteine,
      4. Name: 120110C-11.mgf-105808.xls
      5. PublicationRef: PMID23936051
  14. 29605
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel21-22
      3. ModificationList: acetylated residue, monohydroxylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine, neutral loss,
      4. Name: 120306okamoto-M11.mgf-105517.xls
      5. PublicationRef: PMID23936051
  15. 29563
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel7-8
      3. ModificationList: monohydroxylated residue, acetylated residue, S-carboxamidoethyl-L-cysteine, deaminated residue, neutral loss,
      4. Name: 110603okamoto78.mgf-ine.xls
      5. PublicationRef: PMID23936051
  16. 29592
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel17-18
      3. ModificationList: monohydroxylated residue, acetylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine,
      4. Name: 120112S09.mgf-102949.xls
      5. PublicationRef: PMID23936051
  17. 29569
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel19-20
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, deaminated residue, neutral loss,
      4. Name: 110603okamoto1920.mgf-ine.xls
      5. PublicationRef: PMID23936051
  18. 29595
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel1-2
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, neutral loss, acetylated residue, deaminated residue,
      4. Name: 120306okamoto-M01.mgf-104512.xls
      5. PublicationRef: PMID23936051
  19. 29578
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel11-12
      3. ModificationList: deaminated residue, monohydroxylated residue, acetylated residue, S-carboxamidoethyl-L-cysteine, neutral loss,
      4. Name: 120110C-06.mgf-105209.xls
      5. PublicationRef: PMID23936051
  20. 29564
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel9-10
      3. ModificationList: monohydroxylated residue, deaminated residue, acetylated residue, S-carboxamidoethyl-L-cysteine,
      4. Name: 110603okamoto910.mgf-ine.xls
      5. PublicationRef: PMID23936051
  21. 29607
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel3-4
      3. ModificationList: monohydroxylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, neutral loss,
      4. Name: 120118P02.mgf-121217.xls
      5. PublicationRef: PMID23936051
  22. 29568
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel17-18
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, deaminated residue, neutral loss,
      4. Name: 110603okamoto1718.mgf-ine.xls
      5. PublicationRef: PMID23936051
  23. 29589
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel11-12
      3. ModificationList: monohydroxylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine, neutral loss, acetylated residue,
      4. Name: 120112S06.mgf-102817.xls
      5. PublicationRef: PMID23936051
  24. 29612
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel13-14
      3. ModificationList: monohydroxylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, neutral loss,
      4. Name: 120118P07.mgf-121819.xls
      5. PublicationRef: PMID23936051
  25. 29582
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel19-20
      3. ModificationList: S-carboxamidoethyl-L-cysteine, deaminated residue, monohydroxylated residue, acetylated residue, neutral loss,
      4. Name: 120110C-10.mgf-105717.xls
      5. PublicationRef: PMID23936051
  26. 29611
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel11-12
      3. ModificationList: monohydroxylated residue, deaminated residue, acetylated residue, S-carboxamidoethyl-L-cysteine, neutral loss,
      4. Name: 120118P06.mgf-121727.xls
      5. PublicationRef: PMID23936051
  27. 29593
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel19-20
      3. ModificationList: monohydroxylated residue, deaminated residue, acetylated residue, S-carboxamidoethyl-L-cysteine, neutral loss,
      4. Name: 120112S10.mgf-103009.xls
      5. PublicationRef: PMID23936051
  28. 29590
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel13-14
      3. ModificationList: monohydroxylated residue, deaminated residue, acetylated residue, S-carboxamidoethyl-L-cysteine,
      4. Name: 120112S07.mgf-102859.xls
      5. PublicationRef: PMID23936051
  29. 29614
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel17-18
      3. ModificationList: monohydroxylated residue, acetylated residue, S-carboxamidoethyl-L-cysteine, deaminated residue, neutral loss,
      4. Name: 120118P09.mgf-121910.xls
      5. PublicationRef: PMID23936051
  30. 29594
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel21-22
      3. ModificationList: acetylated residue, monohydroxylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine, neutral loss,
      4. Name: 120112S11.mgf-103029.xls
      5. PublicationRef: PMID23936051
  31. 29580
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel15-16
      3. ModificationList: monohydroxylated residue, acetylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine,
      4. Name: 120110C-08.mgf-105501.xls
      5. PublicationRef: PMID23936051
  32. 29567
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel15-16
      3. ModificationList: monohydroxylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine, acetylated residue,
      4. Name: 110603okamoto1516.mgf-ine.xls
      5. PublicationRef: PMID23936051
  33. 29616
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel21-22
      3. ModificationList: monohydroxylated residue, acetylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine, neutral loss,
      4. Name: 120118P11.mgf-122012.xls
      5. PublicationRef: PMID23936051
  34. 29579
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel13-14
      3. ModificationList: deaminated residue, acetylated residue, monohydroxylated residue, S-carboxamidoethyl-L-cysteine, neutral loss,
      4. Name: 120110C-07.mgf-105352.xls
      5. PublicationRef: PMID23936051
  35. 29601
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel13-14
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, deaminated residue, neutral loss,
      4. Name: 120306okamoto-M07.mgf-105140.xls
      5. PublicationRef: PMID23936051
  36. 29581
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel17-18
      3. ModificationList: monohydroxylated residue, acetylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine, neutral loss,
      4. Name: 120110C-09.mgf-105605.xls
      5. PublicationRef: PMID23936051
  37. 29565
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel11-12
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, deaminated residue,
      4. Name: 110603okamoto1112mgf-.ine.xls
      5. PublicationRef: PMID23936051
  38. 29599
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel9-10
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, deaminated residue,
      4. Name: 120306okamoto-M05.mgf-104849.xls
      5. PublicationRef: PMID23936051
  39. 29588
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel9-10
      3. ModificationList: acetylated residue, S-carboxamidoethyl-L-cysteine, monohydroxylated residue, deaminated residue,
      4. Name: 120112S05.mgf-102737.xls
      5. PublicationRef: PMID23936051
  40. 29577
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel9-10
      3. ModificationList: monohydroxylated residue, acetylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine, neutral loss,
      4. Name: 120110C-05.mgf-105018.xls
      5. PublicationRef: PMID23936051
  41. 29615
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel19-20
      3. ModificationList: monohydroxylated residue, deaminated residue, neutral loss, acetylated residue, S-carboxamidoethyl-L-cysteine,
      4. Name: 120118P10.mgf-121938.xls
      5. PublicationRef: PMID23936051
  42. 29584
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel1-2
      3. ModificationList: monohydroxylated residue, acetylated residue, S-carboxamidoethyl-L-cysteine, deaminated residue,
      4. Name: 120112S01.mgf-102446.xls
      5. PublicationRef: PMID23936051
  43. 29570
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel21-22
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, deaminated residue, neutral loss,
      4. Name: 110603okamoto2122.mgf-ine.xls
      5. PublicationRef: PMID23936051
  44. 29585
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel3-4
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue,
      4. Name: 120112S02.mgf-102523.xls
      5. PublicationRef: PMID23936051
  45. 29587
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel7-8
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, deaminated residue, acetylated residue,
      4. Name: 120112S04.mgf-102647.xls
      5. PublicationRef: PMID23936051
  46. 29571
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel23-24
      3. ModificationList: deaminated residue, acetylated residue, monohydroxylated residue, S-carboxamidoethyl-L-cysteine, neutral loss,
      4. Name: 110603okamoto2324.mgf-ine.xls
      5. PublicationRef: PMID23936051
  47. 29602
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel15-16
      3. ModificationList: monohydroxylated residue, acetylated residue, S-carboxamidoethyl-L-cysteine, deaminated residue,
      4. Name: 120306okamoto-M08.mgf-105229.xls
      5. PublicationRef: PMID23936051
  48. 29586
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel5-6
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, deaminated residue, neutral loss, acetylated residue,
      4. Name: 120112S03.mgf-102546.xls
      5. PublicationRef: PMID23936051
  49. 29606
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel1-2
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, deaminated residue, acetylated residue,
      4. Name: 120118P01.mgf-121123.xls
      5. PublicationRef: PMID23936051
  50. 29598
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel7-8
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, deaminated residue, acetylated residue,
      4. Name: 120306okamoto-M04.mgf-104728.xls
      5. PublicationRef: PMID23936051
  51. 29600
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel11-12
      3. ModificationList: monohydroxylated residue, neutral loss, acetylated residue, S-carboxamidoethyl-L-cysteine, deaminated residue,
      4. Name: 120306okamoto-M06.mgf-105006.xls
      5. PublicationRef: PMID23936051
  52. 29575
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel5-6
      3. ModificationList: monohydroxylated residue, deaminated residue, acetylated residue, S-carboxamidoethyl-L-cysteine, neutral loss,
      4. Name: 120110C-03.mgf-104633.xls
      5. PublicationRef: PMID23936051
  53. 29561
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel3-4
      3. ModificationList: monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue,
      4. Name: 110603okamoto34.mgf-ine.xls
      5. PublicationRef: PMID23936051
  54. 29613
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel15-16
      3. ModificationList: monohydroxylated residue, deaminated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, neutral loss,
      4. Name: 120118P08.mgf-121848.xls
      5. PublicationRef: PMID23936051
  55. 29576
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel7-8
      3. ModificationList: deaminated residue, monohydroxylated residue, S-carboxamidoethyl-L-cysteine, acetylated residue, neutral loss,
      4. Name: 120110C-04.mgf-104851.xls
      5. PublicationRef: PMID23936051
  56. 29610
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel9-10
      3. ModificationList: S-carboxamidoethyl-L-cysteine, acetylated residue, monohydroxylated residue, deaminated residue, neutral loss,
      4. Name: 120118P05.mgf-121634.xls
      5. PublicationRef: PMID23936051
  57. 29566
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Gel13-14
      3. ModificationList: monohydroxylated residue, acetylated residue, deaminated residue, neutral loss, S-carboxamidoethyl-L-cysteine,
      4. Name: 110603okamoto1314.mgf-ine.xls
      5. PublicationRef: PMID23936051