PXD000500-1

PXD000500 is an original dataset announced via ProteomeXchange.

Title	Arabidopsis mitochondrial proteome during a diurnal cycle
Description	We surveyed the heterogeneity of the mitochondrial proteome and its function during a typical night and day cycle in Arabidopsis shoots. This used a staged, quantitative analysis of the proteome across 10 time points covering 24 h of the life of 3-week-old Arabidopsis shoots grown under 12-h dark and 12-h light conditions. Results were queried against an in-house Arabidopsis database comprising ATH1.pep (release 7) from The Arabidopsis Information Resource and the Arabidopsis mitochondrial and plastid protein sets (the combined database contained a total of 30,700 protein sequences with 12,656,682 residues) using the Mascot search engine version 2.2 and utilizing error tolerances of +-1.2 Da for MS and +-0.6 Da for MS/MS, 'enzyme' set to trypsin, 'maximum missed cleavages' set to 1, variable modifications of oxidation (Met) and carbamidomethyl (Cys), instrument set to ESI-TRAP, and peptide charge set at 2+ and 3+. ATH1.pep is a non-redundant database with systematically named protein sequences based on Arabidopsis genome sequencing and annotation. PRIDE XML files with accession numbers 10471–10525 and without peptide/protein identifications have already been made public.
HostingRepository	PRIDE
AnnounceDate	2013-10-09
AnnouncementXML	Submission_2013-10-09_02:10:39.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000500
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Chun Pong Lee
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; neutral loss: 63.998285; iodoacetic acid derivatized residue; iodoacetamide derivatized residue
Instrument	selected ion m/z

Revision	Datetime	Status	ChangeLog Entry
0	2013-10-07 07:49:32	ID requested
⏵ 1	2013-10-09 02:10:48	announced
⏵ 1	2013-10-09 02:41:19	announced
2	2014-07-28 00:49:46	announced	Updated project metadata.
3	2024-10-07 09:10:02	announced	2024-10-07: Updated project metadata.

Dataset with its publication pending

submitter keyword: Arabidopsis, plant, mitochondria, diurnal cycle, LC-MS/MS

Chun Pong Lee
contact affiliation	Department of Plant Sciences, University of Oxford
contact email	chun.lee@plants.ox.ac.uk
Prof. A. Harvey Millar
contact attribute	harvey.millar@uwa.edu.au
contact affiliation	ARC CoE Plant Energy Biology, University of Western Australia
contact email	harvey.millar@uwa.edu.au
Dr. Chun Pong Lee
contact attribute	cplee@graduate.uwa.edu.au
contact affiliation	ARC CoE Plant Energy Biology, University of Western Australia
contact email	cplee@graduate.uwa.edu.au

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/2013/10/PXD000500

• PRIDE
  1. 31375
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Spot 16
     3. ModificationList: monohydroxylated residue,
     4. Name: Mito_Diurnal_Spot16
     5. PublicationRef: pending
  2. 31388
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Spot 28
     3. ModificationList: monohydroxylated residue,
     4. Name: Mito_Diurnal_Spot28
     5. PublicationRef: pending
  3. 31397
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Spot 36
     3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
     4. Name: Mito_Diurnal_Spot36
     5. PublicationRef: pending
  4. 31369
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Spot 10
     3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
     4. Name: Mito_Diurnal_Spot10
     5. PublicationRef: pending
  5. 31416
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Spot 53
     3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
     4. Name: Mito_Diurnal_Spot53
     5. PublicationRef: pending
  6. 31418
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Spot 55
     3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
     4. Name: Mito_Diurnal_Spot55
     5. PublicationRef: pending
  7. 31377
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Spot 18
     3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
     4. Name: Mito_Diurnal_Spot18
     5. PublicationRef: pending
  8. 31374
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Spot 15
     3. ModificationList: monohydroxylated residue,
     4. Name: Mito_Diurnal_Spot15
     5. PublicationRef: pending
  9. 31415
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Spot 52
     3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
     4. Name: Mito_Diurnal_Spot52
     5. PublicationRef: pending
  10. 31379
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 2
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot2
      5. PublicationRef: pending
  11. 31406
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 44
      3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot44
      5. PublicationRef: pending
  12. 31401
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 4
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot4
      5. PublicationRef: pending
  13. 31368
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 1
      3. ModificationList: monohydroxylated residue, neutral loss, iodoacetic acid derivatized residue,
      4. Name: Mito_Diurnal_Spot1
      5. PublicationRef: pending
  14. 31400
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 39
      3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot39
      5. PublicationRef: pending
  15. 31413
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 50
      3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot50
      5. PublicationRef: pending
  16. 31390
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 3
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot3
      5. PublicationRef: pending
  17. 31378
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 19
      3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot19
      5. PublicationRef: pending
  18. 31396
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 35
      3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
      4. Name: Mito_Diurnal_Spot35
      5. PublicationRef: pending
  19. 31383
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 23
      3. ModificationList: monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot23
      5. PublicationRef: pending
  20. 31384
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 24
      3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot24
      5. PublicationRef: pending
  21. 31399
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 38
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
      4. Name: Mito_Diurnal_Spot38
      5. PublicationRef: pending
  22. 31385
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 25
      3. ModificationList: monohydroxylated residue,
      4. Name: Mito_Diurnal_Spot25
      5. PublicationRef: pending
  23. 31419
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 6
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot6
      5. PublicationRef: pending
  24. 31371
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 12
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
      4. Name: Mito_Diurnal_Spot12
      5. PublicationRef: pending
  25. 31392
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 31
      3. ModificationList: monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot31
      5. PublicationRef: pending
  26. 31382
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 22
      3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
      4. Name: Mito_Diurnal_Spot22
      5. PublicationRef: pending
  27. 31387
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 27
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
      4. Name: Mito_Diurnal_Spot27
      5. PublicationRef: pending
  28. 31410
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 48
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot48
      5. PublicationRef: pending
  29. 31422
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 9
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
      4. Name: Mito_Diurnal_Spot9
      5. PublicationRef: pending
  30. 31404
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 42
      3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot42
      5. PublicationRef: pending
  31. 31403
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 41
      3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot41
      5. PublicationRef: pending
  32. 31411
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 49
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot49
      5. PublicationRef: pending
  33. 31370
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 11
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot11
      5. PublicationRef: pending
  34. 31408
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 46
      3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot46
      5. PublicationRef: pending
  35. 31394
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 33
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot33
      5. PublicationRef: pending
  36. 31381
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 21
      3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot21
      5. PublicationRef: pending
  37. 31395
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 34
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
      4. Name: Mito_Diurnal_Spot34
      5. PublicationRef: pending
  38. 31417
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 54
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
      4. Name: Mito_Diurnal_Spot54
      5. PublicationRef: pending
  39. 31407
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 45
      3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
      4. Name: Mito_Diurnal_Spot45
      5. PublicationRef: pending
  40. 31372
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 13
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot13
      5. PublicationRef: pending
  41. 31389
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 29
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot29
      5. PublicationRef: pending
  42. 31393
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 32
      3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot32
      5. PublicationRef: pending
  43. 31421
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 8
      3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
      4. Name: Mito_Diurnal_Spot8
      5. PublicationRef: pending
  44. 31414
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 51
      3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot51
      5. PublicationRef: pending
  45. 31380
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 20
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot20
      5. PublicationRef: pending
  46. 31386
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 26
      3. ModificationList: monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot26
      5. PublicationRef: pending
  47. 31373
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 14
      3. ModificationList: monohydroxylated residue,
      4. Name: Mito_Diurnal_Spot14
      5. PublicationRef: pending
  48. 31376
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 17
      3. ModificationList: monohydroxylated residue,
      4. Name: Mito_Diurnal_Spot17
      5. PublicationRef: pending
  49. 31420
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 7
      3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot7
      5. PublicationRef: pending
  50. 31412
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 5
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot5
      5. PublicationRef: pending
  51. 31405
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 43
      3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
      4. Name: Mito_Diurnal_Spot43
      5. PublicationRef: pending
  52. 31402
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 40
      3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot40
      5. PublicationRef: pending
  53. 31391
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 30
      3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
      4. Name: Mito_Diurnal_Spot30
      5. PublicationRef: pending
  54. 31409
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 47
      3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
      4. Name: Mito_Diurnal_Spot47
      5. PublicationRef: pending
  55. 31398
      1. InstrumentRef: INSTRUMENT_1
      2. Label: Spot 37
      3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
      4. Name: Mito_Diurnal_Spot37
      5. PublicationRef: pending