PXD000385-1

PXD000385 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Amniocyte lysate proteome
Description	Down syndrome (DS), caused by an extra copy of chromosome 21, affects 1 in 750 live births and is characterised by cognitive impairment and a constellation of congenital defects. Currently, little is known about the molecular pathogenesis and no direct genotype-phenotype relationship has yet been confirmed. Since DS amniocytes are expected to have a distinct biological behaviour compared to normal amniocytes, we hypothesise that relative quantification of proteins produced from trisomy and euploid (chromosomally normal) amniocytes will reveal dysregulated molecular pathways. Chromosomally normal- and Trisomy 21-amniocytes were quantitatively analyzed by using Stable Isotope Labeling of Amino acids in Cell culture and tandem mass spectrometry. The most extensive proteome of amniocytes and amniotic fluid has been generated and differentially expressed proteins from amniocytes with Trisomy 21 revealed molecular pathways that seem to be most significantly affected by the presence of an extra copy of chromosome 21. Mass spectra were analyzed using Mascot (version 2.2, Matrix Science), executing a spectral search against a concatenated International Protein Index (IPI) human protein database (version 3.54 containing 39,925 entries) and a decoy database. Parameters included: trypsin enzyme specificity, SILAC double measurements of Lys6 and Arg8, 1 missed cleavage, minimum peptide length of 7 amino acids, minimum of 1 unique peptide, top 6 MS/MS peaks per 100 Da, peptide mass tolerance of 20 ppm for precursor ion and MS/MS tolerance of 0.5 Da. Oxidation of methionine and N-terminal protein acetylation for variable modifications and cysteine caramidomethylation for fixed modification. All entries were filtered using a false positive rate of 1% both at the peptide and protein levels, and false positives were removed. Quantification via normalised H/L ratios was based on minimum of 3 peptide ratio counts. Protein group entries with a normalised ratio significance B score of =< 0.05 or significance A score of =< 0.05 were retained for further analysis.
HostingRepository	PRIDE
AnnounceDate	2013-09-27
AnnouncementXML	Submission_2013-09-27_05:59:51.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000385
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	E Diamandis
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; neutral loss: 63.998285
Instrument	radial ejection linear ion trap

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-31 02:18:35	ID requested
⏵ 1	2013-09-27 05:07:56	announced
⏵ 1	2014-07-28 00:43:33	announced
2	2013-09-27 05:59:51	announced	Add reference
2	2014-08-08 01:54:25	announced	Updated project metadata.
3	2024-10-07 09:02:49	announced	2024-10-07: Updated project metadata.

Publication List

Cho CK, Drabovich AP, Karagiannis GS, Mart, í, nez-Morillo E, Dason S, Dimitromanolakis A, Diamandis EP, Quantitative proteomic analysis of amniocytes reveals potentially dysregulated molecular networks in Down syndrome. Clin Proteomics, 10(1):2(2013) [pubmed]

Cho CK, Drabovich AP, Karagiannis GS, Mart, í, nez-Morillo E, Dason S, Dimitromanolakis A, Diamandis EP, Quantitative proteomic analysis of amniocytes reveals potentially dysregulated molecular networks in Down syndrome. Clin Proteomics, 10(1):2(2013) [pubmed]

Keyword List

submitter keyword: cell culture, LC-MSMS

submitter keyword: cell culture, LC-MSMS

Contact List

E Diamandis
contact affiliation	Pathology and Laboratory Medicine
contact email	edumartinezmorillo@gmail.com

Full Dataset Link List

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/2013/09/PXD000385

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/2013/09/PXD000385

Repository Record List

[ + ]

PRIDE
1. 30472
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 2
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 2
  5. PublicationRef: PMID23394617
2. 30493
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 4
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 4
  5. PublicationRef: PMID23394617
3. 30481
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 2
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 2
  5. PublicationRef: PMID23394617
4. 30476
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 6
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 6
  5. PublicationRef: PMID23394617
5. 30488
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 9
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 9
  5. PublicationRef: PMID23394617
6. 30473
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 3
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 3
  5. PublicationRef: PMID23394617
7. 30494
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 5
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 5
  5. PublicationRef: PMID23394617
8. 30478
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 8
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 8
  5. PublicationRef: PMID23394617
9. 30480
  1. InstrumentRef: INSTRUMENT_1
  2. Label: lysates
  3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue,
  4. Name: Amniocytes
  5. PublicationRef: PMID23394617
10. 30479
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 9
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 9
  5. PublicationRef: PMID23394617
11. 30485
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 6
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 6
  5. PublicationRef: PMID23394617
12. 30471
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 1
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 1
  5. PublicationRef: PMID23394617
13. 30474
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 4
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 4
  5. PublicationRef: PMID23394617
14. 30496
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 7
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 7
  5. PublicationRef: PMID23394617
15. 30486
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 7
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 7
  5. PublicationRef: PMID23394617
16. 30477
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 7
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 7
  5. PublicationRef: PMID23394617
17. 30497
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 8
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 8
  5. PublicationRef: PMID23394617
18. 30491
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 2
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 2
  5. PublicationRef: PMID23394617
19. 30487
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 8
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 8
  5. PublicationRef: PMID23394617
20. 30482
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 3
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 3
  5. PublicationRef: PMID23394617
21. 30499
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 2
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 2
  5. PublicationRef: PMID23394617
22. 30490
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 1
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 1
  5. PublicationRef: PMID23394617
23. 30489
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 10
  3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 10
  5. PublicationRef: PMID23394617
24. 30475
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 5
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 5
  5. PublicationRef: PMID23394617
25. 30498
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 1
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 1
  5. PublicationRef: PMID23394617
26. 30495
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 6
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 6
  5. PublicationRef: PMID23394617
27. 30484
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 5
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
  4. Name: Amniocytes (lysates) - Experiment 5
  5. PublicationRef: PMID23394617
28. 30470
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 1
  3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue,
  4. Name: Amniocytes (lysates) - Experiment 1
  5. PublicationRef: PMID23394617
29. 30492
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 3
  3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue,
  4. Name: Amniocytes (lysates) - Experiment 3
  5. PublicationRef: PMID23394617
30. 30483
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Exp 4
  3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue,
  4. Name: Amniocytes (lysates) - Experiment 4
  5. PublicationRef: PMID23394617