PXD017471 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | New label free methods for protein relative quantification applied to the investigation of animal model of Huntington Disease. |
Description | Spectral Counts approaches (SpCs) are largely employed for the comparison of protein expression profiles in label free differential proteomics applications. Similarly, to other comparative methods, also SpCs based approaches require a normalization procedure before Fold Changes (FC) calculation. Here, we propose new Complexity Based Normalization (CBN) methods that introduced a variable adjustment factor (f), related to the complexity of the sample, both in terms of total number of identified proteins (CBN(P)) and as total number of spectral counts (CBN(S)). Both these new methods were compared with the Normalized Spectral Abundance Factor (NSAF) and the Spectral Counts log Ratio (Rsc), by using standard protein mixtures. Finally, to test the robustness and the effectiveness of the CBNs methods, they were employed for the comparative analysis ofcortical protein extract fromzQ175 mouse brains, model of Huntington Disease (HD), and control animals. On standard mixtures, both CBN methods showed an excellent behavior in terms of reproducibility and coefficients of variation (CVs) in comparison to the other SpCs approaches. Moreover, the CBN(S) was demonstrated to be more sensitive in detecting small difference in proteins amount when applied on biological samples in comparison to CBN(P). |
HostingRepository | PRIDE |
AnnounceDate | 2020-08-18 |
AnnouncementXML | Submission_2020-08-18_06:40:26.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Marianna Caterino |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | iodoacetamide derivatized residue |
Instrument | LTQ Orbitrap |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-02-12 03:01:12 | ID requested | |
⏵ 1 | 2020-08-18 06:40:26 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Label free methods |
spectral counts normalization |
complexity-based correction factor |
Huntington Disease mice models |
Contact List
Maria Monti |
contact affiliation | Department of Chemical Sciences, University of Naples 'FedericoII', Naples, Italy; CEINGE scarl Advanced Biotechnology, Facility of Proteomics, Naples, Italy |
contact email | montimar@unina.it |
lab head | |
Marianna Caterino |
contact affiliation | University of Naples 'Federico II' |
contact email | marianna.caterino@unina.it |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD017471
- Label: PRIDE project
- Name: New label free methods for protein relative quantification applied to the investigation of animal model of Huntington Disease.