PXD017471

PXD017471 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-12 03:01:12	ID requested
⏵ 1	2020-08-18 06:40:26	announced

Dataset with its publication pending

submitter keyword: Label free methods

spectral counts normalization

complexity-based correction factor

Huntington Disease mice models

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

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/pride/data/archive/2020/08/PXD017471

PRIDE project URI

• PRIDE
  1. PXD017471
     1. Label: PRIDE project
     2. Name: New label free methods for protein relative quantification applied to the investigation of animal model of Huntington Disease.