PXD003400-2

PXD003400 is an original dataset announced via ProteomeXchange.

Title	Filter-aided sample preparation depends on filter unit shape
Description	One of the main goals of shotgun proteomics studies is to identify by mass spectrometry as many proteins as possible, often from low-protein samples, in order to help answer important biological questions. All experimental steps need to be optimized to achieve a thorough proteomic analysis. One of the most important is an optimal extraction and solubilization of proteins through the use of detergents, chaotropes, and reducing agents. Although very efficient in solubilizing membrane proteins, the presence of these detergents, such as SDS, negatively affects the LC/MS analysis and limits protein identifications, and therefor they need to be removed before LC-MS analysis. Filter-aided sample preparation (FASP) is a generally accepted method for removal of detergents and chaotropes used for protein extraction as well as non-proteinaceous compounds such as salts, nucleic acids and lipids. Another critical aspect of proteomic analyses is the starting amount of protein in the sample. There is still little information about the efficacy of FASP method for protein-limited samples. The aim of this study was to compare two methods for SDS removal, ethanol precipitation versus FASP and we evaluate the effectiveness of FASP method using different filtration devices, as well as RIPA (0.1% SDS) and high-SDS (2%SDS) lysis buffers applied to low (1µg) and high (10-100µg) protein amounts.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:14:35.683.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chiara guerrera
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-01-04 05:08:02	ID requested
1	2020-11-05 02:27:41	announced
⏵ 2	2024-10-22 05:14:36	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Technical

submitter keyword: Human, FASP, LC-MS/MS

Ida Chiara Guerrera
contact affiliation	Proteomics Platform Necker, PPN-3P5, Structure federative de recherche SFR Necker, Universite Paris Descartes, Paris, FRANCE
contact email	chiara.guerrera@inserm.fr
lab head
Chiara guerrera
contact affiliation	Necker proteomics, INSERM
contact email	chiara.guerrera@inserm.fr
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/2020/11/PXD003400

PRIDE project URI

• PRIDE
  1. PXD003400
     1. Label: PRIDE project
     2. Name: Filter-aided sample preparation depends on filter unit shape