PXD009068

PXD009068 is an original dataset announced via ProteomeXchange.

Title	A generic normalization method for proper quantification in untargeted proteomics screening
Description	The label-free quantitative mass spectrometry methods, in particular the SWATH-MS approach, have gained popularity and became a powerful technique for comparison of large datasets. In the present work, it is introduced the use of recombinant proteins as internal standards for untargeted label-free methods. The proposed internal standard strategy reveals a similar intragroup normalization capacity when compared with the most common normalization methods, with the additional advantage of maintaining the overall proteome changes between groups (which are lost using the methods referred above). Thus, proving to be able to maintain a good performance even when large qualitative and quantitative differences in sample composition are observed, such as the ones induced by biological regulation (as observed in secretome and other biofluids’ analyses) or by enrichment approaches (such as immunopurifications). Moreover, it corresponds to a cost-effective alternative, easier to implement than the current stable-isotope labeling internal standards, therefore being an appealing strategy for large quantitative screening, as clinical cohorts for biomarker discovery.
HostingRepository	PRIDE
AnnounceDate	2019-08-19
AnnouncementXML	Submission_2019-08-19_01:21:07.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sandra Anjo
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Aequorea victoria; NCBI TaxID: 6100;
ModificationList	S-carboxamidoethyl-L-cysteine; methylthiolated residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-28 07:02:35	ID requested
⏵ 1	2019-08-19 01:21:08	announced

Dataset with its publication pending

ProteomeXchange project tag: Reference

curator keyword: Technical

submitter keyword: Internal Standard, SWATH-MS, Proteomics screening, Biofluids, Data normalization

Bruno Manadas
contact affiliation	Center for Neuroscience and Cell Biology – University of Coimbra
contact email	bmanadas@gmail.com
lab head
Sandra Anjo
contact affiliation	​Center for Neuroscience and Cell Biology – University of Coimbra
contact email	sandra.isabel.anjo@gmail.com
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/2019/08/PXD009068

PRIDE project URI

• PRIDE
  1. PXD009068
     1. Label: PRIDE project
     2. Name: A generic normalization method for proper quantification in untargeted proteomics screening