PXD018152

PXD018152 is an original dataset announced via ProteomeXchange.

Title	proteiNorm – A user-friendly tool for normalization and analysis of TMT and label-free protein quantification
Description	The technological advances in mass spectrometry allow us to collect more comprehensive data with higher quality and increasing speed. With the rapidly increasing amount of data generated, the need for streamlining analyses becomes more apparent. Proteomic data is known to be often affected by systemic bias from unknown sources, and failing to adequately normalize the data can lead to erroneous conclusions. To allow researchers to easily evaluate and compare different normalization methods via a user-friendly interface, we have developed “proteiNorm”. The current implementation of proteiNorm accommodates preliminary filter on peptide and sample level, followed by an evaluation of several popular normalization methods and visualization of missing value. The user then selects an adequate normalization method and one of several imputation methods used for the subsequent comparison of different differential abundance/expression methods and estimation of statistical power. The application of proteiNorm and interpretation of its results is demonstrated on a Tandem Mass Tag mass spectrometry example data set, where the proteome of three different breast cancer cell lines was profiled with and without hydroxyurea treatment. With proteiNorm, we provide a user-friendly tool to identify an adequate normalization method and to select an appropriate method for a differential abundance/expression analysis.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-08_18:38:58.787.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD018152
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Stephanie Byrum
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-23 09:14:23	ID requested
⏵ 1	2021-09-08 18:38:59	announced

Graw S, Tang J, Zafar MK, Byrd AK, Bolden C, Peterson EC, Byrum SD, proteiNorm - A User-Friendly Tool for Normalization and Analysis of TMT and Label-Free Protein Quantification. ACS Omega, 5(40):25625-25633(2020) [pubmed]

submitter keyword: Proteomics, Normalization, Differential analysis

Stephanie Diane Byrum
contact affiliation	1. Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 2. Arkansas Children's Research Institute
contact email	sbyrum@uams.edu
lab head
Stephanie Byrum
contact affiliation	UAMS
contact email	sbyrum@uams.edu
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/2021/09/PXD018152

PRIDE project URI

• PRIDE
  1. PXD018152
     1. Label: PRIDE project
     2. Name: proteiNorm – A user-friendly tool for normalization and analysis of TMT and label-free protein quantification