PXD019881

PXD019881 is an original dataset announced via ProteomeXchange.

Title	Isobaric matching between runs and novel PSM-level normalization in MaxQuant strongly improve reporter ion-based quantification - Peli1 knock-out mice dataset
Description	Isobaric labeling has the promise of combining high sample multiplexing with precise quantification. However, normalization issues and the missing value problem of complete n-plexes hamper quantification across more than one n-plex. Here we introduce two novel algorithms implemented in MaxQuant that substantially improve the data analysis with multiple n-plexes. First, isobaric matching between runs (IMBR) makes use of the three-dimensional MS1 features to transfer identifications from identified to unidentified MS/MS spectra between LC-MS runs in order to utilize reporter ion intensities in unidentified spectra for quantification. On typical datasets, we observe a significant gain in quantifiable n-plexesMS/MS spectra that can be used for quantification. Second, we introduce a novel PSM-level normalization, applicable to data with and without common reference channel. It is a weighted median-based method, in which the weights reflect the number of ions that were used for fragmentation. On a typical dataset, we observe complete removal of batch effects and dominance of the biological sample grouping after normalization. This dataset is one of the datasets used for the study. It is TMT 10-plex with a reference channel.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:07:36.421.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sung-Huan Yu
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-18 22:44:32	ID requested
1	2020-06-21 22:20:57	announced
2	2020-09-07 22:55:46	announced	2020-09-08: Updated publication reference for PubMed record(s): 32892627.
⏵ 3	2024-10-22 05:07:41	announced	2024-10-22: Updated project metadata.

Yu SH, Kyriakidou P, Cox J, Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification. J Proteome Res, 19(10):3945-3954(2020) [pubmed]

10.1021/acs.jproteome.0c00209;

submitter keyword: match between runs, normalization, tandem mass tag,isobaric labeling, multiplexed quantification

Jürgen Cox
contact affiliation	Max Planck Institute of Biochemistry
contact email	cox@biochem.mpg.de
lab head
Sung-Huan Yu
contact affiliation	Max Planck Institute of BIochemistry
contact email	shyu@biochem.mpg.de
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/2020/06/PXD019881

PRIDE project URI

• PRIDE
  1. PXD019881
     1. Label: PRIDE project
     2. Name: Isobaric matching between runs and novel PSM-level normalization in MaxQuant strongly improve reporter ion-based quantification - Peli1 knock-out mice dataset