PXD055647

PXD055647 is an original dataset announced via ProteomeXchange.

Title	Sensitive and accurate proteome profiling of embryogenesis using Real-Time Search and TMTproC quantification
Description	Multiplexed proteomics has become a powerful tool for investigating biological systems. Using balancer-peptide conjugates (e.g., TMTproC complementary ions) in the MS2 spectra for quantification circumvents the ratio distortion problem inherent in multiplexed proteomics. However, TMTproC quantification scans require long Orbitrap transients and extended ion injection times to achieve sufficient ion statistics and spectral resolution. Real-Time Search (RTS) algorithms have demonstrated increased speed and sensitivity by selectively informing precursor peak quantification. Here, we combine complementary ion quantification with Real-Time Search (TMTproC-RTS) to enhance sensitivity while maintaining accuracy and precision in quantitative proteomics at the MS2 level. We demonstrate the utility of this method by quantifying protein dynamics during the embryonic development of Drosophila melanogaster (fly), Ciona robusta (sea squirt), and Xenopus laevis (frog). We quantify 7.6k, 8.6k, and 12.7k proteins in each organism, which is an improvement of 12%, 13%, and 14%, respectively, compared to naive TMTproC analysis. For all three organisms, the newly acquired data outperform previously published datasets and provides a diverse, deep, and accurate database of protein dynamics during embryogenesis which will advance the study of evolutionary comparison in early embryogenesis.
HostingRepository	PRIDE
AnnounceDate	2025-01-17
AnnouncementXML	Submission_2025-01-17_12:39:00.871.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alex Johnson
SpeciesList	scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355; scientific name: Ciona intestinalis x Ciona robusta; NCBI TaxID: 2893330; scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue
Instrument	Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-06 17:51:54	ID requested
⏵ 1	2025-01-17 12:39:01	announced

10.1016/J.MCPRO.2024.100899;

submitter keyword: Ciona, TMTpro, Xenopus,Drosophila, multiplexing, Ascend

Martin Wuhr
contact affiliation	Princeton University
contact email	aj10@princeton.edu
lab head
Alex Johnson
contact affiliation	Princeton University
contact email	aj10@princeton.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/2025/01/PXD055647

PRIDE project URI

• PRIDE
  1. PXD055647
     1. Label: PRIDE project
     2. Name: Sensitive and accurate proteome profiling of embryogenesis using Real-Time Search and TMTproC quantification