PXD062540-1

PXD062540 is an original dataset announced via ProteomeXchange.

Title	Complement Reporter Ion Quantification with a Quadrupole-Ion Trap Instrument
Description	Proteomics workflows have traditionally been divided into discovery-based and targeted approaches, with instrumentation optimized for each. Discovery experiments typically utilize high-resolution analyzers such as the Orbitrap™, while targeted workflows rely on the sensitivity and specificity of triple quadrupole systems. Recently, a quadrupole-ion trap instrument (Stellar™ MS), demonstrated superior performance for targeted applications compared to traditional triple quadrupoles. In this study, we expand the capabilities of this platform to multiplexed shotgun proteomics using complement reporter ion quantification in an ion trap (iTMTproC). Benchmarking with standards shows that iTMTproC achieves quantification accuracy and interference reduction comparable to MultiNotch MS3 on the Orbitrap Fusion Lumos™, a dedicated quadrupole-ion trap-Orbitrap™ tribrid instrument for this method. We further validate the approach through a developmental time-series analysis of vertebrate embryos, revealing data quality equivalent to MultiNotch MS3 with greater sensitivity. These findings significantly extend the functionality of targeted instrumentation, underscoring the versatility of quadrupole-ion trap systems and providing cost-effective access to highly accurate quantitative multiplexed shotgun proteomics.
HostingRepository	PRIDE
AnnounceDate	2025-09-08
AnnouncementXML	Submission_2025-09-07_17:42:07.092.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD062540
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Edward Cruz
SpeciesList	scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos; Orbitrap Ascend; Stellar

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-02 14:55:13	ID requested
⏵ 1	2025-09-07 17:42:07	announced

10.1021/acs.jproteome.5c00356;

Cruz ER, Johnson ANT, Pujari V, Zhang Q, Nguyen T, Stadlmeier M, Wang J, Jacob CC, McAlister GC, Remes PM, W, ü, hr M, Expanding Targeted Instrumentation for Discovery Applications: Complement Reporter Ion Quantification with a Quadrupole-Ion Trap Instrument. J Proteome Res, 24(9):4611-4622(2025) [pubmed]

10.6019/PXD062540;

submitter keyword: Stellar, complement reporter ion,quadrupole-ion trap, multiplexed shotgun proteomics

Martin Wuhr
contact affiliation	Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, USA
contact email	wuhr@princeton.edu
lab head
Edward Cruz
contact affiliation	Princeton University
contact email	ercruz@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/2025/09/PXD062540

PRIDE project URI

• PRIDE
  1. PXD062540
     1. Label: PRIDE project
     2. Name: Complement Reporter Ion Quantification with a Quadrupole-Ion Trap Instrument