PXD055915-1

PXD055915 is an original dataset announced via ProteomeXchange.

Title	msSIM for single-cell proteomic analysis
Description	We report the development of the spectral library-based multiplex segmented Selected Ion Monitoring (SLB-msSIM) method, a novel approach that significantly improves sensitivity and robustness for single-cell analysis. Single-cell MS data is acquired using the msSIM technique, which sequentially applies multiple isolation cycles with the quadrupole, utilizing a wide isolation window in each cycle to accumulate and store precursor ions in the C-trap for a single scan in the Orbitrap. Proteomic identification is achieved through spectral matching with a well-defined spectral library. We employed the SLB-msSIM method to explore cellular heterogeneity across multiple cell lines and to analyze cellular trajectories during epithelial-mesenchymal transition.
HostingRepository	PRIDE
AnnounceDate	2025-10-13
AnnouncementXML	Submission_2025-10-13_00:04:12.881.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lakmini Senavirathna
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-16 13:41:02	ID requested
⏵ 1	2025-10-13 00:04:13	announced

10.1002/pmic.70037;

Senavirathna L, Ma C, Duong VA, Tsai HY, Chen R, Pan S, SLB-msSIM: A Spectral Library-Based Multiplex Segmented SIM Platform for Single-Cell Proteomic Analysis. Proteomics, 25(19):50-61(2025) [pubmed]

submitter keyword: selected ion monitoring,single-cell proteomics, cancer cell heterogeneity

Seng pan
contact affiliation	The University of Texas Health Science Center at Houston. Institute of Molecular Medicine, Houston, TX, USA
contact email	sheng.pan@uth.tmc.edu
lab head
Lakmini Senavirathna
contact affiliation	University of Texas Health Science Center at Houston
contact email	herath.lakmini.senavirathna@uth.tmc.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/2025/10/PXD055915

PRIDE project URI

• PRIDE
  1. PXD055915
     1. Label: PRIDE project
     2. Name: msSIM for single-cell proteomic analysis