PXD075509-1

PXD075509 is an original dataset announced via ProteomeXchange.

Title	E.coli total RNA digests higer-collision dissociation energies test in LC-MS/MS
Description	Four open-source software suites for the analysis of oligonucleotide data from tandem MS have been reported. These tools are all based on matching theoretical spectral libraries generated by silico digestion. While some software publications have included simple comparisons with previously published tools, a discussion of oligonucleotide identification within complex backgrounds is lacking. In this study, we acquired multiple complex oligonucleotide datasets using an Orbitrap instrument to evaluate various search engines (Ariadne, RNAModMapper, NASE and Pytheas) and assess their performance in terms of accuracy, false discovery rate (FDR), performance at certain FDR, consensus of oligonucleotide identification, consistency of outputs in chemical measurements, and unknown modification discovery.In this study, we prepared two sets of samples, which involve three RNase T1 digested and three RNase A digested E. coli total RNA. Then, digests were analyzed by LC-MS/MS.
HostingRepository	PRIDE
AnnounceDate	2026-03-11
AnnouncementXML	Submission_2026-03-11_11:02:54.703.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jing Feng
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: NEWT:562;
ModificationList	monomethylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2026-03-11 10:50:18	ID requested
⏵ 1	2026-03-11 11:02:55	announced

Dataset with its publication pending

submitter keyword: E.coli RNA, HCD, Oligonucleotide, LC-MS/MS

Xiang Zhang
contact affiliation	University of Louisville, Department of Chemistry, Louisville, KY 40208, USA
contact email	xiang.zhang@louisville.edu
lab head
Jing Feng
contact affiliation	University of Louisville
contact email	jing.feng@louisville.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/2026/03/PXD075509

PRIDE project URI

• PRIDE
  1. PXD075509
     1. Label: PRIDE project
     2. Name: E.coli total RNA digests higer-collision dissociation energies test in LC-MS/MS