PXD062360

PXD062360 is an original dataset announced via ProteomeXchange.

Title	Understanding m/z range settings for MS/MS scans: a case study with intact glycopeptides
Description	Several practical considerations dictate the scan range, or breadth of ion m/z values, that can be transmitted through ion guides in mass spectrometers (MS). Voltage settings must be balanced to minimize low m/z cutoffs while also generating effective pseudopotential wells for high m/z ions to maximize transmission of ion populations of interest. The scan range is particularly impactful in glycoproteomics, because glycopeptide identification typically relies on low mass-to-charge (m/z) glycan-derived oxonium ions and higher m/z peptide fragments that retain glycan modifications. Common practice suggests a so-called “5-10-15 rule” when setting scan ranges, which defines the upper m/z value to be used for the scan based on a multiple of the first m/z value. While this axiom has very real implications for transmitting diverse ion populations in full MS scans, adhering to this strategy can unnecessarily limit analytical information available in glycopeptide MS/MS spectra. Here, we explore the implications of following or breaking the 5-10-15 rule in MS/MS scans for glycopeptide characterization on a quadrupole-Orbitrap-linear ion trap Tribrid MS system (Orbitrap Ascend). We show that breaking the 5-10-15 rule does not lead to a significant loss of fragment ion transmission at either extreme of the m/z range. We demonstrate this concept for glycopeptides fragmented with higher-energy collisional dissociation (HCD), electron-transfer dissociation (ETD), and electron-transfer/higher-energy collision dissociation (EThcD). We use this case study to discuss the concepts important to using the 5-10-15 rule wisely and when it can be practically ignored, such as using large m/z ranges to improve glycopeptide characterization.
HostingRepository	PRIDE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-07_16:10:59.607.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tim S Veth
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	complex glycosylation
Instrument	Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-28 13:31:31	ID requested
⏵ 1	2026-06-07 16:11:00	announced

10.1021/jasms.5c00352;

Veth TS, Kothlow K, Riley NM, Range Settings for MS/MS Scans: A Case Study with Intact Glycopeptides. J Am Soc Mass Spectrom, 37(4):872-883(2026) [pubmed]

submitter keyword: glycobiology, glycopeptides,Mass spectrometry, mass range

Nicholas M. Riley
contact affiliation	University of Washington, Department Chemistry, Seattle, WA, 98195
contact email	nmriley@uw.edu
lab head
Tim S Veth
contact affiliation	University of Washington
contact email	tveth@uw.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD062360
     1. Label: PRIDE project
     2. Name: Understanding m/z range settings for MS/MS scans: a case study with intact glycopeptides