PXD022367

PXD022367 is an original dataset announced via ProteomeXchange.

Title	MaxQuant.Live enables enhanced selectivity and identification of peptides modified by endogenous SUMO and ubiquitin
Description	Small ubiquitin-like modifiers (SUMOs) and ubiquitin are frequent post-translational modifications of proteins that play pivotal roles in all cellular processes. We previously reported mass spectrometry-based proteomics methods that enable profiling of lysines modified by endogenous SUMO or ubiquitin in an unbiased manner, without requiring genetic engineering. Here we investigated the applicability of precursor mass filtering enabled by MaxQuant.Live (MQL) to our SUMO and ubiquitin proteomics workflows, which efficiently avoided sequencing of precursors too small to be modified but otherwise indistinguishable by mass-to-charge ratio. Using peptide mass filtering, we achieved much higher precursor selectivity, ultimately resulting in up to 30% more SUMO and ubiquitin sites identified from replicate samples. Real-time ‘untargeting’ of unmodified peptides by MQL resulted in 90% SUMO-modified precursor selectivity from a 25% pure sample, demonstrating great applicability for digging deeper into ubiquitin-like modificomes. We adapted the mass filtering strategy to the new Exploris 480 mass spectrometer, achieving comparable gains in SUMO precursor selectivity and identification rates. Collectively, mass filtering via MQL significantly increased identification rates of SUMO- and ubiquitin-modified peptides from the exact same samples, without the requirement for prior knowledge or spectral libraries.
HostingRepository	PRIDE
AnnounceDate	2022-02-14
AnnouncementXML	Submission_2022-02-13_16:50:13.846.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ivo Hendriks
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitinylated lysine; sumoylated lysine
Instrument	Orbitrap Exploris 480; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-05 00:35:52	ID requested
1	2021-02-04 22:48:02	announced
2	2021-02-11 22:36:29	announced	2021-02-12: Updated publication reference for PubMed record(s): 33539096.
⏵ 3	2022-02-13 16:50:14	announced	2022-02-14: Updated project metadata.

Hendriks IA, Akimov V, Blagoev B, Nielsen ML, MaxQuant.Live Enables Enhanced Selectivity and Identification of Peptides Modified by Endogenous SUMO and Ubiquitin. J Proteome Res, 20(4):2042-2055(2021) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: peptide mass filtering,SUMO, MQL, ubiquitin, MaxQuant.Live, precursor untargeting

Michael Lund Nielsen
contact affiliation	Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
contact email	michael.lund.nielsen@cpr.ku.dk
lab head
Ivo Hendriks
contact affiliation	Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
contact email	ivo.a.hendriks@gmail.com
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/2021/02/PXD022367

PRIDE project URI

• PRIDE
  1. PXD022367
     1. Label: PRIDE project
     2. Name: MaxQuant.Live enables enhanced selectivity and identification of peptides modified by endogenous SUMO and ubiquitin