PXD018758

PXD018758 is an original dataset announced via ProteomeXchange.

Title	Leveraging immonium ions for identifying and targeting acyl-lysine modifications in proteomic datasets
Description	Acyl modifications vary greatly in terms of elemental composition and site of protein modification. Developing methods to identify these modifications more confidently can help assess the scope of these modifications in large proteomic datasets. Herein we analyze the utility of acyl-lysine immonium ions for identifying the modifications in proteomic datasets. We demonstrate that the cyclized immonium ion is a strong indicator of acyl-lysine presence when its rank or relative abundance compared to other ions within a spectrum is considered. Utilizing a stepped collision energy method in a shotgun experiment highlights the immonium ion strongly. Implementing an analysis that accounted for features within each MS2 spectra, this method allows peptides with short chain acyl-lysine modifications to be clearly identified in complex lysates. Immonium ions can also be used to validate novel acyl-modifications; in this study we report the first examples of 3-hydroxylpimelyl-lysine modification and validate them using immonium ions. Overall these results solidify the use of the immonium ion as a marker for acyl-lysine modifications in complex proteomic datasets.
HostingRepository	PRIDE
AnnounceDate	2020-09-09
AnnouncementXML	Submission_2020-09-08_23:34:43.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD018758
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Janine Fu
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Butyryl; Crotonyl; Oxidation; Acetyl; Carbamidomethyl; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue; butanoylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-23 01:34:37	ID requested
⏵ 1	2020-09-08 23:34:44	announced

Muroski JM, Fu JY, Nguyen HH, Ogorzalek Loo RR, Loo JA, Leveraging Immonium Ions for Targeting Acyl-Lysine Modifications in Proteomic Datasets. Proteomics, 21(3-4):e2000111(2021) [pubmed]

submitter keyword: Lysine acetylation, Lysine acylation, 3-hydroxypimelylation, immonium ion, BSA, LC-MS/MS, Stepped Collision Energy

Joseph A. Loo
contact affiliation	Department of Chemistry and Biochemistry, University of California, Los Angeles, CA,USA David Geffen School of Medicine, Department of Biological Chemistry, University of California, Los Angeles, CA, USA UCLA-DOE Institute, University of California, Los Angeles, CA, USA UCLA Molecular Biology Institute, University of California, Los Angeles, CA, USA
contact email	jloo@chem.ucla.edu
lab head
Janine Fu
contact affiliation	University of California, Los Angeles
contact email	janinefu@chem.ucla.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD018758
     1. Label: PRIDE project
     2. Name: Leveraging immonium ions for identifying and targeting acyl-lysine modifications in proteomic datasets