PXD032235-1

PXD032235 is an original dataset announced via ProteomeXchange.

Title	Pitfalls and Solutions in Mass Spectrometry-based Identification of Protein Glycation
Description	Protein glycation is a type of post-translational modification (PTM) involving complex non-enzymatic reactions of reducing sugars or reactive dicarbonyls with proteins, generating a heterogeneous group of advanced glycation end-products (AGEs) such as carboxymethyllysine (CML). In bottom-up proteomics, 2-iodoacetamide (IAA) is the most commonly used reagent for cysteine alkylation before trypsin digestion, which exogenously gives a carbamidomethylation (CAM) group on the side chain of cysteine residue. However, offisite alkylation of IAA can occur at the protein N-terminus and other amino acid residues such as lysine residue. Here, for the first time, we provided evidence that IAA alkylation can result in false-positive identifications of CML, and N-isopropylacrylamide (NIPAM) can be used as an IAA alternative to avoid these pitfalls.
HostingRepository	PRIDE
AnnounceDate	2023-01-24
AnnouncementXML	Submission_2023-01-24_00:44:43.362.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Humphrey, WendongMa
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetic acid derivatized residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-11 10:56:18	ID requested
⏵ 1	2023-01-24 00:44:43	announced
2	2023-11-14 08:57:01	announced	2023-11-14: Updated project metadata.

submitter keyword: CAM, post-translational modification, human, IAA, N-isopropylcarbamidoethylation, NIPAM, CM, CML, cell line, Q-Exactive, N-isopropylacrylamide, Hela, 2-iodoacetamide, Orbitrap, carboxymethylation, Escherichia coli, E. coli, PTM, kidney,Protein glycation, HEK293, carboxymethyllysine, LC-MS/MS, AGE, NIPCAE, carbamidomethylation, advanced glycation end-product

Terence Chuen WaiPoon
contact affiliation	Pilot Laboratory, Institute of Translational Medicine, Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau, China
contact email	tcwpoon@um.edu.mo
lab head
Humphrey, WendongMa
contact affiliation	Faculty of Health Sciences, University of Macau
contact email	humartel93@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/2023/01/PXD032235

PRIDE project URI

• PRIDE
  1. PXD032235
     1. Label: PRIDE project
     2. Name: Pitfalls and Solutions in Mass Spectrometry-based Identification of Protein Glycation