PXD007071-2

PXD007071 is an original dataset announced via ProteomeXchange.

Title	The impact of commonly used alkylating agents on artefactual peptide modification
Description	Iodoacetamide is by far the most commonly used agent for alkylation of cysteine during sample preparation for proteomics. An alternative, 2-chloroacetamide, has been recently suggested to reduce the alkylation of residues other than cysteine, such as the N-terminus, Asp, Glu, Lys, Ser, Thr and Tyr. Here, we show that although 2-chloroacetamide reduces the level of off-target alkylation, it exhibits a range of adverse effects. The most significant of these was methionine oxidation, which increases to a maximum of 40% of all Met containing peptides compared to 2-5% with iodoacetamide. Increases were also observed for mono and dioxidised tryptophan. No additional differences between the alkylating reagents were observed for a range of other post-translational modifications and digestion parameters. The adverse impact of 2-chloroacetamide on methionine oxidation suggest it is not the ideal alkylating reagent for proteomics.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:39:06.250.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Peter Hains
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2017-07-18 02:30:22	ID requested
1	2017-08-16 00:33:05	announced
⏵ 2	2024-10-22 04:39:13	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.7b00022;

Hains PG, Robinson PJ, The Impact of Commonly Used Alkylating Agents on Artifactual Peptide Modification. J Proteome Res, 16(9):3443-3447(2017) [pubmed]

curator keyword: Technical

submitter keyword: post-translational modification, cysteine alkylation, artefact, N-terminal alkylation,Alkylation

Philip J Robinson
contact affiliation	ProCan and the Cell Signalling Units, Children’s Medical Research Institute, The University of Sydney, 214 Hawkesbury Rd, Westmead, NSW Australia, 2145.
contact email	PRobinson@cmri.org.au
lab head
Peter Hains
contact affiliation	Children's Medical Research Institute
contact email	phains@cmri.org.au
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/2017/08/PXD007071

PRIDE project URI

• PRIDE
  1. PXD007071
     1. Label: PRIDE project
     2. Name: The impact of commonly used alkylating agents on artefactual peptide modification