PXD014000

PXD014000 is an original dataset announced via ProteomeXchange.

Title	‘Shotgun’ Proteome Analyses Do Not Require Alkylation of Cysteine
Description	It is a common belief that reduction of disulfide bridges and alkylation of thiols in proteins are indispensable steps in proteomic sample preparation. Since this chemical procedure is often incomplete and prone to side reactions and can results in various artefacts we reexamined its importance. We found that the reduction and alkylation do not increase the depth of analysis and quality of proteomic quantification therefore these steps are unessential in shotgun-type investigations of proteomes. Moreover, we found that compared to a standard procedure using iodoacetamide for thiol-alkylation, sample preparation under conditions protecting thiols from oxidation improves quality of peptides and allows identifying of 10-20% more peptides and proteins. Excluding the thiol-alkylation from proteomic sample preparation, shorten the workflows, and decreases the probability of biases resulting from occurrence of artificially modified peptides.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:50:38.166.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jacek Wisniewski
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2019-05-23 23:59:04	ID requested
1	2020-01-21 07:23:23	announced
2	2020-01-21 07:29:36	announced	2020-01-21: Updated publication reference for DOI(s): 10.1016/j.aca.2019.12.007.
3	2020-09-22 06:54:32	announced	2020-01-21: Updated publication reference for DOI(s): 10.1016/j.aca.2019.12.007. 2020-09-22: Updated publication reference for PubMed record(s): 31987133. 2020-09-22: Updated publication reference for DOI(s): 10.1016/j.aca.2019.12.007.
⏵ 4	2023-11-14 08:50:38	announced	2023-11-14: Updated project metadata.

Wi, ś, niewski JR, Zettl K, Pilch M, Rysiewicz B, Sadok I, 'Shotgun' proteomic analyses without alkylation of cysteine. Anal Chim Acta, 1100():131-137(2020) [pubmed]

curator keyword: Technical

submitter keyword: thiol alkylation,iodoacetamide,Shotgun proteomics

Jacek R Wisniewski
contact affiliation	Max Planck Institute of Biochemistry Martinsried, Germany
contact email	jwisniew@biochem.mpg.de
lab head
Jacek Wisniewski
contact affiliation	Proteomics
contact email	jwisniew@biochem.mpg.de
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/2020/01/PXD014000

PRIDE project URI

• PRIDE
  1. PXD014000
     1. Label: PRIDE project
     2. Name: ‘Shotgun’ Proteome Analyses Do Not Require Alkylation of Cysteine