PXD009600

PXD009600 is an original dataset announced via ProteomeXchange.

Title	Updated in-gel digestion for protein analysis by mass spectrometry
Description	The in-gel digestion of proteins for analysis by liquid chromatograph mass spectrometry has been used since the early 1990s. Although several improvements have contributed to increasing the quality of the data obtained, many recent publications still use sub-optimal approaches. We present an updated in-gel digestion protocol. We show that alternative reducing, alkylating agents and tryptic digestion buffers increase peptide and protein identification and reduce incubation times. Our results indicate that a simultaneous and short, high temperature reduction and alkylation reaction using Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) and chloroacetamide (CAA) with a subsequent gel wash improve protein identification and sequence coverage, diminish peptide side reactions. Additionally, use of 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid buffer (HEPES) allows a significant reduction in the digestion time improving trypsin performance and increasing the peptide recovery. The updated in-gel digestion protocol described here is highly efficient and offers flexibility to be incorporated in any proteomic laboratory.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:44:54.193.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Juan Ramon Hernandez-Fernaud
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2018-04-25 06:01:19	ID requested
1	2018-10-02 03:50:51	announced
⏵ 2	2024-10-22 04:44:57	announced	2024-10-22: Updated project metadata.

Goodman JK, Zampronio CG, Jones AME, Hernandez-Fernaud JR, Updates of the In-Gel Digestion Method for Protein Analysis by Mass Spectrometry. Proteomics, 18(23):e1800236(2018) [pubmed]

10.1002/pmic.201800236;

curator keyword: Technical

submitter keyword: proteomics, mass spectrometry,in-gel digestion, trypsin

Juan Ramon Hernandez Fernaud
contact affiliation	Manager
contact email	jrfernau@ull.edu.es
lab head
Juan Ramon Hernandez-Fernaud
contact affiliation	Universidad de La Laguna
contact email	jrfernaud@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/2018/10/PXD009600

PRIDE project URI

• PRIDE
  1. PXD009600
     1. Label: PRIDE project
     2. Name: Updated in-gel digestion for protein analysis by mass spectrometry