PXD012738-1

PXD012738 is an original dataset announced via ProteomeXchange.

Title	LysargiNase Enhances the Protein Identification on FFPE Samples
Description	Formalin-Fixed Paraffin-Embedded (FFPE) samples are treasure for proteomic studies of disease. However, their usage is hampered for proteomics study because of the crosslink among proteins, and protein vs nucleic acid. Even worse, other covalent chemical modifications like methylation introduced by formaldehyde interfere trypsin digestion. We applied LysargiNase for the first time in FFPE samples, and systematically compared the samples digested by LysargiNase with commonly used tryptic samples. A total of 33095 peptides and 3559 proteins were identified with LysargiNase and trypsin combined in two replicates. LysargiNase increased peptide identification by 19.3% and protein identification by 13.3% on the basis of trypsin. Consistently, LysargiNase increased C terminal peptide identification by 47.7%. Moreover, LysargiNase showed less missed-cleavage rate (54.5%) at methylated sites than trypsin (74.5%), contributing to the identification of methylated peptides in FFPE samples.
HostingRepository	iProX
AnnounceDate	2019-02-15
AnnouncementXML	Submission_2019-05-15_20:50:48.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shu Liu
SpeciesList	scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2019-02-17 07:37:29	ID requested
⏵ 1	2019-05-15 20:50:49	announced

Liu S, Xu F, Yin Y, Zhang J, Wang F, Li Y, Xu P, LysargiNase enhances protein identification on the basis of trypsin on formalin-fixed paraffin-embedded samples. Rapid Commun Mass Spectrom, 33(17):1381-1389(2019) [pubmed]

submitter keyword: FFPE, proteome, Trypsin, LysargiNase, methylation, mouse liver

Ping Xu
contact affiliation	National Center for Protein Sciences (Beijing)
contact email	xuping@mail.ncpsb.org
lab head
Shu Liu
contact affiliation	National Center for Protein Sciences (Beijing)
contact email	liushulr@126.com
dataset submitter

iProX dataset URI