PXD042929

PXD042929 is an original dataset announced via ProteomeXchange.

Title	Functional identification of protocadherin alpha 9 (PCDHA9) as a candidate causative gene for amyotrophic lateral sclerosis
Description	Mice were sacrificed after anesthesia by isoflurane following neck cutting. The spinal cord L3-L5 was taken and frozen in liquid nitrogen immediately and the ventral horn of the bilateral spinal cord (about 400um thick in gray matter area) was collected at low temperature. The samples were digested with Ripa lysate (containing 4% sodium dodecyl sulfate, protease inhibitors and phosphatase inhibitors). The protein concentrations were detected using a BCA protein assay kit (Thermo Scientific, Rockford, IL). Protein digestion was performed using the filter-aided proteome preparation (FASP) method. After digested with sequencing grade trypsin (Promega, Madison, WI) at 37 °C overnight, the resultant tryptic peptides were labeled with acetonitrile-dissolved TMT reagents (Thermo Scientific, Rockford, IL) by incubation at room temperature in dark for 2 h. The labeling reaction was stopped by 5% hydroxylamine, then equal amounts of labeled samples were mixed before prefractionation with reversed phase (RP)-high performance liquid chromatography (HPLC). Sample prefractionation was performed using an offline basic RP-HPLC approach. The LC-MS/MS analysis was performed using an Orbitrap Fusion™ Lumos™ Tribrid™ mass spectrometer (Thermo Scientific, Rockford, IL Waltham, MA) coupled online to an Easy-nLC 1200 in the data-dependent mode. The database search was performed for all raw MS files using the software MaxQuant (version 1.6). The Mus musculus proteome sequence database downloaded from uniProt (https://www.uniprot.org/) was applied to search the data. The functional results were analyzed by GO analysis.
HostingRepository	iProX
AnnounceDate	2023-06-12
AnnouncementXML	Submission_2024-03-18_20:14:30.593.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jie Zhong
SpeciesList	scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-12 20:23:43	ID requested
1	2023-06-12 20:24:16	announced
⏵ 2	2024-03-18 20:14:31	announced	2024-03-19: Update information.

Zhong J, Wang C, Zhang D, Yao X, Zhao Q, Huang X, Lin F, Xue C, Wang Y, He R, Li XY, Li Q, Wang M, Zhao S, Afridi SK, Zhou W, Wang Z, Xu Y, Xu Z, PCDHA9 as a candidate gene for amyotrophic lateral sclerosis. Nat Commun, 15(1):2189(2024) [pubmed]

submitter keyword: PCDHA9, mouse spinal cord, GO analysis.

Zhiheng Xu
contact affiliation	Institute of Genetics and Developmental Biology
contact email	zhxu@genetics.ac.cn
lab head
Jie Zhong
contact affiliation	Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
contact email	Jiezhong@genetics.ac.cn
dataset submitter

iProX dataset URI