PXD000334

PXD000334 is an original dataset announced via ProteomeXchange.

Title	Proteomics quality and standard: from a regulatory perspective
Description	Cultured mouse lymphoma cells were lysed with a buffer containing 50 mM Tris-HCl (pH 8.0) and 8 M Urea with or without a protease inhibitor cocktail (Sigma). The lysates were desalted and digested with sequencing-grade modified trypsin (Promega). Different amounts of peptides were analyzed using nanoflow RPLC-MS/MS on a linear ion trap mass spectrometer (LTQ XL, Thermo Electron, San Jose, CA). The raw MS/MS data were searched using SEQUEST running under BioWorks (Rev. 3.3.1 SP1) (Thermo Electron, San Jose, CA) against a mouse IPI proteome database (Version 3.62) downloaded from the European Bioinformatics Institute (EBI) (http://www.ebi.ac.uk). For the SEQUEST analysis, the peptide mass tolerance was set as 2.0 Da and the fragment ion tolerance was 1.0 Da. A tryptic enzyme restriction with a maximum of two internal missed cleavage sites was used. The Xcorr versus charge state values were filtered at Xcorr ≥ 1.7 for [M+H]1+ ions, ≥ 2.5 for [M+2H]2+ ions, ≥ 3.2 for [M+3H]3+ ions, and P ≤ 0.01 and ΔCn ≥ 0.08 were applied for identification of all fully tryptic peptides. The peptide ion chromatogram was extracted using a minimum intensity threshold of 100, mass tolerance of 2.0 amu and smoothing point of 5, and the area of the extracted ion chromatographic (XIC) peak was integrated and calculated using the PepQuan module in Bioworks (Thermo Electron, San Jose, CA).
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:37:32.183.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Li-Rong Yu
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-10 13:54:33	ID requested
1	2022-06-06 10:53:06	announced
⏵ 2	2024-10-22 05:37:33	announced	2024-10-22: Updated project metadata.

10.1016/j.jprot.2013.11.024;

Gu Q, Yu LR, Proteomics quality and standard: from a regulatory perspective. J Proteomics, 96():353-9(2014) [pubmed]

submitter keyword: biomarker qualification,mouse, proteomics, standards, mass spectrometry, quality control, regulatory decision, LC-MS/MS

Li-Rong Yu
contact affiliation	National Center for Toxicological Research, FDA
contact email	lirong.yu@fda.hhs.gov
lab head
Li-Rong Yu
contact affiliation	National Center for Toxicological Research, FDA
contact email	lirong.yu@fda.hhs.gov
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/2022/02/PXD000334

PRIDE project URI

• PRIDE
  1. PXD000334
     1. Label: PRIDE project
     2. Name: Proteomics quality and standard: from a regulatory perspective