PXD038522

PXD038522 is an original dataset announced via ProteomeXchange.

Title	Data for manuscript, “An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples”
Description	Clinical BALF samples are rich in biomolecules, including proteins, and useful for molecular studies of lung health and disease. However, MS based proteomic analysis of BALF is impeded by the dynamic range of protein abundance, and potential for interfering contaminants. We have developed a workflow that eliminates these challenges. By combining high abundance protein depletion, protein trapping, clean-up, and in-situ tryptic digestion, our workflow is compatible with both qualitative and quantitative MS-based proteomic analysis. The workflow includes collection of endogenous peptides for peptidomic analysis of BALF, if desired, as well as amenability to offline semi-preparative or microscale fractionation of peptide mixtures prior to LC-MS/MS analysis, for increased depth of analysis. We show the effectiveness of this workflow on BALF samples from COPD patients. Overall, our workflow should allow MS-based proteomics to be applied to a wide variety of studies focused on BALF clinical samples.
HostingRepository	PRIDE
AnnounceDate	2023-04-05
AnnouncementXML	Submission_2023-04-05_12:57:39.104.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	DanielleWeise
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; 2-pyrrolidone-5-carboxylic acid (Gln); L-methionine removal; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-03 17:19:43	ID requested
⏵ 1	2023-04-05 12:57:39	announced

Dataset with its publication pending

submitter keyword: Bronchoalveolar lavage fluid

BALF

quantitative proteomics

mass spectrometry

sample preparation

lung disease

Timothy J.Griffin
contact affiliation	Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, USA
contact email	tgriffin@umn.edu
lab head
DanielleWeise
contact affiliation	University of Minnesota
contact email	ostr0103@umn.edu
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/2023/04/PXD038522

PRIDE project URI

• PRIDE
  1. PXD038522
     1. Label: PRIDE project
     2. Name: Data for manuscript, “An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples”