PXD028136-1

PXD028136 is an original dataset announced via ProteomeXchange.

Title	Evaluation of disposable-trap column nanoLC-FAIMS-MS/MS for the proteomic analysis of FFPE tissue
Description	Proteomic biomarker discovery using formalin-fixed paraffin-embedded (FFPE) tissue requires robust workflows to support the analysis of large cohorts of patient samples. It also requires finding a reasonable balance between achieving high proteomic depth and limiting overall analysis time. To this end, we evaluated the merits of online coupling of disposable trap column nano-flow liquid chromatography, high-field asymmetric-waveform ion-mobility spectrometry (FAIMS) and tandem mass spectrometry (nLC-FAIMS-MS/MS). The data shows that ≤ 600 ng of peptide digest should be loaded onto the chromatographic part of the system. Careful characterization of the FAIMS settings enabled the choice of optimal combinations of compensation voltages (CV) as a function of the employed LC gradient time. We found nLC-FAIMS-MS/MS to be on par with stage tip-based off-line high pH reversed phase fractionation in terms of proteomic depth and reproducibility of protein quantification (coefficient of variation ≤ 15% for 90 % of all proteins) but requiring 50% less sample and substantially reducing sample handling. Using FFPE material from lymph node, lung and prostate tissue as examples, we show that nLC-FAIMS-MS/MS can identify 5-6,000 proteins from the respective tissue within a total of 3 hours of analysis time.
HostingRepository	PRIDE
AnnounceDate	2021-11-02
AnnouncementXML	Submission_2021-11-02_06:53:25.435.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Stephan Eckert
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	mono N-acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-26 04:05:11	ID requested
⏵ 1	2021-11-02 06:53:25	announced

Dataset with its publication pending

submitter keyword: Human, Quantitative proteomics, clinical proteomics, FFPE, high field asymmetric waveform ion mobility spectrometry (FAIMS), LC-FAIMS-MS/MS

Bernhard Kuster
contact affiliation	1 Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany 2 German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany 3 Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising, Germany
contact email	kuster@tum.de
lab head
Stephan Eckert
contact affiliation	Technical University of Munich
contact email	stephan.eckert@tum.de
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/2021/11/PXD028136

PRIDE project URI

• PRIDE
  1. PXD028136
     1. Label: PRIDE project
     2. Name: Evaluation of disposable-trap column nanoLC-FAIMS-MS/MS for the proteomic analysis of FFPE tissue