PXD008493

PXD008493 is an original dataset announced via ProteomeXchange.

Title	Assessment of sample preparation bias in mass spectrometry-based proteomics
Description	For mass spectrometry-based proteomics, the selected sample preparation strategy is a key determinant for information that will be obtained. However, the corresponding selection is often not based on a fit-for-purpose evaluation. Here we report a comparison of in-gel (IGD), in-solution (ISD), on-filter (OFD), and on-pellet digestion (OPD) workflows on the basis of targeted (QconCAT-multiple reaction monitoring (MRM) method for mitochondrial proteins) and discovery proteomics (data dependent acquisition, DDA) analyses using three different human head and neck tissues (i.e. nasal polyps, parotid gland, and palatine tonsils). Our study reveals differences between the sample preparation methods, for example with respect to protein and peptide losses, quantification variability, protocol-induced methionine oxidation and asparagine/glutamine deamidation as well as identification of cysteine containing peptides. Moreover, none of the methods performed best for all types of tissues, which seemingly argues against the existence of a universal sample preparation method for proteome analysis.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:42:27.031.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD008493
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Horvatovich Péter
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-19 01:25:56	ID requested
1	2018-04-06 06:29:56	announced
⏵ 2	2024-10-22 04:42:34	announced	2024-10-22: Updated project metadata.

10.6019/PXD008493;

Klont F, Bras L, Wolters JC, Ongay S, Bischoff R, Halmos GB, Horvatovich P, Assessment of Sample Preparation Bias in Mass Spectrometry-Based Proteomics. Anal Chem, 90(8):5405-5413(2018) [pubmed]

10.1021/acs.analchem.8b00600;

ProteomeXchange project tag: Chromosome-centric Human Proteome Project (C-HPP), Human Proteome Project

curator keyword: Technical

submitter keyword: parotid gland, proteomics, palatine tonsils,nasal polyps, sample preparation

Peter Horvatovich
contact affiliation	University of Groningen Faculty of Mathematics and Natural Sciences Department of Pharmacy Analytical Biochemistry Building 3226, Room 6.9 Antonius Deusinglaan 1 9713 AV Groningen Internal Zip Code XB20 P.O. Box 196 9700 AD Groningen The Netherlands Telephone: +31-(0)50-363 3341 Fax: +31 (0)50 363 7582 Mobile: +31 (0)6 2459 7203 Email: p.l.horvatovich@rug.nl Homepage: www.biomac.nl
contact email	p.l.horvatovich@rug.nl
lab head
Horvatovich Péter
contact affiliation	Faculty of Science and Engineering, Groningen Research Institute of Pharmacy, Analytical Biochemistry, University of Groningen, 9713 AV Groningen, The Netherlands
contact email	p.l.horvatovich@rug.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008493
     1. Label: PRIDE project
     2. Name: Assessment of sample preparation bias in mass spectrometry-based proteomics