PXD014524

PXD014524 is an original dataset announced via ProteomeXchange.

Title	A simple peptide quantification approach for MS-based proteomics quality control
Description	Despite its growing popularity and use, bottom-up proteomics remains a complex analytical methodology. Its general workflow consists of three main steps: sample preparation, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and computational data analysis. Quality assessment of the different steps and components of this workflow is instrumental to identify technical flaws and to avoid loss of precious measurement time and sample material. However, assessment of the extent of sample losses along the sample preparation protocol, in particular after proteolytic digestion, is not yet routinely implemented because of the lack of an accurate and straightforward method to quantify peptides. Here, we report on the use of a microfluidic UV/visible spectrophotometer to quantify MS-ready peptides directly in MS loading solvent, consuming only 2 µl of sample. We compared the performance of the microfluidic spectrophotometer with a standard device and determined the optimal sample amount for LC-MS/MS analysis on a Q Exactive HF mass spectrometer using a dilution series of a commercial K562 cell digest. Careful evaluation of selected LC and MS parameters allowed us to define 3 µg as an optimal peptide amount to be injected on this particular LC-MS/MS system. Finally, using tryptic digests from human HEK293T cells and showed that injecting equal peptide amounts, rather than approximate ones, results in less variable LC-MS/MS and protein quantification data. The obtained quality improvement together with easy implementation of the approach makes it possible to routinely quantify MS-ready peptides as a next step in daily proteomics quality control.
HostingRepository	PRIDE
AnnounceDate	2020-11-06
AnnouncementXML	Submission_2021-01-06_06:58:41.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD014524
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Teresa Mendes Maia
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Acetyl
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-09 01:12:27	ID requested
1	2020-03-13 00:52:38	announced
2	2020-11-06 08:37:15	announced	2020-11-06: Updated project metadata.
⏵ 3	2021-01-06 06:58:41	announced	2020-11-06: Updated project metadata. 2021-01-06: Updated publication reference for PubMed record(s): 32258910.

Maia TM, Staes A, Plasman K, Pauwels J, Boucher K, Argentini A, Martens L, Montoye T, Gevaert K, Impens F, Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control. ACS Omega, 5(12):6754-6762(2020) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: peptide quantitation, bottom-up proteomics, quality control, method optimization

Francis Impens
contact affiliation	VIB Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium. VIB Proteomics Core, VIB, 9000 Ghent, Belgium. Department for Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.
contact email	francis.impens@vib-ugent.be
lab head
Teresa Mendes Maia
contact affiliation	VIB Proteomics Core
contact email	teresa.maia@vib-ugent.be
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/2020/07/PXD014524

PRIDE project URI

• PRIDE
  1. PXD014524
     1. Label: PRIDE project
     2. Name: A simple peptide quantification approach for MS-based proteomics quality control