PXD024893

PXD024893 is an original dataset announced via ProteomeXchange.

Title	Online-2D nanoLC-MS for crude serum proteome profiling: assessing sample preparation impact on proteome composition
Description	Although current LC-MS technology permits scientists to efficiently screen clinical samples in translational research, e.g. steroids, biogenic amines and even plasma or serum proteomes, in a daily routine, maintaining the balance between throughput and analytical depth is still a limiting factor. A typical approach to enhance the proteome depth is employing offline 2-dimensional (2D) fractionation techniques before nanoLC-MS/MS analysis. These additional sample preparation steps usually require extensive sample manipulation, which could result in sample alteration and sample loss. The consequent results variability increase the risk of false discovery, regardless of time-intensive sample preparation workload. Here we present and compare 1D-nanoLC-MS with an automated online-2D high-pH RP x low pH RP separation method for deep proteome profiling using a nanoLC system coupled to a high-resolution accurate-mass mass spectrometer. The proof-of-principle study permitted the identification of ca. 500 proteins with ~10,000 peptides in 15 enzymatically digested crude serum samples collected from healthy donors in 3 laboratories across Europe. The developed method identified 60% more peptides in comparison with conventional 1D nanoLC-MS/SM analysis with ca. 4 times lower throughput while retaining the quantitative information. Serum sample preparation artifacts were revealed by applying unsupervised classification techniques, and, therefore, must be taken into account while planning multicentric biomarker discovery and validation studies. Overall, this novel method reduces sample complexity and boosts the number of peptide and protein identifications without the need for extra sample handling procedures for samples equivalent to less than 1 µL of blood, which expands the space for potential biomarker discovery by looking deeper into the composition of biofluids.
HostingRepository	PRIDE
AnnounceDate	2021-07-12
AnnouncementXML	Submission_2021-07-11_21:43:56.653.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Runsheng Zheng
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-22 00:19:22	ID requested
1	2021-07-09 05:32:19	announced
⏵ 2	2021-07-11 21:43:57	announced	2021-07-12: Updated project metadata.

10.1021/ACS.ANALCHEM.1C01291;

Zheng R, Govorukhina N, Arrey TN, Pynn C, van der Zee A, Marko-Varga G, Bischoff R, Boychenko A, Online-2D NanoLC-MS for Crude Serum Proteome Profiling: Assessing Sample Preparation Impact on Proteome Composition. Anal Chem, 93(28):9663-9668(2021) [pubmed]

submitter keyword: Peptide Fractionation, Blood, nanoLC-MS, 1D nanoLC-MS,Proteome Profiling, Crude Serum, High-Resolution Accurate Mass-Spectrometry, Online-2D nanoLC-MS

Alexander Boychenko
contact affiliation	Thermo Fisher Scientific
contact email	oleksandr.boychenko@thermofisher.com
lab head
Runsheng Zheng
contact affiliation	Thermo Fisher Scientific
contact email	runsheng.zheng@thermofisher.com
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/2021/07/PXD024893

PRIDE project URI

• PRIDE
  1. PXD024893
     1. Label: PRIDE project
     2. Name: Online-2D nanoLC-MS for crude serum proteome profiling: assessing sample preparation impact on proteome composition