PXD048358

PXD048358 is an original dataset announced via ProteomeXchange.

Title	Refinement of paramagnetic bead–based digestion protocol for automatic sample preparation using an artificial neural network
Description	Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and high-throughput alternative for protein extraction and digestion. Here, a refined paramagnetic bead–based digestion protocol is described for Opentrons® OT-2 platform (OT-2) as a versatile, reproducible, and affordable alternative for the automatic sample preparation for MS analysis. For this purpose, an artificial neural network (ANN) was applied to maximize the number of peptides without missed cleavages identified in HeLa extract by combining factors such as the quantity (µg) of trypsin/Lys-C and beads (MagReSyn® Amine), % (w/v) SDS, % (v/v) acetonitrile (ACN), and time of digestion (h). ANN model predicted the optimal conditions for the digestion of 50 µg of HeLa extract, pointing to the use of 2.5% (w/v) SDS and 300 µg of beads for sample preparation and long-term digestion (16h) with 0.15 µg Lys-C and 2.5 µg trypsin (≈ 1:17 ratio). Based on the results of the ANN model, the manual protocol was automated in OT-2. The performance of the automatic protocol was evaluated with different sample types, including human plasma, rat bile, Arabidopsis thaliana leaves, Escherichia coli cells, and mouse tissue cortex, showing great reproducibility and low sample-to-sample variability in all cases. Notwithstanding, we must highlight the performance of this method in the preparation of a challenging biological fluid as bile, a proximal fluid that is rich in bile salts, bilirubin, cholesterol, and fatty acids, among other MS interferents. Compared to other protocols described in the literature for the extraction of digestion of bile proteins, our method allowed to identify exclusively 9.91% (x proteins), thus contributing to improving the coverage of the bile proteome.
HostingRepository	PRIDE
AnnounceDate	2024-05-31
AnnouncementXML	Submission_2024-05-31_09:40:48.245.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD048358
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sergio Ciordia
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-09 10:26:39	ID requested
⏵ 1	2024-05-31 09:40:49	announced

Ciordia S, Santos FM, Dias JML, Lamas JR, Paradela A, Alvarez-Sola G, Á, vila MA, Corrales F, Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network. Talanta, 274():125988(2024) [pubmed]

10.6019/PXD048358;

10.1016/j.talanta.2024.125988;

submitter keyword: Bile,magnetic beads, protein aggregation, SP3 protein digestion, artificial neural network

Fernando Corrales Izquierdo
contact affiliation	Functional Proteomics Lab, National Center for Biotechnology (CNB-CSIC)
contact email	fcorrales@cnb.csic.es
lab head
Sergio Ciordia
contact affiliation	Spanish National Center for Biotechnology
contact email	sciordia@cnb.csic.es
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/2024/05/PXD048358

PRIDE project URI

• PRIDE
  1. PXD048358
     1. Label: PRIDE project
     2. Name: Refinement of paramagnetic bead–based digestion protocol for automatic sample preparation using an artificial neural network