PXD051148-1

PXD051148 is an original dataset announced via ProteomeXchange.

Title	Repurposed 3D Printer Allows Economical and Programmable Fraction Collection for Proteomics of Nanogram Scale Samples
Description	In this work we describe the construction and application of a repurposed 3D-printer as a fraction collector. We utilise a nanoLC to ensure minimal volumes and surfaces although any LC can be coupled. The setup operates as a high-pH fractionation system capable of effectively working with nanogram scales of lysate digests. The 2D RP-RP system demonstrated superior proteome coverage over single-shot data-dependent acquisition (DDA) analysis using only 5 ng of human cell lysate digest with performance increasing with increasing amounts of material. We found that the fractionation system allowed over 60% signal recovery at the peptide level and, more importantly, we observed improved protein level intensity coverage which indicates the complexity reduction afforded by the system outweighs the sample losses endured. The application of data-independent acquisition (DIA) and wide window acquisition (WWA) to fractionated samples allowed nearly 8,000 proteins to be identified from 50 ng of material. The utility of the 2D system was further investigated for phosphoproteomics (>21,000 phosphosites from 50 µg starting material) and pull-down type experiments and showed substantial improvements over single-shot experiments. We show that the 2D RP-RP system is highly versatile and powerful tool for many proteomics workflows.
HostingRepository	PRIDE
AnnounceDate	2024-07-12
AnnouncementXML	Submission_2024-07-12_07:44:25.035.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eduardo Shigueo Kitano
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2024-04-02 04:35:36	ID requested
⏵ 1	2024-07-12 07:44:25	announced

Kitano ES, Nisbet G, Demyanenko Y, Kowalczyk KM, Iselin L, Cross S, Castello A, Mohammed S, Repurposed 3D Printer Allows Economical and Programmable Fraction Collection for Proteomics of Nanogram Scale Samples. Anal Chem, 96(28):11439-11447(2024) [pubmed]

10.1021/acs.analchem.4c01731;

submitter keyword: DDA DIA WWA LC-MS/MS, phosphoproteome,Proteomics, Two-dimensional peptide separation, RNA-binding protein

Shabaz Mohammed
contact affiliation	Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, United Kingdom; Department of Chemistry, University of Oxford, OX1 3TA, Oxford, 16 United Kingdom; Rosalind Franklin Institute, Harwell Campus, OX11 0QX Didcot, United Kingdom
contact email	shabaz.mohammed@chem.ox.ac.uk
lab head
Eduardo Shigueo Kitano
contact affiliation	The Rosalind Franklin Institute and Department of Pharmacology, University of Oxford
contact email	eduardo.kitano@pharm.ox.ac.uk
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/2024/07/PXD051148

PRIDE project URI

• PRIDE
  1. PXD051148
     1. Label: PRIDE project
     2. Name: Repurposed 3D Printer Allows Economical and Programmable Fraction Collection for Proteomics of Nanogram Scale Samples