PXD005345

PXD005345 is an original dataset announced via ProteomeXchange.

Title	Integrated Mass Spectrometry Imaging and Omics Workflows on the Same Tissue Section Using Parafilm-Assisted Microdissection
Description	In this work, we demonstrate the use of grid-aided, parafilm-assisted microdissection to perform MALDI MS imaging and shotgun proteomics and metabolomics in a combined workflow and using only a single tissue section. The grid is generated by microspotting of acid dye 25 using a piezoelectric microspotter. In the gas phase, the dye is detectable as a free radical species, and its distribution can be superimposed with ion images generated by tissue components, then used as a guide to locate regions of interest and aid during manual microdissection. Subjecting the dissected pieces to the modified Folch method allows to separate the metabolic components from the proteins. The proteins can then be subjected to overnight digestion under controlled conditions to improve protein identification yields. The proof of concept experiment on rat brain generated 162 and 140 metabolite assignments from three ROIs (cerebellum, hippocampus and midbrain/hypothalamus) in positive and negative mode, respectively, and 890, 1,303 and 1,059 unique protein accessions. Integrated metabolite and protein overrepresentation analysis identified pathways associated with the biological functions of each ROI, most of which were not identified when looking at the protein and metabolite lists individually. This combined MALDI MS imaging and multi-omics approach benefits from the advantages of both methods (molecular mapping from MSI and increased depth of coverage from shotgun proteomics and metabolomics), and further extends the amount of information that can be generated from single tissue sections.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:34:11.750.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jusal Quanico
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-11-14 06:18:48	ID requested
1	2017-03-20 09:08:00	announced
⏵ 2	2024-10-22 04:34:17	announced	2024-10-22: Updated project metadata.

Quanico J, Franck J, Wisztorski M, Salzet M, Fournier I, Integrated mass spectrometry imaging and omics workflows on the same tissue section using grid-aided, parafilm-assisted microdissection. Biochim Biophys Acta Gen Subj, 1861(7):1702-1714(2017) [pubmed]

10.1016/j.bbagen.2017.03.006;

curator keyword: Technical

submitter keyword: proteomics, lipidomics, MALDI MS imaging,parafilm-assisted microdissection

Michel Salzet
contact affiliation	Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM)-INSERM U1192, Université de Lille 1, France
contact email	michel.salzet@univ-lille1.fr
lab head
Jusal Quanico
contact affiliation	PRISM- University of Lille 1
contact email	jusal.quanico@univ-lille1.fr
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/2017/03/PXD005345

PRIDE project URI

• PRIDE
  1. PXD005345
     1. Label: PRIDE project
     2. Name: Integrated Mass Spectrometry Imaging and Omics Workflows on the Same Tissue Section Using Parafilm-Assisted Microdissection