PXD040720

PXD040720 is an original dataset announced via ProteomeXchange.

Title	Testing TMT-SPS-MS3 and label free approach in recalcitrant Mago (Mangifera indica L.) peel tissues
Description	Significant progress has been observed in recent years in proteomics tools. However, minimal application of the newest proteomic tools has been massively applied in plant recalcitrant tissues in non-model fruits. This constant occurrence constrains the progress in understanding essential molecular processes during postharvest shelf life (PSL) of fleshy fruits. In fact, comparative proteomic studies in fruit like mango, guava, papaya, and avocado are minimal. Therefore, we set up a label free quantitation (LFQ) and TMT-SPS-MS3 pipeline for comparative study of mango peels during PSL. Our protocol included different protein extraction and peptide fractionation before mass spectrometry analysis. In doing so we were able to confidently identify 4,400 proteins with high confidence, among which 1087 were differentially accumulated. The combination of phenolic protein extraction, high-pH reverse-phase peptide fractionation and LFQ exhibited the best approach for relative quantification, but other protein extraction, peptide fractionation and data acquisition showed significant complementation. LFQ and Byonic also allowed the determination of intact N-glyco peptides on proteins such as the desiccation-related protein, which molecular dynamics analysis support the occurrence of N-glycans providing stability of the protein. Our study represents the first massive proteomics comparison of mango peels during PSL.
HostingRepository	PRIDE
AnnounceDate	2024-01-29
AnnouncementXML	Submission_2024-01-29_10:12:15.837.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Miguel Elizalde
SpeciesList	scientific name: Mangifera indica (Mango); NCBI TaxID: 29780;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-09 05:55:09	ID requested
⏵ 1	2024-01-29 10:12:16	announced

10.1002/PMIC.202300239;

submitter keyword: protein extraction,proteomics, postharvest shelf life, mango peel

Dr. Eliel Ruiz May
contact affiliation	Instituto de Ecologia A.C.
contact email	eliel.ruiz@inecol.mx
lab head
Miguel Elizalde
contact affiliation	Instituto de Ecolog'ia A.C.
contact email	jose.elizalde@inecol.mx
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/2024/01/PXD040720

PRIDE project URI

• PRIDE
  1. PXD040720
     1. Label: PRIDE project
     2. Name: Testing TMT-SPS-MS3 and label free approach in recalcitrant Mago (Mangifera indica L.) peel tissues