PXD040451

PXD040451 is an original dataset announced via ProteomeXchange.

Title	Data independent acquisition mass spectrometry (DIA-MS) analysis of FFPE rectal cancer samples offers in depth proteomics characterization of response to neoadjuvant chemoradiotherapy
Description	A total of 97 LARC patients treated at the Institute for Oncology and Radiology of Serbia in the period of 2018-2019 were included in the study. Patients were treated with long-course chemoradiotherapy (CRT): Radiotherapy (RT) was delivered with a total dose of 50.4 Gy in 28 fractions; concomitant chemotherapy (5-FU, 350 mg/m2 daily) and Leucovorin (25 mg/m2 daily) was administered during the first and the fifth week of RT. Patients were evaluated in week 6-8 after treatment completion with pelvic MRI scan and rigid proctoscopy. Pathohistological response after surgery was assessed according to tumor regression grading (TRG) categories by Mandard. Twenty biopsy samples taken at diagnosis were used for proteomic analysis, 9 responders (R, TRG 1-2), and 11 non-responders (NR, TRG 3-5), in order to achieve the maximum range of different molecular features potentially associated with response.
HostingRepository	PRIDE
AnnounceDate	2023-11-21
AnnouncementXML	Submission_2023-11-21_08:40:08.025.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Martina Samiotaki
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-27 06:09:37	ID requested
⏵ 1	2023-11-21 08:40:08	announced

10.3390/ijms242015412;

Stanojevic A, Samiotaki M, Lygirou V, Marinkovic M, Nikolic V, Stojanovic-Rundic S, Jankovic R, Vlahou A, Panayotou G, Fijneman RJA, Castellv, í, -Bel S, Zoidakis J, Cavic M, Data-Independent Acquisition Mass Spectrometry Analysis of FFPE Rectal Cancer Samples Offers In-Depth Proteomics Characterization of the Response to Neoadjuvant Chemoradiotherapy. Int J Mol Sci, 24(20):(2023) [pubmed]

submitter keyword: proteomics,data independent acquisition mass spectrometry, neoadjuvant chemoradiotherapy, rectal cancer

Dr Milena Cavic
contact affiliation	Institute for Oncology and Radiology of Serbia Department of Experimental Oncology Pasterova 14, 11000 Belgrade, Serbia
contact email	milena.cavic@ncrc.ac.rs
lab head
Martina Samiotaki
contact affiliation	Protein Analysis Laboratory B.S.R.C. "Alexander Fleming", Alexander Fleming Street 34 16672, Vari, Greece
contact email	samiotaki@fleming.gr
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/2023/11/PXD040451

PRIDE project URI

• PRIDE
  1. PXD040451
     1. Label: PRIDE project
     2. Name: Data independent acquisition mass spectrometry (DIA-MS) analysis of FFPE rectal cancer samples offers in depth proteomics characterization of response to neoadjuvant chemoradiotherapy