PXD032137 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Identification of plasma proteins associated with oesophageal cancer chemotherapeutic treatment outcomes using SWATH-MS |
Description | Oesophageal adenocarcinoma (OAC) is an aggressive cancer with a five-year survival of <15%, and the incidence is predicted to double within the next 20 years. Current neo-adjuvant chemotherapy treatment strategies only benefit a minority (20-30%) of patients and there are currently no methods available to differentiate between responders and non-responders. Here we performed quantitative proteomics using Sequential Window Acquisition of all THeoretical fragment-ion spectra-Mass Spectrometry (SWATH-MS) on albumin/IgG-depleted and non-depleted plasma samples from 23 patients with locally advanced OAC or oesophageal gastric junction cancers prior to treatment. Individuals were grouped based on tumour regression (TRG) score (TRG1-3 vs TRG4 and 5) after chemotherapy and differentially abundant proteins were compared using univariate and multivariate analyses. Protein depletion led to the identification of around twice as many proteins in the samples compared to non-depletion. SWATH-MS revealed significant quantitative differences in the abundance of several proteins (p<0.05) between the two groups. These included all three c1q subunit proteins, C1QA, C1QB and C1QC, which were of higher abundance in the low TRG group (higher degree of regression in response to treatment). Of those that were found to be of higher abundance in the high TRG group, GSTP1 was found to exhibit the lowest p-value (univariate analysis) and highest accuracy and Cohen’s kappa value (multivariate analysis). The concentrations of c1q complex and GSTP1 were further examined and validated using ELISA-based assays. This study provides quantitative information relating to differences in the plasma proteome that underpin response to chemotherapeutic treatment in oesophageal cancers. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:55:50.485.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Sally Shirran |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | iodoacetamide derivatized residue |
Instrument | TripleTOF 5600 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-03-09 00:39:19 | ID requested | |
1 | 2022-08-22 04:10:25 | announced | |
⏵ 2 | 2023-11-14 08:55:51 | announced | 2023-11-14: Updated project metadata. |
Publication List
Guo N, Minas G, Synowsky SA, Dunne MR, Ahmed H, McShane R, Bhardwaj A, Donlon NE, Lorton C, O'Sullivan J, Reynolds JV, Caie PD, Shirran SL, Lynch AG, Stewart AJ, Arya S, Identification of plasma proteins associated with oesophageal cancer chemotherapeutic treatment outcomes using SWATH-MS. J Proteomics, 266():104684(2022) [pubmed] |
Keyword List
submitter keyword: MAGIC regimen, oesophageal cancer, data-independent acquisition, quantitative proteomics,chemotherapy |
Contact List
Swati Arya |
contact affiliation | School of Medicine, University of St Andrews, St Andrews, KY16 9TF, United Kingdom. |
contact email | sa212@st-andrews.ac.uk |
lab head | |
Sally Shirran |
contact affiliation | University of St Andrews |
contact email | ss101@st-andrews.ac.uk |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD032137
- Label: PRIDE project
- Name: Identification of plasma proteins associated with oesophageal cancer chemotherapeutic treatment outcomes using SWATH-MS