Dataset Information

Label-free LC-MS proteomics of oral squamous cell carcinoma patients and healthy controls: proteomics

ABSTRACT: This study compared serum proteomic expressions of 41 oral squamous cell carcinoma patients and 44 healthy controls. The data was acquired with UDMSE in resolution mode and targeted fragmentation with DIA. This project consist of two parallel projects: proteomic and N-glycopeptidomic projects. This is the proteomic project. Due to in-parallel N-glycoproteomic analysis the abundant serum proteins were included in the proteomics.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Serum

DISEASE(S): Oral Squamous Cell Carcinoma

SUBMITTER: Sakari Joenväärä

LAB HEAD: Prof. Risto Renkonen

PROVIDER: PXD055139 | Pride | 2026-02-09

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20200902_OSCC_SEC_P_07.raw.zip	Raw
	20200902_OSCC_SEC_P_08.raw.zip	Raw
	20200902_OSCC_SEC_P_09.raw.zip	Raw
	20200902_OSCC_SEC_P_10.raw.zip	Raw
	20200902_OSCC_SEC_P_100.raw.zip	Raw

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Publications

Disease-specific N-glycopeptides in serum of patients with oral squamous cell carcinoma.

Tohmola Tiialotta T Joenväärä Sakari S Dickinson Amy A Mäkitie Antti A Silén Suvi S

Scientific reports 20250902 1

The incidence of oropharyngeal cancers is increasing due to human papilloma virus (HPV); however, this phenomenon does not explain the rising incidence of oral cancers, for which the reason remains unknown. These cancers are typically diagnosed at an advanced stage, which adversely affects the prognosis. Improved methods for early detection, such as blood-based biomarkers, could significantly improve patient outcomes. We investigated quantitative and qualitative differences in serum protein N-gl ...[more]

PMID: 40890283

Similar Datasets

Project description:This is the proteomics part of the above project. Purpose: No blood-based biomarkers to detect OPSCC early before symptoms develop or before clinically visible. Diagnosis is solely based on histology of a visible tumour. Most OPSCC patients are diagnosed at an advanced stage, which leads to significant morbidity and poor survival. If high-risk patients were identified with blood-based biomarkers before clear clinical manifestations, tumours could be detected and treated at an earlier stage. Causes of OPSCC include smoking, alcohol misuse, and human papillomavirus (HPV). Tumours are separated according to WHO recommendations into HPV+ OPSCC and HPV- OPSCC using the proxy histological marker p16. We additionally separated our patients into these groups to determine whether the serum glycopeptides would differ between HPV+ and HPV- tumours, as these are distinct clinical entities. Patients and Methods: Pre-treatment sera from 74 patients with OPSCC (including 26 p16- tumours and 48 p16+ tumours) and 12 controls were used, collected between the years 2012 and 2015 at the Department of Otorhinolaryngology – Head and Neck Surgery, Helsinki University Hospital, Helsinki, Finland. Samples were grouped as follows: early stage p16+ OPSCC (stage I only), early stage p16- OPSCC (stage I-II), p16+ (any stage), p16- (any stage), controls. In-parallel quantitative bulk serum proteomics and serum glycopeptidomics were performed. Results: We identified 78 bulk proteins in the serum, of which 33 significantly differed between early-stage p16- OPSCC and controls, 22 between early-stage p16+ OPSCC and controls, 1 between early-stage p16+ and early-stage p16- OPSCCs, and 30 between all p16+ and p16- OPSCCs. We identified glycopeptides from proteins including but not limited to alpha-1-antitrypsin, haptoglobin, and Immunoglobulin heavy constant alpha 1, and compared these with the protein expression levels in each comparison. Conclusions: We have identified novel serum glycopeptide biomarkers detect early-stage OPSCCs, to be evaluated further as a diagnostic panel to detect preclinical OPSCC in at-risk patients.