Summary of Study ST003801

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002375. The data can be accessed directly via it's Project DOI: 10.21228/M8N83P This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST003801
Study Title	Salivary Metabolome Profiling in Oral Cancer Patients: A Comparative Study.
Study Summary	Objectives: The present study is conducted to investigate the biochemical and pathophysiological changes in saliva of non-smokers controls and oral cancer patients. Materials and methods: Saliva samples collected from a total of 16 oral cancer participants, and 26 non-smoking control individuals were subjected to untargeted metabolomics analysis. Metabolites from the saliva samples of all the participants were analyzed and processed via MetaboScape software version 4 (Bruker, Darmstadt, Germany). Results: We identified 59 differentially abundant salivary metabolites in the comparisons between controls and oral cancer samples. Among the 59 metabolites, 33 were significantly different in oral cancer participants. The top five most abundant metabolites in oral cancer were N-Acetyl-L-alanine, L-Carnitine, Trimethylamine, Acetaminophen, and Oxypurinol.. Conclusions: Salivary metabolomic profiling revealed distinct metabolic alterations in oral cancer patients compared to controls, highlighting potential biomarkers for disease detection and monitoring. Clinical Relevance: Our findings underscore the profound impact of oral cancer on oral biochemistry, potentially predisposing individuals to oncogenic transformations.
Institute	Sharjah Institute for Medical Research
Last Name	Facility
First Name	Core
Address	M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah, Sharjah, UAE, Sharjah, 000, United Arab Emirates
Email	tims-tof@sharjah.ac.ae
Phone	+971 6 5057656
Submit Date	2025-03-11
Raw Data Available	Yes
Raw Data File Type(s)	mzML, d
Analysis Type Detail	LC-MS
Release Date	2025-09-11
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002375
Project DOI:	doi: 10.21228/M8N83P
Project Title:	Salivary Metabolome Profiling in Oral Cancer Patients: A Comparative Study.
Project Summary:	Objectives: The present study is conducted to investigate the biochemical and pathophysiological changes in saliva of non-smokers controls and oral cancer patients. Materials and methods: Saliva samples collected from a total of 16 oral cancer participants, and 26 non-smoking control individuals were subjected to untargeted metabolomics analysis. Metabolites from the saliva samples of all the participants were analyzed and processed via MetaboScape software version 4 (Bruker, Darmstadt, Germany). Results: We identified 59 differentially abundant salivary metabolites in the comparisons between controls and oral cancer samples. Among the 59 metabolites, 33 were significantly different in oral cancer participants. The top five most abundant metabolites in oral cancer were N-Acetyl-L-alanine, L-Carnitine, Trimethylamine, Acetaminophen, and Oxypurinol.. Conclusions: Salivary metabolomic profiling revealed distinct metabolic alterations in oral cancer patients compared to controls, highlighting potential biomarkers for disease detection and monitoring. Clinical Relevance: Our findings underscore the profound impact of oral cancer on oral biochemistry, potentially predisposing individuals to oncogenic transformations.
Institute:	Sharjah Institute for Medical Research
Last Name:	Facility
First Name:	Core
Address:	M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah, Sharjah, UAE, Sharjah, 000, United Arab Emirates
Email:	tims-tof@sharjah.ac.ae
Phone:	+971 6 5057656

Subject:

Subject ID:	SU003935
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA416388	Saliva Control 22-02_40_1_3285	non-smoking control
SA416389	Saliva Control 26-02_44_1_3293	non-smoking control
SA416390	Saliva Control 26-01_44_1_3292	non-smoking control
SA416391	Saliva Control 25-02_43_1_3291	non-smoking control
SA416392	Saliva Control 25-01_43_1_3290	non-smoking control
SA416393	Saliva Control 24-02_42_1_3289	non-smoking control
SA416394	Saliva Control 24-01_42_1_3288	non-smoking control
SA416395	Saliva Control 23-02_41_1_3287	non-smoking control
SA416396	Saliva Control 23-01_41_1_3286	non-smoking control
SA416397	Saliva Control 01-01_19_1_3242	non-smoking control
SA416398	Saliva Control 01-02_19_1_3243	non-smoking control
SA416399	Saliva Control 06-02_24_1_3253	non-smoking control
SA416400	Saliva Control 10-01_28_1_3260	non-smoking control
SA416401	Saliva Control 09-02_27_1_3259	non-smoking control
SA416402	Saliva Control 09-01_27_1_3258	non-smoking control
SA416403	Saliva Control 08-02_26_1_3257	non-smoking control
SA416404	Saliva Control 08-01_26_1_3256	non-smoking control
SA416405	Saliva Control 07-02_25_1_3255	non-smoking control
SA416406	Saliva Control 07-01_25_1_3254	non-smoking control
SA416407	Saliva Control 06-01_24_1_3252	non-smoking control
SA416408	Saliva Control 11-01_29_1_3262	non-smoking control
SA416409	Saliva Control 05-02_23_1_3251	non-smoking control
SA416410	Saliva Control 05-01_23_1_3250	non-smoking control
SA416411	Saliva Control 04-02_22_1_3249	non-smoking control
SA416412	Saliva Control 04-01_22_1_3248	non-smoking control
SA416413	Saliva Control 03-02_21_1_3247	non-smoking control
SA416414	Saliva Control 03-01_21_1_3246	non-smoking control
SA416415	Saliva Control 02-02_20_1_3245	non-smoking control
SA416416	Saliva Control 02-01_20_1_3244	non-smoking control
SA416417	Saliva Control 10-02_28_1_3261	non-smoking control
SA416418	Saliva Control 11-02_29_1_3263	non-smoking control
SA416419	Saliva Control 21-02_39_1_3283	non-smoking control
SA416420	Saliva Control 17-01_35_1_3274	non-smoking control
SA416421	Saliva Control 21-01_39_1_3282	non-smoking control
SA416422	Saliva Control 20-02_38_1_3281	non-smoking control
SA416423	Saliva Control 20-01_38_1_3280	non-smoking control
SA416424	Saliva Control 19-02_37_1_3279	non-smoking control
SA416425	Saliva Control 19-01_37_1_3278	non-smoking control
SA416426	Saliva Control 18-02_36_1_3277	non-smoking control
SA416427	Saliva Control 18-01_36_1_3276	non-smoking control
SA416428	Saliva Control 17-02_35_1_3275	non-smoking control
SA416429	Saliva Control 16-02_34_1_3273	non-smoking control
SA416430	Saliva Control 12-01_30_1_3264	non-smoking control
SA416431	Saliva Control 16-01_34_1_3272	non-smoking control
SA416432	Saliva Control 15-02_33_1_3271	non-smoking control
SA416433	Saliva Control 15-01_33_1_3270	non-smoking control
SA416434	Saliva Control 14-02_32_1_3269	non-smoking control
SA416435	Saliva Control 14-01_32_1_3268	non-smoking control
SA416436	Saliva Control 13-02_31_1_3267	non-smoking control
SA416437	Saliva Control 13-01_31_1_3266	non-smoking control
SA416438	Saliva Control 12-02_30_1_3265	non-smoking control
SA416439	Saliva Control 22-01_40_1_3284	non-smoking control
SA416356	P08-02-4764	Oral cancer
SA416357	P01-01-4749	Oral cancer
SA416358	P01-02-4750	Oral cancer
SA416359	P02-01-4751	Oral cancer
SA416360	P02-02-4752	Oral cancer
SA416361	P03-01-4753	Oral cancer
SA416362	P03-02-4754	Oral cancer
SA416363	P04-01-4755	Oral cancer
SA416364	P04-02-4756	Oral cancer
SA416365	P05-01-4757	Oral cancer
SA416366	P05-02-4758	Oral cancer
SA416367	P06-01-4759	Oral cancer
SA416368	P06-02-4760	Oral cancer
SA416369	P07-02-4762	Oral cancer
SA416370	P08-01-4763	Oral cancer
SA416371	P07-01-4761	Oral cancer
SA416372	P09-01-4765	Oral cancer
SA416373	P13-02-4774	Oral cancer
SA416374	P16-02-4780	Oral cancer
SA416375	P16-01-4779	Oral cancer
SA416376	P15-02-4778	Oral cancer
SA416377	P15-01-4777	Oral cancer
SA416378	P09-02-4766	Oral cancer
SA416379	P14-01-4775	Oral cancer
SA416380	P14-02-4776	Oral cancer
SA416381	P13-01-4773	Oral cancer
SA416382	P12-02-4772	Oral cancer
SA416383	P12-01-4771	Oral cancer
SA416384	P11-02-4770	Oral cancer
SA416385	P11-01-4769	Oral cancer
SA416386	P10-02-4768	Oral cancer
SA416387	P10-01-4767	Oral cancer

Showing results 1 to 84 of 84

Showing results 1 to 84 of 84

Collection:

Collection ID:	CO003928
Collection Summary:	Saliva collection and storage To investigate the development of oral cancer, we recruited 42 participants and divided them into two groups: 26 control participants (mean age: 34.08 ± 2.8 years), and 16 oral cancer patients (mean age: 51 ± 6.5 years). The study protocol was approved by the Research Ethics Committee (REC-22–06–18) in accordance with ethical principles, including the Helsinki Declaration. All methods and procedures adhered to relevant guidelines and regulations, ensuring informed consent and the maintenance of privacy and confidentiality. Inclusion criteria for this study included oral cancer patients and non-smokers aged 20 years or older who served as the control group. The patients enrolled in the study was histologically confirmed for primary oral squamous cell carcinoma. Exclusion criteria included pregnancy and active oral inflammation. Participants were instructed to refrain from eating, smoking, and drinking for two hours and to thoroughly rinse their mouths to prevent sample contamination before initiating sample collection. Samples were transported in ice containers to the laboratory, where they were centrifuged for 5 minutes at 5000 rpm at 4°C to remove cell debris. The supernatants were then frozen at -80°C until further analysis.
Sample Type:	Saliva

Treatment:

Treatment ID:	TR003944
Treatment Summary:	No treatment were given. Saliva samples collected from a total of 16 oral cancer participants, and 26 non-smoking control individuals were subjected to untargeted metabolomics analysis

Sample Preparation:

Sampleprep ID:	SP003941
Sampleprep Summary:	Metabolites extraction and sample preparation Samples were thawed at room temperature, and 100 µL from each sample is mixed with 300 µL methanol (≥99.9%, LC–MS CHROMASOLV) for protein precipitation. After vortexing and incubating at −20 °C for 2 hours, the samples were vortexed again, centrifuged at 14,000 rpm for 15 minutes, and the supernatants transferred to glass vials. These supernatants were then evaporated in a SpeedVac EZ-2 Plus (GeneVac, Ipswich, UK) at a controlled temperature of 35–40 °C to prevent heat-sensitive metabolite degradation. The dried extracts were resuspended in 200 µL of deionized water containing 0.1% formic acid (LC-MS CHROMASOLV, Honeywell, Seelze, Germany), vortexed for 2 minutes for thorough mixing, and filtered using a 0.45 µm hydrophilic nylon syringe filter to remove particulates before LC-MS/MS analysis. To assess reproducibility, equal volumes (10 µL) of all samples were pooled to create a quality control (QC) sample, which is placed in the autosampler at 4 °C for analysis.

Sampleprep ID:

SP003941

Sampleprep Summary:

Metabolites extraction and sample preparation Samples were thawed at room temperature, and 100 µL from each sample is mixed with 300 µL methanol (≥99.9%, LC–MS CHROMASOLV) for protein precipitation. After vortexing and incubating at −20 °C for 2 hours, the samples were vortexed again, centrifuged at 14,000 rpm for 15 minutes, and the supernatants transferred to glass vials. These supernatants were then evaporated in a SpeedVac EZ-2 Plus (GeneVac, Ipswich, UK) at a controlled temperature of 35–40 °C to prevent heat-sensitive metabolite degradation. The dried extracts were resuspended in 200 µL of deionized water containing 0.1% formic acid (LC-MS CHROMASOLV, Honeywell, Seelze, Germany), vortexed for 2 minutes for thorough mixing, and filtered using a 0.45 µm hydrophilic nylon syringe filter to remove particulates before LC-MS/MS analysis. To assess reproducibility, equal volumes (10 µL) of all samples were pooled to create a quality control (QC) sample, which is placed in the autosampler at 4 °C for analysis.

Chromatography:

Chromatography ID:	CH004740
Chromatography Summary:	The LC-MS/MS analysis was performed using an ultra-high-performance liquid chromatography (UHPLC) system (Bruker Daltonik GmbH, Bremen, Germany) coupled with a quadrupole time-of-flight (QTOF) mass spectrometer. The system featured an electrospray ionization (ESI) source, a solvent delivery system pump (Elute UHPLC HPG 1300), an autosampler, and a thermostat-controlled column compartment. The operating system was Windows 10 Enterprise 2016 LTSB, and the software utilized included Bruker Compass HyStar 5.0 SR1 Patch1 (5.0.37.1) and Compass 4.1, Version 6.2. Two mobile phases were employed: Phase A, comprising water with 0.1% formic acid, and Phase B, comprising acetonitrile with 0.1% formic acid. The gradient program initiated with a flow rate of 0.25 ml/min with 99% A and 1% B from 0 to 2 minutes, transitioning to 1% A and 99% B from 2 to 17 minutes. This was maintained from 17 to 20 minutes, followed by a return to 99% A and 1% B from 20 to 20.1 minutes. The flow rate was adjusted to 0.35 mL/min from 20.1 to 28.5 minutes, and subsequently reverted to 0.25 mL/min at 28.5 to 30 minutes. 10µL from each sample was injected and metabolites were separated on a Hamilton® Intensity Solo 2 C18 column (100 mm × 2.1 mm × 1.8 µm), with the oven temperature maintained at 35 °C.
Instrument Name:	Bruker Elute
Column Name:	Hamilton Intensity Solo 2 C18 (100 x 2.1mm, 1.8um)
Column Temperature:	35 °C
Flow Gradient:	The gradient program initiated with a flow rate of 0.25 ml/min with 99% A and 1% B from 0 to 2 minutes, transitioning to 1% A and 99% B from 2 to 17 minutes. This was maintained from 17 to 20 minutes, followed by a return to 99% A and 1% B from 20 to 20.1 minutes. The flow rate was adjusted to 0.35 mL/min from 20.1 to 28.5 minutes, and subsequently reverted to 0.25 mL/min at 28.5 to 30 minutes.
Flow Rate:	0.25mL/min - 0.35 mL/min
Solvent A:	100% Water; 0.1% Formic Acid
Solvent B:	100% acetonitrile; 0.1% Formic Acid
Chromatography Type:	Reversed phase

Analysis:

Analysis ID:	AN006249
Analysis Type:	MS
Chromatography ID:	CH004740
Num Factors:	2
Num Metabolites:	176
Units:	AU