DOI: 10.5281/zenodo.7941230
title: A Gas Chromatography – Ion Mobility Spectrometry dataset for colorectal cancer diagnostic of 56 urine samples corresponding to 29 subjects.

description: <strong>Contents of the dataset</strong> The dataset includes the set of urine samples in .mea format, which can be<br> read using the GCIMS R package. It also contains analytical standards in the same format, used for quality<br> control of the equipment and as a retention time alignment reference. If you want to preview the data, you do not need to download the full Urines.zip<br> and AnalyticalStandards.zip files, but rather use the smaller UrinesDemo.zip and<br> AnalyticalStandardsDemo.zip, with a subset of just three samples of the whole<br> dataset. Besides the actual measurements, you will find the annotations.csv and<br> reference_peaks.csv files, with sample annotations and some reference peaks<br> identified in the samples. See further details below. <br> <strong>Sample collection</strong> Urine samples from 29 subjects were collected at Hospital de Reus. 15 subjects<br> were diagnosed with colorectal cancer, 14 subjects were controls. The study<br> protocol was approved by the Ethics Committee of Hospital de Reus (study<br> approval no. 074/2018). Samples were aliquoted and frozen at -80ºC for storage. <strong>Sample preparation</strong><br> Sample preparation improves urine preservation by blocking bacterial growth in<br> the urine, and favours volatile extraction. It also adds an internal standard<br> for verification of instrument variability. <em>Stock solution preparation</em> Dissolve 11.69 g of NaCl in about 35 mL deionized water and add 6.5 mg sodium<br> azide (NaN3). Once dissolved, add 5.50 mL 5M HCl and mark up to volume with<br> deionized water until the final volume is 50mL. The HCl 5M is used to obtain<br> an acid pH. The pH is controlled with a pH test paper. The final pH level must<br> be 2 or below. The NaCl favors the volatile extraction, and the NaN3 omits<br> the bacterial growth in the urine. <em>Internal standard solution preparation</em><br> The 4-flurobenzaldehyde is located in retention time around 200 seconds and<br> can be used as an internal standard. Prepare a methanol stock solution using 100 ml of methanol grade for<br> preparative chromatography and 200 ml of distilled water. Mix 5 mL of 4-fluorobenzaldehyde with 100 mL of the methanol stock solution. Dilute the previous mixture in 400 mL of mili-Q water. <br> <em>Sample preparation</em><br> Aliquotes were thawed before analysis. Once thawed, 300uL of the stock solution<br> were added to the urine sample, and 1.5 ml of the acidified urine sample were<br> transferred into a 20ml vial, ensuring only the supernatant of the sample<br> is transferred. Finally, 20 mL of the internal standard solution is added to the sample. <strong>GC-IMS Analysis</strong> Samples were analyzed with a GC-IMS FlavourSpec® instrument from<br> G.A.S. Dortmund (Dortmund, Germany). Samples were incubated for 15 minutes<br> at 60ºC, the flow rate of the drift gas was set at 200 ml/min, and the carrier<br> gas was set 11 ml/min. Both the drift and carrier gas were Nitrogen 5.0. The GC<br> and IMS temperature were set at 60ºC and the measurement time lasted 33 minutes. Besides the urines, a set of measurements of a ketone mixture was also analyzed<br> at least once per day as an analytical standard control of the equipment. The mixture<br> included 6 ketones (2-butanone, 2-pentanone, 2-hexanone, 2-heptanone,<br> 2-ocatanone and 2-nonanone). This mixture is measured in the same conditions as<br> the urine samples. Samples are provided in the native instrument format (.mea format), that can be<br> read with the GCIMS R package or with the instrument software. <strong>Sample annotations</strong> The dataset includes a CSV file with sample annotations. The annotations include the following information: Diagnostic: Either ColorectalCancer or Control Sex: Either Male or Female Sample volume (in ml) Fasting: Whether the sample was collected with the patient in fasting conditions Age in years Weight_kg Height_cm BMI Smoker: TRUE/FALSE, whether the patient smoked Diseases: Whether the patient suffered from ArterialHypertension, CardiacFailure, Cholesterol, Dyslipidemia, Fibromyalgia or Tuberculosis AnalysisDateTime: Date and time of the GC-IMS analysis of the sample <br> <strong>Reference peaks</strong> Some peaks were manually annotated to ease the alignment of the samples and explore<br> alignment solutions. While manual peak labelling is not generally required, we<br> attach those reference peaks as well and their locations, in case they are of<br> interest. These reference peaks are found at reference_peaks.csv.