A Gas Chromatography – Ion Mobility Spectrometry dataset for colorectal cancer diagnostic of 56 urine samples corresponding to 29 subjects.

Contents of the dataset

The dataset includes the set of urine samples in .mea format, which can be
read using the GCIMS R package.

It also contains analytical standards in the same format, used for quality
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
and AnalyticalStandards.zip files, but rather use the smaller UrinesDemo.zip and
AnalyticalStandardsDemo.zip, with a subset of just three samples of the whole
dataset.

Besides the actual measurements, you will find the annotations.csv and
reference_peaks.csv files, with sample annotations and some reference peaks
identified in the samples.

See further details below.

Sample collection

Urine samples from 29 subjects were collected at Hospital de Reus. 15 subjects
were diagnosed with colorectal cancer, 14 subjects were controls. The study
protocol was approved by the Ethics Committee of Hospital de Reus (study
approval no. 074/2018).

Samples were aliquoted and frozen at -80ºC for storage.

Sample preparation
 

Sample preparation improves urine preservation by blocking bacterial growth in
the urine, and favours volatile extraction. It also adds an internal standard
for verification of instrument variability.

Stock solution preparation

Dissolve 11.69 g of NaCl in about 35 mL deionized water and add 6.5 mg sodium
azide (NaN3). Once dissolved, add 5.50 mL 5M HCl and mark up to volume with
deionized water until the final volume is 50mL. The HCl 5M is used to obtain
an acid pH. The pH is controlled with a pH test paper. The final pH level must
be 2 or below. The NaCl favors the volatile extraction, and the NaN3 omits
the bacterial growth in the urine.

Internal standard solution preparation
 

The 4-flurobenzaldehyde is located in retention time around 200 seconds and
can be used as an internal standard.

Prepare a methanol stock solution using 100 ml of methanol grade for
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.

Sample preparation
 

Aliquotes were thawed before analysis. Once thawed, 300uL of the stock solution
were added to the urine sample, and 1.5 ml of the acidified urine sample were
transferred into a 20ml vial, ensuring only the supernatant of the sample
is transferred.

Finally, 20 mL of the internal standard solution is added to the sample.

GC-IMS Analysis

Samples were analyzed with a GC-IMS FlavourSpec® instrument from
G.A.S. Dortmund (Dortmund, Germany). Samples were incubated for 15 minutes
at 60ºC, the flow rate of the drift gas was set at 200 ml/min, and the carrier
gas was set 11 ml/min. Both the drift and carrier gas were Nitrogen 5.0. The GC
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
at least once per day as an analytical standard control of the equipment. The mixture
included 6 ketones (2-butanone, 2-pentanone, 2-hexanone, 2-heptanone,
2-ocatanone and 2-nonanone). This mixture is measured in the same conditions as
the urine samples.

Samples are provided in the native instrument format (.mea format), that can be
read with the GCIMS R package or with the instrument software.

Sample annotations

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

Reference peaks

Some peaks were manually annotated to ease the alignment of the samples and explore
alignment solutions. While manual peak labelling is not generally required, we
attach those reference peaks as well and their locations, in case they are of
interest.

These reference peaks are found at reference_peaks.csv.