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| Preanalytical bias | |
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| Patients information | Age, gender, ethnicity |
| Disease subtype and/or severity |
| Medical background |
| Health background |
| Smoking status, alcohol intake, diet, other risk factors |
| Drug treatments |
| Patient position (seated/standing/lying), daily moment of collection |
| Type of control (healthy or disease) |
| Location of sample collection (single or multisite) |
| Study inclusion and exclusion criteria |
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| Sample characteristics | Number of individuals |
| Type (blood, serum, plasma, urine, cerebrospinal fluid, cell lysate, etc.) |
| Source (banked or prospectively collected) |
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| Sample-handling procedures | Collection protocols (initial processing, procedure, timing, type of anticoagulant, type of tubes, number of sites, etc.) |
| Storage procedures (time, aliquoting, storage materials, temperature, freeze-thaw cycles, etc.) |
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| Analytical bias | |
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| Sample-Processing procedures | Fractionation and depletion methods |
| Processing steps (denaturation, buffer components, delipidation, etc.) |
| Liquid handling methods (automated or manual, technique, equipment, etc.) |
|
| Experimental protocols | Array types |
| Sample pH and dilution factor |
| Quantity of sample loading and position on arrays |
| Sample binding, washing and drying procedures |
| Matrix addition (type and method) |
| Instruments settings |
| Number of instruments, locations |
| Environmental factors (temperature, humidity percentage) |
|
| Data analysis methods | Spectrum processing (baseline subtraction, normalization, alignment, noise reduction, etc.) |
| Peak labelling |
| Feature selection, statistical analysis |
| Classification approaches |
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