Challenges for Biomarker Discovery in Body Fluids Using SELDI-TOF-MS

Table 2

Advantages and limitations of body fluids particularly useful for biomarker discovery.

Body fluids	Advantages	Limitations	Recommendations
Serum	(i) established sample banks often composed of serum aliquots (retrospective studies),	(i) presence of various products derived from coagulation cascade,	(i) use standardized collection protocol,
	(ii) proteins and peptides that “survive” to the clotting procedure exhibit a stability that can be exploited in routine clinical applications.	(ii) biomarker with poor stability during coagulation process will not be detected in serum,	(ii) keep sample during 1 hour at RT to allow clotting process before centrifugation,
		(iii) possible influence of the disease on coagulation process.	(iii) preserve on ice after clotting. Aliquoting and freezing (−80^∘C) cannot be done immediately.
Plasma	(i) more rapidly processed than serum (interesting for emergency diagnosis),	(i) interference with chip surface (i.e. heparin tube),	(i) use standardized collection protocol,
	(ii) larger final volume of fluid after processing than with serum,	(ii) sample dilution in citrate tube,	(ii) carefully choose the type of anticoagulants (EDTA tubes are preferable),
	(iii) more stable than serum due to the inhibition of coagulation cascade.	(iii) possible interference of EDTA with protein binding on IMAC surface,	(iii) use platelet-poor plasma,
		(iv) SELDI-TOF spectra less rich in peaks number and intensity than serum.	(iv) centrifuge, aliquot and freeze (−80^∘C) as soon as possible. If not possible, keep at RT to avoid cold platelet activation.
Dry blood	(i) medical staff not needed for collection,	(i) elution step to recover sample from filter paper.	(i) keep dry specimens at RT for 3–4 hours in horizontal position,
	(ii) low blood volume necessary,		(ii) store at −20^∘C.
	(iii) easy storage and transport.
Saliva	(i) easy and noninvasive sampling,	(i) low volume collected,	(i) always collect with the same method (stimulated or not) and at the same moment of the day,
	(ii) medical staff not needed for collection,	(ii) presence of many proteases and unspecific materials such as food residues or microorganisms,	(ii) centrifuge to remove insoluble material, aliquot and freeze at −80^∘C.
		(iii) level of certain plasma proteins are not reflected in saliva.
Urine	(i) easy and noninvasive collection,	(i) fluctuation of protein concentration overtime and according to renal integrity,	(i) use standardized collection protocol,
	(ii) medical staff not needed for collection,	(ii) presence of salts and proteins in low concentration.	(ii) concentrate the samples,
	(iii) obtained in large volume.		(iii) centrifuge, aliquot and freeze at −80^∘C,
			(iv) normalization with creatinine content.