A mass spectrometry based method and a software tool to assess degradation status of serum samples to be used in proteomics for biomarker discovery

Integrity of serum samples is a major concern for biomarker discovery in many fields, including oncology. A gradual degradation of the fibrinopeptide A (fpA) as a result of the preservation process was already observed. In this work, we investigated this process to define a method for the assessment of sera integrity based on the total amount of fpA and its degradation pattern. SeraDeg software was developed. It identifies fpA fragments in spectra and extracts their abundances. The SeraDeg Quality Score (SDQS) is finally determined for each spectrum depending on its total fpA abundance and on the ratio of its higher mass versus lower mass fragments abundances. Spectra were evaluated for the total amount of fpA and the percent contribution of its fragments. The total fpA abundance is significantly lower in cryo-preserved samples than in fresh sera. Moreover, fresh sera present higher percentages of the most intact forms of fpA. Four relevant fpA fragments were identified. We developed and made available on-line SeraDeg, a software able to screen serum spectra, compute fpA related parameters and assign quality scores. SeraDeg was validated using spectra from a set of 250 samples. Biological significance The susceptibility of fpA to degradation suggests its use as quality indicator of cryo-preserved serum samples. SeraDeg can support the adoption of this method which may especially be useful in differential sero-proteomics for wide-range biomarker discovery. Moreover, it discloses the doors to a critical re-evaluation of previous experiments in light of the quality of serum samples as assessed by fpA degradation analysis.