Abstract
Background High quality clinical samples are critical for meaningful interpretation of data obtained in both basic and translational medicine. More specifically, optimized pre-analysis handling to bio-sample is crucial for avoiding biased analysis in a clinical setting. A universally applicable method for the evaluation of sample quality and pre-analysis handling is therefore in great demand.MethodsThe fingerprint pattern of low molecular weight (LMW) peptides in sera is directly associated with sample quality and handling process. Previous studies for enrichment/isolation of LMW peptides have shown that LMW peptides can be enriched by silica meso-porous material in a sensitive and high-throughput manner. Here, a peptide profile approach utilizing mesoporous silica chip-based sample preparation combined with MALDI MS analysis was used as a new platform for evaluation of bio-sample quality. Rat sera were selected as model sample and analyzed according to their LMW peptide fingerprint spectra.ResultsThis novel method can complete the entire sample preparation procedure in a short period of time (<40 min), requires minimum amounts of sample (<10 µL), is of high sensitivity (LOD 10 ng/mL) as well as high reproducibility (CV% < 15%). According to the acquired LMW peptide spectra, we were able to distinguish the serum samples processed under different conditions (including different storage temperature, time, and freezing/thaw cycles) with the help of bioinformatics tools (principle composition analysis and significant difference analysis), and identify the samples that had significantly changed due to the inappropriate processing. Based on the percentage of significantly changed peaks in LMW peptide mass spectrum after handling, a judgment standard was established that can be used to evaluate the status of preservation of a biological sample. In addition, our principle study established recommendations for storage time, storage temperature and freeze/thaw conditions.ConclusionOur novel method for analysis of bio-samples allows for effective identification of variations in composition within samples, and provides a cost-effective tool for simple sample manipulation in a clinical setting.
Highlights
High quality clinical samples are critical for meaningful interpretation of data obtained in both basic and translational medicine
Performance of mesoporous chip as enrichment platform of low molecular weight (LMW) peptides in serum In order to evaluate the sensitivity of the matrix assisted laser desorption ionization mass spectrometry (MS) approach based on mesoporous chip enrichment, we tested serum samples spiked with synthesized standard peptide (Mw 1338) in different concentrations
We have discovered that the LMW peptide profiles enabled by the meso-porous chip were able to effectively represent the differentiation of samples stored at different temperatures, and the extent of variation of peptide spectra highly correlated with temperature, implying that this proposed approach can be utilized to evaluate the variation of sample quality caused by the handling procedure
Summary
High quality clinical samples are critical for meaningful interpretation of data obtained in both basic and translational medicine. A universally applicable method for the evaluation of sample quality and pre-analysis handling is in great demand. Both basic and translational medical researches depend on the availability of high quality clinical samples, which. Liang et al Clin Proteom (2016) 13:34 They can be released from activated, dying, or lysed neutrophils or mononuclear phagocytes during sample process [5]. These enzymes will hydrolyze serum proteins and peptides, and as a consequence change the proteomic pattern of the sample. Considering the large number of specimens commonly involved in clinical tests, the testing methods used should ideally be fast, consume little sample volume, compatible with high-throughput technology, available for easy manipulation, and cost-effective; besides, the results of the sample analysis should reflect the changes that have occurred in the sample since collection
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