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Mesoporous silica chip: enabled peptide profiling as an effective platform for controlling bio-sample quality and optimizing handling procedure

View Article: PubMed Central - PubMed

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.

Methods: The 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.

Results: This 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.

Conclusion: Our 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.

No MeSH data available.


PCA of serums froze at −80 °C and then thawed at 4 °C for 1–5 cycles
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Fig11: PCA of serums froze at −80 °C and then thawed at 4 °C for 1–5 cycles

Mentions: Afterwards, we further investigated the impact of freezing frequency. Serums were repeatedly froze at −80 °C and then thawed at 4 °C for 1–5 cycles, and then compared with the original fresh serums. As shown in PCA analysis (Fig. 11), when the cycles of freezing/thaw were lower than three times, the frozen/thawed serums were hard to discern from fresh serums. When the freezing/thaw cycles exceeded 4 times, the frozen/thawed serums were separated from the fresh serums completely (Fig. 11). The same trends can also be concluded from the comparison of Psd values (Fig. 12). The Psd values were almost constant and only around 20% when freezing times were less than 3. However, as freezing times increased to 5, the Psd value was over 40%, implying a serious change of serum proteome (Fig. 12).Fig. 11


Mesoporous silica chip: enabled peptide profiling as an effective platform for controlling bio-sample quality and optimizing handling procedure
PCA of serums froze at −80 °C and then thawed at 4 °C for 1–5 cycles
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5120552&req=5

Fig11: PCA of serums froze at −80 °C and then thawed at 4 °C for 1–5 cycles
Mentions: Afterwards, we further investigated the impact of freezing frequency. Serums were repeatedly froze at −80 °C and then thawed at 4 °C for 1–5 cycles, and then compared with the original fresh serums. As shown in PCA analysis (Fig. 11), when the cycles of freezing/thaw were lower than three times, the frozen/thawed serums were hard to discern from fresh serums. When the freezing/thaw cycles exceeded 4 times, the frozen/thawed serums were separated from the fresh serums completely (Fig. 11). The same trends can also be concluded from the comparison of Psd values (Fig. 12). The Psd values were almost constant and only around 20% when freezing times were less than 3. However, as freezing times increased to 5, the Psd value was over 40%, implying a serious change of serum proteome (Fig. 12).Fig. 11

View Article: PubMed Central - PubMed

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.

Methods: The 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.

Results: This 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.

Conclusion: Our 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.

No MeSH data available.