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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 the serums stored at different temperatures (−190, −80, −20, 4 and 25 °C) for 48 days
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Fig7: PCA of the serums stored at different temperatures (−190, −80, −20, 4 and 25 °C) for 48 days

Mentions: This trend was further demonstrated from the analysis of samples stored for 48 days. The obvious changes of spectra can even be distinguished directly at the temperature of 4 and −20 °C (Fig. 6). In the PCA analysis, all the sample groups separated completely from the fresh samples except for the −190 °C group (Fig. 7), and the general freezing condition such as −20 °C is no longer appropriate. Besides, after stored for 48 day, the percentage of m/z peaks showing significant difference enhanced obviously compared with the samples stored 9 day, and still showed the highly dependent on temperatures (Fig. 5). To our surprise, the sample stored in ultra-low temperature freezer (−80 °C) also showed significant difference from the fresh samples and the Psd value reached 40%, which probably should be attributed to unstable temperature due to the frequent opening of the freezer door during this long period. These results suggested that as the storage time prolonged, a temperature-lowered and more stable condition is required.Fig. 6


Mesoporous silica chip: enabled peptide profiling as an effective platform for controlling bio-sample quality and optimizing handling procedure
PCA of the serums stored at different temperatures (−190, −80, −20, 4 and 25 °C) for 48 days
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig7: PCA of the serums stored at different temperatures (−190, −80, −20, 4 and 25 °C) for 48 days
Mentions: This trend was further demonstrated from the analysis of samples stored for 48 days. The obvious changes of spectra can even be distinguished directly at the temperature of 4 and −20 °C (Fig. 6). In the PCA analysis, all the sample groups separated completely from the fresh samples except for the −190 °C group (Fig. 7), and the general freezing condition such as −20 °C is no longer appropriate. Besides, after stored for 48 day, the percentage of m/z peaks showing significant difference enhanced obviously compared with the samples stored 9 day, and still showed the highly dependent on temperatures (Fig. 5). To our surprise, the sample stored in ultra-low temperature freezer (−80 °C) also showed significant difference from the fresh samples and the Psd value reached 40%, which probably should be attributed to unstable temperature due to the frequent opening of the freezer door during this long period. These results suggested that as the storage time prolonged, a temperature-lowered and more stable condition is required.Fig. 6

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.