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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.


Linear correlation of MS intensities with peptide concentrations in the range from 10 to 500 ng/mL
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Fig2: Linear correlation of MS intensities with peptide concentrations in the range from 10 to 500 ng/mL

Mentions: In order to evaluate the sensitivity of the MS approach based on mesoporous chip enrichment, we tested serum samples spiked with synthesized standard peptide (Mw 1338) in different concentrations. As illustrated in Fig. 1, a strong signal for the standard peptide at m/z 1339 was detected at the concentrations tested. This standard peak was resolved from the background even at a concentration as low as 10 ng/mL. A good linear correlation with R2 = 0.996 was obtained in the range of 10–500 ng/mL, as shown in Fig. 2. These results confirmed the good performances of mesoporous chip-enabled MALDI MS approach in the relative quantitative analysis. Repeated test of one same serum sample in the different well on the mesoporous chip also showed good reproducibility, and the CV% of five endogenous m/z peaks from the peptide MS pattern respectively are 12.6% (m/z 1561.41), 6.6% (m/z 1553.37), 10.6% (m/z 1552.39), 5.8% (m/z 1394.66), 9.0% (m/z 897.62).Fig. 1


Mesoporous silica chip: enabled peptide profiling as an effective platform for controlling bio-sample quality and optimizing handling procedure
Linear correlation of MS intensities with peptide concentrations in the range from 10 to 500 ng/mL
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Linear correlation of MS intensities with peptide concentrations in the range from 10 to 500 ng/mL
Mentions: In order to evaluate the sensitivity of the MS approach based on mesoporous chip enrichment, we tested serum samples spiked with synthesized standard peptide (Mw 1338) in different concentrations. As illustrated in Fig. 1, a strong signal for the standard peptide at m/z 1339 was detected at the concentrations tested. This standard peak was resolved from the background even at a concentration as low as 10 ng/mL. A good linear correlation with R2 = 0.996 was obtained in the range of 10–500 ng/mL, as shown in Fig. 2. These results confirmed the good performances of mesoporous chip-enabled MALDI MS approach in the relative quantitative analysis. Repeated test of one same serum sample in the different well on the mesoporous chip also showed good reproducibility, and the CV% of five endogenous m/z peaks from the peptide MS pattern respectively are 12.6% (m/z 1561.41), 6.6% (m/z 1553.37), 10.6% (m/z 1552.39), 5.8% (m/z 1394.66), 9.0% (m/z 897.62).Fig. 1

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.