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Achieving Reliable Protein Quantitation Results Using ICAT Reagents, MALDITOF Mass Spectrometry, and Advanced Data Interpretation Tool

nt experiments. Data processing algorithms such as advanced baseline correction, noise reduction, and de-isotoping could be applied to data automatically prior to quantitative analysis. Because of trace amounts of D7 and D6 present in the heavy ICAT reagent, the software allows for a correction factor for these species.

Results

A key element in the software is the flexibility to identify the ICAT reagent pairs based on a theoretical peptide mass list from known protein digests, which could lead to accurate identification of ICAT reagent pairs and therefore reliable quantitative results. For example, the quantitative results from the mass spectrum of the labeled(D8) vs. non-labeled(D0) digested BSA yielded a ratio of 0.91 (vs. theoretical value of 1.0) with a standard deviation of 0.12 (Figure 2 and Table 1).

Alternatively, the VBA software automatically looks for all possible ICAT reagent pairs if the protein digests are not previously identified. False positives could be deleted by applying statistics or re-evaluating the spectrum. For MALDI-TOF analysis, this suppression is often a concern for quantitative analysis because of the complex nature of the sample. Reverse phase separation can improve the dynamic range, as is demonstrated in Figure 3. In this case, the dynamic range for a peptide of interest from a 10-protein mixture is demonstrated by the software to achieve 0.11 (vs. theoretical ratio of 10:1) and 0.03 (vs. theoretical value of 30:1) accurately.

Conclusion

Using MALDI-TOF and advanced data interpretation software, users can achieve reliable quantitative results of affinity-purified ICAT reagent-labeled protein digests. This method can be used as a potential assay to rapidly screen peptides derived from the upand down-regulated proteins that are potential bio-marker candidates in complex mixtures.

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