Correctness of protein identifications of Bacillus subtilis proteome with the indication on potential false positive peptides supported by predictions of their retention times

Abstract

The predictive capability of the retention time prediction model based on quantitative structure-retention relationships (QSRR) was tested. QSRR model was derived with the use of set of peptides identified with the highest scores and originated from 8 known proteins annotated as model ones. The predictive ability of the QSRR model was verified with the use of a Bacillus subtilis proteome digest after separation and identification of the peptides by LC-ESI-MS/MS. That ability was tested with three sets of testing peptides assigned to the proteins identified with different levels of confidence. First, the set of peptides identified with the highest scores achieved in the search were considered. Hence, proteins identified on the basis of more than one peptide were taken into account. Furthermore, proteins identified on the basis of just one peptide were also considered and, depending on the possessed scores, both above and below the assumed threshold, were analyzed in two separated sets. The QSRR approach was applied as the additional constraint in proteomic research verifying results of MS/MS ion search and confirming the correctness of the peptides identifications along with the indication of the potential false positives.

Figure 1

Correlation between experimental and predicted retention times for a set of test peptides obtained from model proteins (n = 21).

Figure 2

Correlation between experimental and predicted retention times for a set of test peptides obtained from Bacillus subtilis proteome. The proteins were identified on the basis of more than one peptide with X_corr above 1.5 (n = 54).

Figure 3

Correlation between experimental and predicted retention times for a set of test peptides obtained from Bacillus subtilis proteome. The proteins were identified on the basis of one peptide with X_corr above 1.5 (n = 41).

Figure 4

Correlation between experimental and predicted retention times for a set of test peptides obtained from Bacillus subtilis proteome. The proteins were identified on the basis of one peptide with X_corr below 1.5 (n = 40).

Figure 5

Percentage of the difference between predicted and experimental retention times (Dt_R) of Bacillus subtilis proteins identified on the basis of one peptide with X_corr below 1.5 (n = 40), over 1.5 (n = 41), and more than one peptide with X_corr over 1.5 (n = 54).