Fig 1.
Example MS data of a of a strain of Salmonella enterica subsp. enterica serovar infantis.
(A) Linear MS data of bacterial cell lysate. (B) The identified protein sequence (hypothetical/YahO) after removal of its 21-residue signal peptide. An asterisk denotes a site of backbone cleavage with its corresponding b-type and/or y-type fragment ions. (C) MS/MS data of the protein ion at m/z 7666. Fragment ions are identified by m/z (theoretical value in parentheses) and their b- or y-type fragment ion designation. (D) The pre-processed and centroided MS/MS data of the protein ion at m/z 7666. Pre-processed and centroided MS/MS data is shown in Fig 1D.
Fig 2.
Workflow for analysis of the selected bacterial proteins.
Fig 3.
Distribution of D-, E-, and N-fragment signal scores.
(A) Histogram of D-, E-, and N- fragment scores. (B) Empirical cumulative distribution functions of D-, E-, and N-fragment scores.
Table 1.
Multivariate regression analysis results.
Fig 4.
Distribution of D-, E-, and N- fragment signal scores with respect to significant explanatory variables.
(A-C) Empirical cumulative distribution functions (eCDF) of D-fragment signal scores. (D) eCDF of N-fragment signal scores. (E-I) eCDF of E-fragment signal scores. Shades of pink represent percentile of significant explanatory variable values.
Fig 5.
Analysis of categorical explanatory variables.
(A) Box plot of fragment signal scores grouped by C-terminal residues adjacent to D. (B) Box plot of fragment signal scores grouped by C-terminal residues adjacent to E. (C) Box plot of fragment signal scores grouped by C-terminal residues adjacent to N. (D) Bar graph comparing the proline fragment signal scores whose adjacent N-terminal adjacent residue was D,E,N or non-D,E,N. (E) Box plot of fragment signal scores grouped by secondary structure of E-residues. Significant explanatory variables p<0.05, p<0.01, p<0.00001 is respectively marked by *,**, and ***** based on the Mann-Whitney U test. Bar graph is displayed as mean ± standard error.
Table 2.
Kruskal-Wallis test of categorical explanatory variables.