gingivalis, including shifts in energy pathways and metabolic end products [13]. Results and discussion selleck chemical Re-analysis using the P. gingivalis strain ATCC 33277 genome annotation The proteomics data previously analyzed using the strain W83 genome annotation [GenBank: AE015924] [9] was recalculated employing the strain specific P. gingivalis EPZ015666 molecular weight strain ATCC 33277 annotation [GenBank: AP009380]. Accurately identifying a proteolytic fragment using mass spectrometry-based shotgun proteomics as coming from a particular protein requires matching the MS data to a protein sequence. Differences in amino acid sequence between the proteins expressed by strain ATCC 33277 and the protein
sequences derived from the strain W83 genome annotation rendered many tryptic peptides from the whole cell digests employed unidentifiable in the original analysis [9]. Given that the quantitative power of the whole cell proteome analysis is dependent on SBI-0206965 order the number of identified peptides [12, 14], the new analysis was expected to give a more complete picture of the differential proteome, an expectation that proved accurate. In addition, some proteins in the strain ATCC 33277 genome are completely absent in the strain W83 genome and were thus qualitatively undetectable in the original analysis. Overall, 1266 proteins were detected with 396 over-expressed and 248 under-expressed proteins
observed from internalized P. gingivalis cells compared to controls (Table 1). Statistics based on multiple hypothesis testing and abundance ratios for all detected proteins can be found in
Additional file 1: Table S1, as well as pseudo M/A plots [15] of the entire dataset. The consensus assignment given in Additional file 1: Table S1 of increased or decreased abundance was based on two inputs, the q-values for comparisons between internalized P. gingivalis and gingival growth medium controls as determined by spectral counting and summed signal intensity from detected peptides that map to a specific ORF [9, 14, 15]. If one or the other of the spectral counting or protein intensity indicated a significant change (q ≤ 0.01) and the other measure showed at least the same direction of change with a log2 ratio of 0.1 or better, then the consensus was considered changed in that direction, coded red for over-expression or green for under-expression. before A simple “”beads on a string”" genomic map of the consensus calls is shown in Fig. 1. Figure 1 Map of relative abundance trends based on the ATCC 33277 gene order and annotation. This plot shows the entire set of consensus calls given in Additional file 1: Table S1 arranged by ascending PGN number [11], which follows the physical order of genes in the genome sequence. Color coding: red indicates increased relative protein abundance for internalized P. gingivalis, green decreased relative abundance, grey indicates qualitative non-detects and black indicates an unused ORF number.