Figure 1. Examples of different approaches to visualizing quantitative proteomics data. (A) Pseudo-abundance ratio measurement (M) vs. overall signal strength (A) plot of 791 P. gingivalis proteins determined by spectral counting. Green indicates under-expression when P. gingivalis was co-incubated with S. gordonii and F. nucleatum; red, over-expression; black, no change in abundance. The solid black lines, LOWESS curves (Cleveland, 1981), indicate boundaries for the region of expected random error about an abundance change of zero, and can also be used to estimate the power to detect abundance change as a function of total spectral counts at any point on the x-axis. (B) An example of proteomics data displayed in genome order, P. gingivalis’ response to co-incubation with S. gordonii by spectral counting. Each circle represents an annotated protein-encoding ORF in the order that it is encoded in the genome. Colored circles show the results of the quantitative proteomic analysis. Green indicates under-expression in P. gingivalis cells co-incubated with S. gordonii compared with P. gingivalis alone; red, over-expression; yellow, proteins that were identified, but showed no statistically significant abundance change; grey, no protein was detected. Blacked out regions indicate ORF numbers for which there is no TIGR annotation. (C) A section of the genomic representation of three M. maripaludis proteome experiments displayed in MEV (Multi-experiment Viewer, www.tm4.org/mev.html). Each row represents an ORF in the order that it is encoded in the genome (MMP1662-1680). Undetected proteins in this range are not shown. The annotation of each ORF is listed at the end of the row. The columns represent experimental conditions. NH4/H2, ammonia-limiting compared with H2-limiting growth conditions; P/H2, phosphate-limiting compared with H2-limiting growth conditions; P/NH4, phosphate-limiting compared with ammonia-limiting growth conditions. The colors represent a gradient of differential abundance between the conditions, from green for over-expression to red for under-expression, with black showing no change in abundance.