Figure 4.

Visualization of data. Visualization of data. All these plots are from the experiment discussed in the text. This Figure illustrates four simple graphs designed to give a quick overview of the data, a) is a scatter plot of the theoretical molecular weight of each identified protein over a certain prophet probability (user-settable) against the scan number. The scan number is the sequential number online MS assigns to each spectra it acquires, and since these spectra are acquired with a given time interval, the scan number can be utilized as a pseudo retention time, b) is a histogram of proteins that are significantly regulated (p < 0.05), and a ProteinProphet probability over 0.6. c) is a mass spectra from one of the peptides used to identify HSP72_HUMAN heat shock-related 70 kDA protein 2. These graphs are generated on the fly and enables the user to assess the quality of the dataset.