Skip to main content

Table 1 User-adjustable options

From: Automated peptide mapping and protein-topographical annotation of proteomics data

Option Variable name Default value Description
Invert H and L -insert off This function enables the user to invert the light to heavy ratios in the ProtXML file to heavy to light ratios.
Validate ASAPratio with Xpress -validate off This function validates the ASAPRatio [8] (Automated Statistical Analysis on Protein Ratio) results with XPRESS [9] results.
Elaborate list of peptides -elaborate off Selecting this function displays the list of all occurrences of a peptide (in case they are identified more than once, by default the tool chooses the peptide with highest Peptide Prophet probability score).
ProteinProphet cutoff -threshold 0.90 This function enables the user to set the cutoff for the ProteinProphet probability score. Any protein with a score less than this cutoff is discarded.
Minimum peptide ratio -rmin -3.0 This function enables the user to set the minimum value allowed for light:heavy ratio of the peptide. This measure is then used for scaling of the peptide ratios.
Maximum peptide ratio -rmax 3.0 This function enables the user to set the maximum value allowed for light:heavy ratio of the peptide. This measure is then used for scaling of the peptide ratios.
Negative no change zone -zn -0.25 This function enables the user to set the negative threshold for light to heavy ratio of the peptide. i.e. the peptide ratios between the Zn and Zp thresholds are categorized together.
Positive no change zone -zp 0.25 This function enables the user to set the positive threshold for light to heavy ratio of the peptide. i.e. the peptide ratios between the Zn and Zp thresholds are categorized together.