For both precursor ion quantification and reporter ion quantification, the application calculates protein and peptide group ratios from the protein and peptide group abundances. The ratios are not calculated from PSM ratios.

You can display a chart of the peptide group ratios, which shows the distribution of peptide group ratios for the selected protein and displays the ratios of the peptide groups associated with the selected protein as a log2-fold change.

Procedure

  1. On the Proteins page of the result file that contains quantification results, select the row of the protein that you are interested in.
  2. Select View > Quan Ratio Distributions, or select Quan Ratios Distribution .
  3. The Quan Ratio Distributions chart opens for reporter ion quantification, or for precursor ion quantification.
  4. Quan Ratio Distributions chart for reporter ion quantification
  5. The Quantification Ratio Distributions chart shows the distribution and spread of the ratios of all peptides belonging to a particular protein. The following figure shows an example for the albumin protein.
  6. Quantification Ratio Distributions chart
  7. The chart shows the distribution of peptide group ratios for each of the ratios reported, as defined in the quantification method for this search. Each of the ratio distribution charts displays the peptide group ratios as the binary logarithm. The logarithmic form is common for such displays, because it provides a reasonable display, even when there is a large spread of the displayed values. In binary logarithmic form, a value of 1 means a two-fold increase, a value of 2 means a four-fold increase, a value of 3 means an eight-fold increase, and so forth.
  8. Each of the separate distribution charts displays the peptide group ratios in three sections. The chart legend explains the meaning of these sections. You can access the chart legend by right-clicking the chart and choosing Show Legend.
  9. The Quan Ratio Distribution charts contain the following three sections:
  10. The first section displays the distribution of the ratios of all peptides considered for calculating the abundance of this protein as a box-and-whisker plot. A box-and-whisker plot is a convenient way of graphically depicting groups of numerical data through a five-number summary: 5 percent lower bound, lower quartile, median, upper quartile, 95 percent upper bound. The range between the lower and upper quartile (this is the range of the box) is also known as the inter-quartile range (IQR) and, like the standard deviation for normally distributed data, is a measure of the spread of the data.
    - The box represents the peptide group ratios between the 25th and the 75th percentiles.
    - The error bars represent the peptide group ratios below the 5th and the 95th percentiles.
    - The blue lines inside the horizontal bar represent the median of the distribution.
  11. The second section (blue circles) displays the distribution of the ratios of all peptide groups considered in calculating the protein abundances.
  12. The third section (red circles) displays the distribution of the ratios of all peptide groups that were not considered in calculating the protein abundance (for example, the peptide group is not unique to this protein or this protein group) according to the rules defined in the quantification method.
  13. Quan Ratio Distributions chart for reporter ion quantification
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    No.DescriptionNo.Description

    1

    95 percent of the peptide ratios are below this point

    4

    5 percent of peptide ratios are below this point

    2

    Distribrution of the peptide ratios considered in calculating the protein abundances

    5

    (blue line) Median of the distribution

    3

    Distribution of the peptide ratios not considered in calculating the protein abundances

    6

    50 percent of the peptide ratios are between the 25th and 75th percentile lines

  14. In addition, each chart displays the median ratio (R) and the inter-quartile range (IQR) in linear and logarithmic format. The header of the chart identifies the protein that the PSM belongs to. Right-click the chart and select Show Legend for the identity of other notations on the chart.