3. What do the various diagrams represent?
The coverage diagram is displayed at the top of the protein page,
on the accession number page as a list and on the protein validation page.
The red sections represent the peptides
that have been identified for the result and their placement along the entire protein length. The opacity is based on the expectation value for that peptide.
The darker the color, the better the expectation value.
Example:
The spectrum diagram is displayed on the peptide page. It represents the mass
spectrum data for the current peptide identification using vertical lines to represent peaks.
The y-axis is the relative intensity.
It is calculated by taking the value from spectrum, dynamic range input parameter
and 'normalizing' the most intense peak with that value.
See the API documentation for
more details on this parameter. The x-axis is the mass range of the spectra data.
The vertical lines represent the peaks. The different colors represent the ion type.
- Red: y ions
- Yellow: y-17 ions
- Blue: b ions
- Green: b-17 ions
- Black: unassigned ions
- Mauve: trivial neutral loss ions
The diagram above the spectrum diagram (showing the sequence with vertical
lines between the residues) represents the b and y ion break down from the spectrum
for assigned ions.
The length of the vertical lines represents the intensity
of the ion peak at that point in the sequence.
The diagram to the left of the spectrum is the delta scatter diagram. The position
of the red and blue 'dots' is based on the identified ion mass (y-axis) and the difference,
in Daltons, between the observed and calculated masses (x-axis). Hover the mouse
over the 'dots' to see the ion mass.
Example:
The diagrams on the details|supporting evidence page are:
- Hyperscore Expectation Function and Convolution Survival Function.
These diagrams represent the values that were used in scoring the spectrum.
Details on the formulae used for this can be found in the paper called:
A Method for Assessing the Statistical Significance of Mass Spectrometry-Based
Protein Identifications Using General Scoring Schemes,
David Fenyö and Ronald C. Beavis, Anal. Chem., 2003, 75, 768-774.
- y and b ion Histograms. The y-axis is the number of peptides and the
x-axis is the number of ions. So in the b ion example below, the first vertical
line means that there were 456 peptides with 0 b ions, the second line is
743 peptides with 1 b ion, the third line is 229 peptides with 2 b ions
and so on. The last value that is shown is the largest non-zero value. In this
case, 3 peptides had 10 b ions.
- Spectra Histogram. A simplified version of the spectrum diagram as shown above.
Example:
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