Spectrum viewer
| Document kind | spectra |
| Drawn from | a file — it can also be previewed in the file manager |
| Formats that open here | MGF · mzML |
| Refuses to draw below | 360px wide |
What it draws
One MS/MS fragment spectrum at a time, as a stick plot: every peak in the peak list is a vertical line at its m/z, its height the intensity relative to the tallest peak in that spectrum (100%). The precursor m/z, when the file declares one, is a dashed line labelled with its value.
When a peptide is given, three more layers appear:
- The fragment ladder above the plot: the peptide's residues, with a mark at every bond. The mark above a bond is the b ion that breaks there (the N-terminal piece), the mark below is the y ion (the C-terminal piece), and a mark is drawn in its series color only when that ion was found in the spectrum.
- Matched sticks recolored by series (b in blue, y in vermillion), the most intense ones labelled with the ion's name. Unmatched peaks stay grey.
- A mass-error strip under the plot, on the same m/z axis: one dot per matched ion at its observed minus theoretical m/z, with the tolerance drawn as dashed bounds either side of zero.
- The theoretical spectrum, mirrored, when you ask for it: every b and y ion of the peptide hangs below the m/z axis facing the observed peaks, solid where a peak matched it and faint where none did. All theoretical sticks are one height, because the score weighs every ion the same.
What opens in it
MGF peak lists (one BEGIN IONS … END IONS block per spectrum, gzipped or not, as PRIDE serves
them) and mzML runs. From an mzML run only the MS/MS spectra are kept; a run holding only
survey (MS1) scans is refused with that count, because it has no fragment spectrum to draw.
What this computes
Nothing is inferred from the peaks alone. An MGF carries peaks, not identities, so no peptide is
guessed: the one the file declares for a spectrum (its SEQ= line) is used, or the one you type.
- Theoretical b and y ions of the peptide, at every fragment charge from 1+ to one below the precursor charge (at least 1+). The peptide is read as ProForma, so modifications are part of the mass.
- Peak matching: each theoretical ion is paired with the nearest observed peak, and the pair is kept only if it lies within the tolerance (in Da, or in ppm of the observed m/z). This is the pairing OpenMS uses.
- HyperScore: the natural log of one plus the summed intensity of the matched peaks, plus the log factorials of the matched b and matched y counts, as OpenMS computes the X!Tandem score. More matched ions of both series raise it far faster than a few intense ones.
- Matched b / y counts, and the mean absolute mass error of the matches in the tolerance's unit.
Reading it
- Relative intensity is per spectrum. 100% is the tallest peak in the spectrum on screen, so two spectra's heights are not comparable.
- A grey stick is unexplained, not noise. It is a peak no b or y ion of this peptide, at these charges and this tolerance, accounts for. Other ion types (a, c, z, internal fragments, neutral losses) are not matched, so a real fragment of those kinds also stays grey.
- The error strip is the check on the tolerance. Matches spread evenly to both dashed bounds suggest the window is admitting chance coincidences; matches clustered on one side of zero suggest a calibration offset.
- A HyperScore is comparable only between matches of the same spectrum, or between spectra scored with the same tolerance and charge. It is not a probability.
Controls
| Control | What it does |
|---|---|
| Spectrum | Steps through the spectra in the file. Changing it clears a typed peptide and charge, so a peptide is never scored against a spectrum it was not given for. Disabled when the file holds one spectrum. |
| Peptide (ProForma) | The peptide whose ions are matched. A peptide that does not parse is refused next to the field, with the reason. |
| Precursor charge | 1+ to 6+. The file's declared charge is marked; it decides the highest fragment charge matched. |
| Tolerance and Tolerance unit | The matching window, in Da or ppm. |
| Mirror theoretical | Draws the peptide's theoretical b and y ions below the axis, matched ones solid. Off until asked; unavailable until a peptide is given. |
| Reset zoom | Returns to the whole m/z range. Drag across the plot to zoom into a range; double-click also resets. |
Hovering a peak reads out its m/z, its relative intensity and, when matched, the ion, its theoretical m/z and the error.
Where it appears
As its own tab on the stage when an MGF or mzML file is opened, and in the file manager's preview. The preview keeps every control, so a spectrum can be annotated before it is opened.
Performance and limits
Every peak is drawn; spectra are hundreds of peaks, not millions. Below 360 px wide the view refuses to draw, because the fragment labels over the sticks overlap and cannot be read.
Related
- Mass spectrometry: scores a spectrum against a peptide with the same matching and HyperScore this view draws, and weighs peptides and their fragment ions.