(New page: This script displays detailed information regarding other peptides that have signals close to the mass-to-charge readings of the peptide in question. The arguments are ''pepid'', ''patter...) |
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== Display Elements == | == Display Elements == | ||
| - | *An overview of the base peptide: | + | *An overview of the base peptide and a form in which retention time and mass tolerances can be changed: |
| - | **The residue sequence. | + | **The residue sequence, followed by the accession number of the protein in which the spectrum detailed below was observed. |
| - | **The mass-to-charge ratio for the base peptide, and the parent ion mass error used in the calculations for signal uniqueness. | + | **'''z''': The charge state of the base peptide. |
| - | **The | + | **'''m/z (q<sub>1</sub>)''': The mass-to-charge ratio for the base peptide, and the parent ion mass error used in the calculations for signal uniqueness. |
| - | **The calculated retention time for the peptide. | + | **'''q<sub>3</sub>''': The parent ion mass delta used to display the table below. This can be changed, and the table below will be modified to reflect the change in the data when the form is resubmitted. |
| - | + | **'''HPLC %ACN''': The calculated retention time for the peptide. The editable field is the retention time delta. This can be changed, and the table below will be modified to reflect the change in the data when the form is resubmitted. | |
| - | + | **'''Sort Base''': Whether to sort the peaks by decreasing intensity or increasing m/z ratio. | |
| - | + | **'''Sample Matrix''': A filter to remove proteins from collision considerations based on a tissue type. E.g., choosing "bone" and resubmitting the form will only check for potential collisions in spectra peaks from proteins that have been identified in that [[Normal_Clinical_Tissue_Alliance|BTO tissue type]]. | |
| - | ** | + | **'''Go''': The submit button. |
| - | ** | + | |
| - | + | *A five-column, colour-coded table containing the details regarding signal uniqueness. | |
| - | + | **'''Base m/z, I''': The m/z ratio and intensity for the peaks associated with this peptide record in the [[[GPM-MRM|MRM database]]]. | |
| - | ***'''Ret δ''': difference from the base peptide of calculated retention time. | + | **'''I''': The intensity of signals from other m/z ratios that fall within the fragment ion delta defined in the form at the top of the page. This field may contain either one number or two numbers separated by a dash (–); in the latter case, the numbers can be interpreted as a range of intensity values at which that m/z ratio has been detected. |
| - | + | **'''Peptides''': the residue sequence of the peptides which create the colliding signal with the base m/z-intensity tuple. | |
| - | ** | + | **'''Ret δ''': the difference from the base peptide of calculated retention time. |
| - | ** | + | **'''Proteins''': a compound field: |
| + | ***A list of proteins in which this peptide is found. | ||
| + | ***A '''+''' icon, depending on the number of proteins in which this peptide is found. Clicking this icon will show or hide the whole list of proteins in which this peptide is found. | ||
| + | **'''"n more" + icon''': a control to show or hide the complete list of peptides with spectra that would collide with the base m/z-Intensity tuple. | ||
| + | |||
| + | *'''Colour coding''': | ||
| + | **'''White background''': Peptides displayed on a white background have a fragment ion mass ''or'' retention time that fall within the deltas specified in the form at the top of the page. This would make the associated base m/z-Intensity signal a poor candidate. | ||
| + | **'''Light green background''': Peptides display on a light green background have a calculated retention time that falls outside the delta defined in the form at the top, but a fragment ion mass within the delta specified in the form at the top. This may make them good candidates. | ||
| + | **'''Dark green background''': m/z-Intensity signals in within the deltas specified at the top do not have collisions within either fragment ion mass or calculated retention time, making them excellent candidates. | ||
This script displays detailed information regarding other peptides that have signals close to the mass-to-charge readings of the peptide in question.
The arguments are pepid, pattern, delta_m, delta_f, and sort_type. pepid is the internal unique identifier for the spectrum associated with this specific peptide in the MRM library. pattern and sort_type are both used to generate links to other GPM resources. delta_m is the mass error range allowable for the parent ion. delta_f is the mass error allowed for any fragment ion.