4. mzPepCalc
mzPepCalc is a very useful tool for calculating fragment ion masses.
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Enter the peptide sequence in the sequence box.
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Modifications like phosphorylation are entered by using specific tokens. Tokens are managed with the "MOD manager" (see section below). For example, pS, pT, and pY correspond to phopsho serine, threonine, and tyrosine.
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Additionally, specific masses can be added to residues by enclosing the mass in brackets. For example, the mass of fragments for angiotensin II phosphate can be displayed by typing: DRV[97.98]YIHPF where [97.98] represents the mass of the phosphate group (H3PO4).
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Set the charge state of the fragment ions you would like to calculate with the spinner box.
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Set the highest charge state precursor you would like to display with the labeled spinner box (‘6’ will calculate from ‘+0’ or unprotonated to ‘+6’ charge state).
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Select # of decimals to display
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Select N-term mod, if applicable
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Select C-term mod, if applicable
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Selection ion type (i.e. b/y or c/z)
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Select mass type (average or monoisotopic)
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Hit calc button to calculate precursor and product ion masses, and display the results in the list boxes.
- CLR clears the current sequence.
- Open opens the “List Bank” (see section below).
- Add will add the current sequence to the List Bank
- MOD will open the “Mod Manager” (see section below).
- Label will annotate the current spectrum with calculated product ions (y/b or c/z) if they are present in the spectrum.
- Clear overlay will remove annotations applied with the label function.
- Copy to clipboard will copy the sequence, precursor, and product ion lists to the clipboard
- You can also copy individual precursors or products by selecting the ion in the corresponding list box, right-clicking, and selecting the appropriate item in the pop-up menu i.e. Copy b-ion to Clipboard.
The list bank is a useful tool to maintain lists of peptides for specific projects.
- Save and load will save and load lists to/from text files.
- Delete will delete the selected entry.
- Clear will clear the list bank.
- Left clicking a sequence in the list bank will send the sequence to the text box in the mzPepCalc and calculate the sequence.
- Edit will allow you to go into “Edit” mode where left clicking allows you to edit the sequence or title of the item:
- You can make custom peptide lists! Place a text file containing a list of sequence{tab}title{enter} in the installation directory/settings folder with the suffix _bpc.txt. When you open list bank, it scans this directory for use defined files and will create a button for each detected list.
- Click edit again to toggle to peptide select mode.
- Clicking standards will load the file PeptideStandards.txt from the mzStudio directory. This is a handy place to store masses for commonly used laboratory peptides like angiotensin.
This is a list of pre-defined post-translational modifications that the mzPepCalc recognizes. For example, caC corresponds to carbamidomethyl cysteine, pS to phosphoserine, and oxM to oxidized methionine. These modifications are currently stored in a text file in the mzStudio installation directory with the path /mz_workbench/files/new_res_list.txt. Individual entries can be edited by double clicking the entry. In addition, entries can be added (New), removed (Delete) and saved (Save). Note, before new modifications are recognized, the mzStudio must be restarted.
From mzPepCalc, it is also possible to display XICs and locate specific product ion spectra. Clicking on a specific calculated charge state displays a window:
- XIC will display an XIC for the specified mz and tolerance
- ‘Find Precursors’ will find MS2 spectra performed on precursors of the specified mz and tolerance.
- Right click in the popup window to close it.