Commands:
Window > Residue Library
The command Window > Residue Library displays the Residue Library Window. The residue library stores the amino acid and modified amino acid symbols, masses and descriptors and allows to define peptide termini. This is the place where the type of fragment ions that are displayed in Sequence Views are defined.
All the information is saved in a residue library file. A saved residue library file is copied to the Arcadiate database file location. The copied version of the file is the actually used one (see command File > Show in Finder)
The window has four sections: Standard Amino Acids, Modified Amino Acids, Termini and Fragment Ion Series. Separate residue libraries can be saved and opened.
Standard Amino Acids: The Standard Amino Acid page defines the standard residues, their names, short codes, average and mono-isotopic masses.
Modified Amino Acids: The Modified Amino Acids page defines modified residues that are based on standard residues. The descriptor of a modified amino acid is the precise text which is used in the output file of database search programmes to describe a modified amino acid. When importing database search files modified amino acid codes are inserted into the peptide sequence based on these descriptors when the option "Insert Modified Amino Acid Code when importing Sequences" in the Arcadiate Preferences is selected (see command Aracdiate > Preferences..., tab Miscellaneous).
Termini: The Termini page defines left and right terminus of the sequences (for amino acids, the N- and C-terminus).
Fragment Ion Series: The Fragment Ion Series page defines which fragment ions will be displayed in the sequence view tables, whether the masses are mono-isotopic or average, their charge state and the polarity.