The name of the protein to be used in the mapping. This is an optional field, as the name is not a necessary input and is only present for the user's convenience.

The sequence of the protein to be used in the mapping. To specify an amino acid sequence the one letter codes for the amino acids should be used. All non-letter characters will be ignored except for '/' and '\' which will be interpreted as the end of a peptide chain.

Examples:

A single peptide chain:

MNYLRRRLSDSNFMANLPNGYMTDLQRPQPPPPPPAAPSPGATTGPATATAERASSAAP

or
      1    *   10    *    20    *   30    *    40    *   50
    1 MNYLRRRLSDSNFMANLPNGYMTDLQRPQPPPPPPAAPSPGATTGPATAT
   51 AERASSAAP

Note: The numbers are only for your convenience, the chains will always be considered as starting at 1.

A pre-defined enzyme to be used in the digestion can be selected here. The following table indicates the meanings of the enzyme names in the drop-down list box.

Name	Cleave at	Don't Cleave at	Terminal	Modification
Trypsin	KR	P	C	none

The maximum number of missed cleavages that are to be allowed for this enzyme in the digestion.

Complete global modifications add the corresponding modification formula to every occurence of the specified amino acid(s). To select more than one, hold the control key down while clicking on your choices. The following table indications the meanings of the modification names in the list box.

Name	Site(s)	Formula
4-vinyl-pyridine (Cys)	C	+C7H7N
Acrylamide (Cys)	C	+C3H5ON
Iodoacetamide (Cys)	C	+C2H3ON
Iodoacetic acid (Cys)	C	+C2H2O2
Performic acid (Cys+O3)	C	+O3
Performic acid (Met+O2)	M	+O2
Performic acid (Met+O)	M	+O

Partial global modifications add the corresponding modification formula to 0 or more (up to the total number of occurences) occurences of the specified amino acid(s). To select more than one, hold the control key down while clicking on your choices. The following table indications the meanings of the modification names in the list box

Name	Site(s)	Formula
4-vinyl-pyridine (Cys)	C	+C7H7N
Acrylamide (Cys)	C	+C3H5ON
Iodoacetamide (Cys)	C	+C2H3ON
Iodoacetic acid (Cys)	C	+C2H2O2
Performic acid (Cys+O3)	C	+O3
Performic acid (Met+O2)	M	+O2
Performic acid (Met+O)	M	+O

If MH+ is selected, the mass of H is subtracted from each mass before the comparison; if M is selected, the masses are not changed.

In this section, enter the average and monoisotopic masses to be mapped to the protein, the error tolerance of these masses, and the charge state of the masses.

Enter the error range for the corresponding masses. You can enter an error for both the monoisotopic and average masses. There are three choices for the units: Daltons (Da), percent (%) and parts-per-million (ppm).

The maximum number of free sulfhdryls allowed in a result model.

The maximum number of peptide fragments combined to create a result model.

The maximum number of cross link attachments in a result model.