Description, Instructions, and Tips for MS-Comp

Instructions for ProteinProspector Programs

Contents of this document:

• Combination Type
• Ion Types
• Nitrogen Rule
• Double Bond Equivalent

• Search Times
• General features of links from program output
• Link from the peptide sequence in program output to MS-Product
• Link from the elemental composition in program output to MS-Isotope
• Modified N or C Terminal Groups
• Modified Cysteine Residues
• User Specified Amino Acid
• Mass (m/z)
• Mass type
• Charge (z)
• AA Composition Ions
• Absent Amino Acids
• Modified Amino Acids Possibly Present
• Instrument

Combination Type

Peptide Elemental
Lists the unique elemental compositions from the list of amino acid combinations reported by the Amino Acid option.

Elemental
Lists the elemental compositions consistent with the search conditions. The elemental compositions returned will obey the nitrogen rule and will have a double bond equivalent within the range expected for a peptide. The elemental compositions are, however, not guaranteed to have corresponding peptides. This option will work at much higher mass than the first two options.

Ion Types

Nitrogen Rule

The nitrogen rule stems from the fact that most of the common elements that have even nominal masses have even valence:

¹²C, valence = 4;
¹⁶O, valence = 2;
²⁸Si, valence = 4;
³²S, valence = 2.

On the other hand most of the elements with odd nominal masses have odd valence:

¹H, valence = 1;
¹⁹F, valence = 1;
³¹P, valence = 3;
³⁵Cl, valence = 1.

Nitrogen is an exception in that it has an even nominal mass but an odd valence:

¹⁴N, valence = 3.

Double Bond Equivalent

DBE = 1 - a/2 + c/2 + d

where:

a = number of atoms with a valence of 1 (H, F, Cl).

b = number of atoms with a valency of 2 (O, S).

c = number of atoms with a valency of 3 (N, P).

d = number of atoms with a valency of 4 (C, Si).

If the value calculated ends in 0.5 then this should be subtracted to get the true value.

Amino Acid	DBE	Elemental Formula	Calculation
A	1.0	C3 H5 N1 O1	3 - 5/2 + 1/2
C	1.0	C3 H5 N1 O1 S1	3 - 5/2 + 1/2
D	2.0	C4 H5 N1 O3	4 - 5/2 + 1/2
E	2.0	C5 H7 N1 O3	5 - 7/2 + 1/2
F	5.0	C9 H9 N1 O1	9 - 9/2 + 1/2
G	1.0	C2 H3 N1 O1	2 - 3/2 + 1/2
H	4.0	C6 H7 N3 O1	6 - 7/2 + 3/2
I	1.0	C6 H11 N1 O1	6 - 11/2 + 1/2
K	2.0	C6 H12 N2 O1	6 - 12/2 + 2/2
L	3.0	C6 H11 N1 O1	6 - 11/2 + 1/2
M	1.0	C5 H9 N1 O1 S1	5 - 9/2 + 1/2
N	3.0	C4 H6 N2 O2	4 - 6/2 + 2/2
P	2.0	C5 H7 N1 O1	5 - 7/2 + 1/2
Q	3.0	C5 H8 N2 O2	5 - 8/2 + 2/2
R	2.0	C6 H12 N4 O1	6 - 12/2 + 4/2
S	1.0	C3 H5 N1 O2	3 - 5/2 + 1/2
T	1.0	C4 H7 N1 O2	4 - 7/2 + 1/2
V	1.0	C5 H9 N1 O1	5 - 9/2 + 1/2
W	8.0	C11 H10 N2 O1	11 - 10/2 + 2/2
Y	5.0	C9 H9 N1 O2	9 - 9/2 + 1/2

The terminal groups and cation then contribute H3 O to the overall elemental formula reducing the DBE by 1.5. Also there is one to add on from the original formula.