886
APPENDIXES
[A5]
For example, for CI2Br, a = 3, b = 1, n = 2, d -~ 1, e = 1, m = 1. Therefore, (a + b) 2 x (d + e) = a2d + 2abd + b2d + a2e + 2abe + b2e. Combination of the terms in the expansion which corresponds to equivalent nominal mass values (0, I, 2 . . . occurrences of a heavy isotope), and substitution of the numerical values for a, b, d, and e, yields the approximate abundance ratio 9 : 15 : 7 : 1. To include contributions from C, N, O, etc., in such cases, the principal isotope peaks (9, 15, 7, and 1 abundance units in the preceding example) can each be treated as "all-light" isotopic species and contributions from 13C, etc., calculated relative to each of those peaks using Eqs. (6) and (7). For example, for dichlorobromobenzene (C6H3C12Br) each of the principal halogen isotope peaks (separated by 2 u) would be accompanied by a first isotope peak due to 13C of (6 x 1.1)%, giving the approximate pattern 9 : 0.60 : 15 : 1.0 : 7 : 0.47 : 1 : 0.07, with each species separated by I u.
A p p e n d i x 5. N o m e n c l a t u r e for P e p t i d e F r a g m e n t I o n s ( P o s i t i v e Ions)*
By
KLAUS BIEMANN
For further discussion of peptide ion nomenclature, see Refs. 1 and 2. N-terminal Ions +
an: H - - ( N H - - C H R - - C O ) n - I - - N H = C H R ~ or
H+
CRnaRnb
H---)(NH--CHR--CO)',_ , - - N H - - C H H+ a n + 1:
b n:
I~,
H--I(NH--CHR--CO)In-I--NH--CH-
H--(NH--CHR--CO)n-I--NH--CHRn--C~---O ÷ n +
cn: H-2(NH--CHR--CO)~n--NH2 * R represents the side chains of the amino acids; Rna and Rnb are the beta substituents of the nth amino acid. 1 p. Roepstorff and J. Fohlman, Biomed. M a s s Spectrom. 11, 601 (1984). 2 K. Biemann, B i o m e d . Environ. M a s s Spectrom. 16, 99 (1988).
METHODS IN ENZYMOLOGY,VOL. 193
Copyright © 1990by Academic Press, Inc. All rightsof reproduction in any form reserved.
[A5]
NOMENCLATURE FOR PEP'rIDE FRAGMENT IONS
H+
887
CRnb
II
dn: H--tNH--CHR--CO],_ ~--NH--CH C-terminal Ion T y p e s H+ vn: HN=CH--CO----~(NH--CHR--CO)'n-~--OU CRnb
H+
II
w n: Xn:
,
,
CH--CO--(NH--CHR--CO)~-I--OH +O~C--NH--CHR~--CO--(NH--CHR--CO)._ 1--OH OF
H+ I I O = C = N - - C H R . - - C O - - ( N H - - C H R - - C O ) . _ j--OH H+ y~: H--'(NH--CHR--CO)~n--OH H+ y,, - 2: ~HN~CR,,--CO--(NH--CHR--CO)I,,-~--OH CR,,'~R,?
II
H÷
,
,
z,,: CH--CO--(NH--CHR--CO),,_ l--OH
Zn +
1:
H÷ • CHR~--CO--INH--CHR--CO)'~-l--OH N o n - S e q u e n c e Specific Ions
I n t e r n a l a c y l ions ( d e n o t e d b y single letter codes) (e.g., G A at m/z 129 for R = H , CH3): H2N--CHR--CO--NH--CHR--C~_O +
Internal immonium ions (denoted by single-letter code followed by the notation - 28): +
HEN--CHR--CO--NH--CHR
Amino acid immonium ions (denoted by single letter code) (e.g., F at m / z 120 f o r R = C6HsCH2): +
HEN==CHR
Loss of amino acid side chains from (M + H) + is denoted as the single letter c o d e o f the amino acid involved, preceded b y a minus sign (e.g., -Vfor[M
+ H - 43] +).
APPENDIXES
[A5]
For example, for CI2Br, a = 3, b = 1, n = 2, d -~ 1, e = 1, m = 1. Therefore, (a + b) 2 x (d + e) = a2d + 2abd + b2d + a2e + 2abe + b2e. Combination of the terms in the expansion which corresponds to equivalent nominal mass values (0, I, 2 . . . occurrences of a heavy isotope), and substitution of the numerical values for a, b, d, and e, yields the approximate abundance ratio 9 : 15 : 7 : 1. To include contributions from C, N, O, etc., in such cases, the principal isotope peaks (9, 15, 7, and 1 abundance units in the preceding example) can each be treated as "all-light" isotopic species and contributions from 13C, etc., calculated relative to each of those peaks using Eqs. (6) and (7). For example, for dichlorobromobenzene (C6H3C12Br) each of the principal halogen isotope peaks (separated by 2 u) would be accompanied by a first isotope peak due to 13C of (6 x 1.1)%, giving the approximate pattern 9 : 0.60 : 15 : 1.0 : 7 : 0.47 : 1 : 0.07, with each species separated by I u.
A p p e n d i x 5. N o m e n c l a t u r e for P e p t i d e F r a g m e n t I o n s ( P o s i t i v e Ions)*
By
KLAUS BIEMANN
For further discussion of peptide ion nomenclature, see Refs. 1 and 2. N-terminal Ions +
an: H - - ( N H - - C H R - - C O ) n - I - - N H = C H R ~ or
H+
CRnaRnb
H---)(NH--CHR--CO)',_ , - - N H - - C H H+ a n + 1:
b n:
I~,
H--I(NH--CHR--CO)In-I--NH--CH-
H--(NH--CHR--CO)n-I--NH--CHRn--C~---O ÷ n +
cn: H-2(NH--CHR--CO)~n--NH2 * R represents the side chains of the amino acids; Rna and Rnb are the beta substituents of the nth amino acid. 1 p. Roepstorff and J. Fohlman, Biomed. M a s s Spectrom. 11, 601 (1984). 2 K. Biemann, B i o m e d . Environ. M a s s Spectrom. 16, 99 (1988).
METHODS IN ENZYMOLOGY,VOL. 193
Copyright © 1990by Academic Press, Inc. All rightsof reproduction in any form reserved.
[A5]
NOMENCLATURE FOR PEP'rIDE FRAGMENT IONS
H+
887
CRnb
II
dn: H--tNH--CHR--CO],_ ~--NH--CH C-terminal Ion T y p e s H+ vn: HN=CH--CO----~(NH--CHR--CO)'n-~--OU CRnb
H+
II
w n: Xn:
,
,
CH--CO--(NH--CHR--CO)~-I--OH +O~C--NH--CHR~--CO--(NH--CHR--CO)._ 1--OH OF
H+ I I O = C = N - - C H R . - - C O - - ( N H - - C H R - - C O ) . _ j--OH H+ y~: H--'(NH--CHR--CO)~n--OH H+ y,, - 2: ~HN~CR,,--CO--(NH--CHR--CO)I,,-~--OH CR,,'~R,?
II
H÷
,
,
z,,: CH--CO--(NH--CHR--CO),,_ l--OH
Zn +
1:
H÷ • CHR~--CO--INH--CHR--CO)'~-l--OH N o n - S e q u e n c e Specific Ions
I n t e r n a l a c y l ions ( d e n o t e d b y single letter codes) (e.g., G A at m/z 129 for R = H , CH3): H2N--CHR--CO--NH--CHR--C~_O +
Internal immonium ions (denoted by single-letter code followed by the notation - 28): +
HEN--CHR--CO--NH--CHR
Amino acid immonium ions (denoted by single letter code) (e.g., F at m / z 120 f o r R = C6HsCH2): +
HEN==CHR
Loss of amino acid side chains from (M + H) + is denoted as the single letter c o d e o f the amino acid involved, preceded b y a minus sign (e.g., -Vfor[M
+ H - 43] +).
