Structure and reactivity of a(n) and a(n) peptide fragments investigated using isotope labeling, tandem mass spectrometry, and density functional theory calculations.
Extensive (15)N labeling and multiple-stage tandem mass spectrometry were used to investigate the fragmentation pathways of the model peptide FGGFL during low-energy collision-induced-dissociation (CID) in an ion-trap mass spectrometer. Of particular interest was formation of a(4) from b(4) and a(4) (a(4)-NH(3)) from a(4) ions correspondingly, and apparent rearrangement and scrambling of peptide sequence during CID. It is suggested that the original FGGF(oxa)b(4) structure undergoes b-type scrambling to form GGFF(oxa). These two isomers fragment further by elimination of CO and (14)NH(3) or (15)NH(3) to form the corresponding a(4)and a(4) isomers, respectively. For ((15)N-F)GGFL and FGG((15)N-F)L the a(4) ion population appears as two distinct peaks separated by 1 mass unit. These two peaks could be separated and fragmented individually in subsequent CID stages to provide a useful tool for exploration of potential mechanisms along the a(4) --> a(4) pathway reported previously in the literature (Vachet et al. J. Am. Chem. Soc.1997, 119, 5481, and Cooper et al. J. Am. Soc. Mass Spectrom.2006, 17, 1654). These mechanisms result in formally the same a(4) structures but differ in the position of the expelled nitrogen atom. Detailed analysis of the observed fragmentation patterns for the separated light and heavy a(4) ion fractions of ((15)N-F)GGFL indicates that the mechanism proposed by Cooper et al. is consistent with the experimental findings, while the mechanism proposed by Vachet et al. cannot account for the labeling data. In addition, a new rearrangement pathway is presented for a(4)-CO ions that effectively transfers the former C-terminal amino acid residue to the N-terminus.
Bythell
Benjamin J
BJ
Department of Molecular Biophysics, German Cancer Research Center, Heidelberg, Germany.
Molesworth
Samuel
S
Osburn
Sandra
S
Cooper
Travis
T
Paizs
Béla
B
Van Stipdonk
Michael
M
D000595:Amino Acid Sequence; D007477:Ions; D008958:Models, Molecular; D015394:Molecular Structure; D009587:Nitrogen Isotopes; D009842:Oligopeptides / Q000737:chemistry; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D053719:Tandem Mass Spectrometry; D013816:Thermodynamics
D007477:Ions; D009587:Nitrogen Isotopes; D009842:Oligopeptides; D010446:Peptide Fragments
Anal Chem. 1993 Oct 15;65(20):2824-34
7504416
Rapid Commun Mass Spectrom. 2000;14(9):746-55
10825012
J Mass Spectrom. 2000 Dec;35(12):1399-406
11180630
Biomed Mass Spectrom. 1984 Nov;11(11):601
6525415
J Phys Chem A. 2008 Feb 14;112(6):1286-93
18215025
J Am Soc Mass Spectrom. 2004 Jan;15(1):103-13
14698560
J Am Chem Soc. 2006 Aug 16;128(32):10364-5
16895391
Biomed Environ Mass Spectrom. 1988 Oct;16(1-12):99-111
3072035
Proc Natl Acad Sci U S A. 1986 Sep;83(17):6233-7
3462691
Rapid Commun Mass Spectrom. 2002;16(5):375-89
11857721
Anal Chem. 1993 Jun 1;65(11):1594-601
8328675
Mass Spectrom Rev. 2005 Jul-Aug;24(4):508-48
15389847
J Am Soc Mass Spectrom. 2008 Dec;19(12):1755-63
18799320
J Am Chem Soc. 2007 May 9;129(18):5887-97
17428052
J Am Soc Mass Spectrom. 2004 Dec;15(12):1810-9
15589757
J Am Soc Mass Spectrom. 2007 Jul;18(7):1291-303
17531501
J Am Soc Mass Spectrom. 2006 Dec;17(12):1654-64
16934997
Nat Rev Mol Cell Biol. 2004 Sep;5(9):699-711
15340378
J Am Chem Soc. 2008 Dec 31;130(52):17774-89
19055406
Anal Chem. 2000 Dec 1;72(23):5804-13
11128940
J Mass Spectrom. 2000 Dec;35(12):1391-8
11180629
J Am Soc Mass Spectrom. 2008 Apr;19(4):609-13
18313327
Rapid Commun Mass Spectrom. 2002;16(6):566-78
11870894
J Am Soc Mass Spectrom. 1998 Apr;9(4):341-4
9879364
J Am Chem Soc. 2005 Dec 14;127(49):17154-5
16332041
J Am Soc Mass Spectrom. 1995 Dec;6(12):1165-74
24214067
J Am Soc Mass Spectrom. 1996 Mar;7(3):233-42
24203294
Nat Methods. 2007 Oct;4(10):787-97
17901868