title: Evidence for sequence scrambling in collision-induced dissociation of y-type fragment ions.
abstract: Sequence scrambling from y-type fragment ions has not been previously reported. In a study designed to probe structural variations among b-type fragment ions, it was noted that y fragment ions might also yield sequence-scrambled ions. In this study, we examined the possibility and extent of sequence-scrambled fragment ion generation from collision-induced dissociation (CID) of y-type ions from four peptides (all containing basic residues near the C-terminus) including: AAAAHAA-NH2 (where "A" denotes carbon thirteen ((13)C1) isotope on the alanine carbonyl group), des-acetylated-α-melanocyte (SYSMEHFRWGKPV-NH2), angiotensin II antipeptide (EGVYVHPV), and glu-fibrinopeptide b (EGVNDNEEGFFSAR). We investigated fragmentation patterns of 32 y-type fragment ions, including y fragment ions with different charge states (+1 to +3) and sizes (3 to 12 amino acids). Sequence-scrambled fragment ions were observed from ~50 % (16 out of 32) of the studied y-type ions. However, observed sequence-scrambled ions had low relative intensities from ~0.1 % to a maximum of ~12 %. We present and discuss potential mechanisms for generation of sequence-scrambled fragment ions. To the best of our knowledge, results on y fragment dissociation presented here provide the first experimental evidence for generation of sequence-scrambled fragments from CID of y ions through intermediate cyclic "b-type" ions.
authors: Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA.
authors: Mahsan
authors: M
authors: Miladi
authors: Brett
authors: B
authors: Harper
authors: Touradj
authors: T
authors: Solouki
mesh_terms: D000595:Amino Acid Sequence; D007477:Ions; D013058:Mass Spectrometry; D009842:Oligopeptides / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry / Q000302:isolation & purification*; D010455:Peptides / Q000737:chemistry*; D000521:alpha-MSH / Q000737:chemistry*
chemical_list: D007477:Ions; D009842:Oligopeptides; D010446:Peptide Fragments; D010455:Peptides; C073965:glutamyl-glycyl-valyl-tyrosyl-valyl-histidyl-prolyl-valine; D000521:alpha-MSH
references: J Am Soc Mass Spectrom. 2009 Feb;20(2):334-9
references: 19013079
references: Rapid Commun Mass Spectrom. 1992 Nov;6(11):651-7
references: 1467549
references: J Am Soc Mass Spectrom. 2011 Jul;22(7):1121-4
references: 21953093
references: Anal Chem. 1993 Oct 15;65(20):2824-34
references: 7504416
references: J Am Chem Soc. 2009 Aug 19;131(32):11503-8
references: 19637928
references: Biomed Mass Spectrom. 1984 Nov;11(11):601
references: 6525415
references: J Am Soc Mass Spectrom. 1996 Mar;7(3):233-42
references: 24203294
references: Chemphyschem. 2009 Apr 14;10(6):883-5
references: 19253930
references: J Phys Chem B. 2010 Nov 25;114(46):15092-105
references: 20973555
references: J Am Chem Soc. 2009 Dec 9;131(48):17528-9
references: 19904982
references: Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9528-33
references: 15210983
references: J Am Soc Mass Spectrom. 2009 Apr;20(4):618-24
references: 19109036
references: Mol Cell Proteomics. 2005 Jun;4(6):835-45
references: 15772112
references: J Am Soc Mass Spectrom. 2010 Dec;21(12):2085-94
references: 20947370
references: Mass Spectrom Rev. 2005 Jul-Aug;24(4):508-48
references: 15389847
references: J Am Soc Mass Spectrom. 2008 Dec;19(12):1771-5
references: 18848466
references: Angew Chem Int Ed Engl. 2012 Jun 25;51(26):6436-8
references: 22615257
references: J Am Soc Mass Spectrom. 2008 Apr;19(4):609-13
references: 18313327
references: Chirality. 1999;11(8):651-8
references: 10467317
references: Anal Chem. 2006 Apr 1;78(7):2113-20
references: 16579588
references: J Am Chem Soc. 2005 Dec 14;127(49):17154-5
references: 16332041
references: J Am Soc Mass Spectrom. 1995 Dec;6(12):1165-74
references: 24214067
references: J Am Soc Mass Spectrom. 2008 Dec;19(12):1781-7
references: 18930410
references: Chem Rev. 2007 Aug;107(8):3568-84
references: 17645314
references: Anal Chem. 2003 Mar 15;75(6):1524-35
references: 12659218
references: Anal Chem. 2002 Oct 1;74(19):4889-94
references: 12380809
references: Anal Chem. 2004 Apr 1;76(7):2083-94
references: 15053674
references: J Am Soc Mass Spectrom. 2010 Aug;21(8):1313-21
references: 20236836
references: Rapid Commun Mass Spectrom. 1994 Sep;8(9):678-86
references: 7524806
references: Nat Methods. 2004 Dec;1(3):195-202
references: 15789030
references: J Phys Chem A. 2008 Feb 14;112(6):1286-93
references: 18215025
references: J Am Soc Mass Spectrom. 2010 Mar;21(3):358-69
references: 20005740
references: Proteomics. 2006 Oct;6(19):5117-31
references: 16955515
references: J Mass Spectrom. 1996 Nov;31(11):1237-43
references: 8946732
references: J Am Chem Soc. 2006 Aug 16;128(32):10364-5
references: 16895391
references: J Am Chem Soc. 2010 Oct 27;132(42):14766-79
references: 20925356
references: Mol Cell Proteomics. 2004 Jan;3(1):1-9
references: 14608001
references: Anal Chem. 2003 May 1;75(9):1963-71
references: 12720328
references: Anal Chem. 1994 Sep 15;66(18):2809-15
references: 7526742
references: Methods. 2011 Aug;54(4):424-31
references: 21277371
references: J Am Chem Soc. 2008 Dec 31;130(52):17644-5
references: 19061412
references: J Am Chem Soc. 2009 Dec 30;131(51):18272-82
references: 19947633
references: J Am Soc Mass Spectrom. 2008 Dec;19(12):1776-80
references: 18639467
references: J Am Soc Mass Spectrom. 2010 Aug;21(8):1352-63
references: 20541953
references: J Proteome Res. 2009 Jun;8(6):3141-7
references: 19368407