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Combined Electron Transfer Dissociation−Collision-Induced Article pubs.acs.org/jpr Combined Electron Transfer Dissociation−Collision-Induced Dissociation Fragmentation in the Mass Spectrometric Distinction of Leucine, Isoleucine, and Hydroxyproline Residues in Peptide Natural Products Kallol Gupta,† Mukesh Kumar,‡ Krishnappa Chandrashekara,§ Kozhalmannom S. Krishnan,‡ and Padmanabhan Balaram*,† † Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India ‡ National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India § Department of Entomology, University of Agricultural Sciences, GKVK, Bangalore 560065, India *S Supporting Information ABSTRACT: Distinctions between isobaric residues have been a major challenge in mass spectrometric peptide sequencing. Here, we propose a methodology for distinction among isobaric leucine, isoleucine, and hydroxyproline, a commonly found post-translationally modified amino acid with a nominal mass of 113 Da, through a combined electron transfer dissociation−collision-induced dissociation approach. While the absence of c and z• ions, corresponding to the Yyy-Xxx (Xxx = Leu, Ile, or Hyp) segment, is indicative of the presence of hydroxyproline, loss of isopropyl (Δm =43 Da) or ethyl radicals (Δm = 29 Da), through collisional activation of z radical ions, are characteristic of leucine or isoleucine, respectively. Radical migration processes permit distinctions even in cases where the specific z• ions, corresponding to the Yyy−Leu or −Ile segments, are absent or of low intensity. This tandem mass spectrometric (MSn) method has been successfully implemented in a liquid chromatography−MSn platform to determine the identity of 23 different isobaric residues from a mixture of five different peptides. The approach is convenient for distinction of isobaric residues from any crude peptide mixture, typically encountered in natural peptide libraries or proteomic analysis. KEYWORDS: isobaric amino acids, electron transfer dissociation, z• ions, collision-induced dissociation, peptaibols, Conus peptides, wasp venom peptides ■ INTRODUCTION isoleucine (residue mass of 113.16 Da).12,23 Further, in many Rapid advances in gas phase fragmentation methodologies, such peptide natural products, post-translational modification of as collision-induced dissociation (CID), electron capture proline residues by hydroxylation leads to the presence of hydroxyproline (Hyp, O), having a residue mass of 113.12 dissociation (ECD), and electron transfer dissociation (ETD), 24 have made mass spectrometry the method of choice for Da. The distinctions among Leu, Ile, and Hyp are often not − determining peptide sequences.1 6 Online liquid chromatog- routine. Hydroxyproline may be distinguished from Leu and Ile raphy−tandem mass spectrometry (LC−MS/MS) procedures by high-resolution mass determination, which requires a mass 23 − are particularly attractive for determining sequences of accuracy of 0.04 Da. Xxx Hyp bonds are often more individual components in complex peptide mixtures, most susceptible to cleavage under CID conditions, giving rise to − frequently encountered in proteomic analysis.7 10 These intense fragment ions that may prove to be useful only in methods have also been extremely valuable in the character- specific cases. The distinctions between Leu and Ile residues ization of peptide mixtures from natural sources.11,12 While the have usually been achieved via high-energy CID (HE-CID) with characteristic neutral losses involving cleavage of the Cβ− conventional CID technique largely yields b and y ions through γ 25−28 C(O)NH amide bond cleavage, fragmentation initiated through C bonds. Under HE-CID conditions, fragmentation of electron capture (ECD/ETD) of the peptide polycation leads different side chains as well as backbone peptide bonds typically to the dissociation of the N−Cα bond, typically generating even gives rise to a complex MS/MS spectrum. The diagnostic − electron c and odd electron z• ions.13 22 Afrequently encountered problem in mass spectral peptide sequencing is Received: January 31, 2011 the need to distinguish between the isobaric residue leucine and Published: November 24, 2011 © 2011 American Chemical Society 515 dx.doi.org/10.1021/pr200091v | J. Proteome Res. 2012, 11, 515−522 Journal of Proteome Research Article fragment ions are often found to be of low intensity, making formic acid (zervamicin IIB and antiameobin II were dissolved assignments ambiguous. Also, under HE-CID conditions, facile in 100% MeOH, containing 0.1% formic acid, and the solutions loss of any acid labile post-translational modification makes the were directly infused into the mass spectrometer), were process of assignment even more difficult. Marshall and co- injected into the mass spectrometer typically at a flow rate of workers have shown extensive characteristic side chain losses of 2 μL/min using an injector pump. The tandem mass different amino acids in ECD spectra, near the precursor m/z spectrometric (MSn) experiments in the direct infusion study region.29 Further, side chain losses from specific radical z• ions were performed manually. After observation of the desired have been shown by Zubarev and co-workers in the hot multiply charged precursor in MS, the precursor ion was electron capture dissociation (HECD) spectra of peptide manually chosen for ETD fragmentation. The ETD reaction polycations.30 The processes of radical migration and radical- time was set at 75 ms for zervamicin and antiamoebin, 85 ms mediated secondary fragmentation have been probed by for Bt2328 and Vt1512, and 100 ms for melittin. All the ETD O’Connor and co-workers through ECD of diprotonated cyclic MS2 experiments were performed using “smart decomposition” peptides.31 Observation of extensive side chain losses and (supplemental activation) that provides a low-background neutral amino acid residues has been explained in terms of a collision gas to increase the product ion abundances through “cascade of free radical reaction” that is initiated from the probable dissociation of the noncovalent bonds (see Dis- precursor where one radical center has been created through cussion). From the MS2 ETD spectra, desired precursor ions the transfer of one electron. Further studies with peptides were subsequently chosen for CID MS3 fragmentation inside containing α-deuterated glycine residues provide experimental the ion trap through collision with He gas. The fragmentation evidence of α-hydrogen abstraction during the process of amplitude (V − ) was kept between 1 and 3. All the p p − radical migration along the peptide backbone.32 A similar experiments were conducted at a scan speed of 8100 m/z s 1. radical nature of the z• ions, formed during ETD The spectra were averaged over 6−10 scans. For LC−MSn fragmentation, has been established by McLuckey and co- analysis, these peptides (5 μL each) were mixed together. The workers through the observation of an oxygen adduct and more LC−MS analysis was performed by coupling the mentioned ion recently through collisional activation of the z• ions.33,34 Using trap mass spectrometer with an Agilent 1100 HPLC system and hot electrons during electron capture dissociation (HECD), the peptide samples were separated on a reverse phase C18 radical-mediated backbone cleavages have been shown to be analytical column (Porshell 120, SB-C18, particle size of 2.7 35,36 μ × useful in effecting the distinction of Leu from Ile, but the m, dimensions of 4.6 mm 150 mm) using a H2O/ technical difficulties in implementing ECD in mass spectrom- acetonitrile mixture (0.1% formic acid) as the solvent system at eters other than FT-ICR MS limit the application of this a flow rate of 0.2 mL/min. The gradient was set from 90% H2O method. McLuckey and co-workers have established that to 100% ACN over 45 min in a linear gradient. The LC−MSn fragment ions obtained under ETD conditions may then be experiments were performed in a data-independent manner. subjected to further CID (ETD−CID) fragmentation for the Before the start of the LC run, the total run time was divided observation of side chain specific losses through radical-induced into different segments as per the retention times of the five cleavages, in a QTRAP instrument, using synthetic model peptides used. In these individual segments, the m/z values of sequences.34 Under conditions of electron transfer dissocia- the precursor ions to be chosen for MS2/MS3 experiments were manually inserted into the acquisition software. During the tion/electron capture dissociation (ETD/ECD) fragmentation, − cleavage of the N−Cα bond at the Pro residue does not lead to LC−MSn study, the scan speed was set to 26000 m/z s 1, and the formation of characteristic c and z• ions due to the typically, the spectra were averaged over three to five scans. The constraints of side chain backbone cyclization in the pyrrolidine ETD reaction time was set at 75 ms for zervamicin and ring.17 The absence of such diagnostic ions can be used to antiamoebin, 85 ms for Bt2328 and Vt1512, and 100 ms for signal the presence of Pro or Hyp residues. Herein, we present melittin. In this case also, smart decomposition (supplemental an extension of these approaches to several peptides of natural activation) was used while acquiring the ETD MS2 spectra. origin containing multiple Leu, Ile, and Hyp residues and Subsequent CID fragmentation was conducted inside the ion further demonstrate the applicability of this method in effective trap through the collision of He gas with the ions of interest. distinction among these
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