Electron transfer dissociation mass spectrometry of peptides containing free cysteine using group XII metals as a charge carrier

Use of group IIB metal ions as charge carriers for collision-induced dissociation of glycopeptide and glycan

RATIONALE

Dissociation of biomolecules by tandem mass spectrometry (MS/MS) generates a variety of fragment ions which provide useful information for the structural characterization of biomolecules. Different fragmentation strategies result in different mass spectra for the same molecule and thus provide distinct features. Charge carriers play important roles in determining the dissociation pathways of the target precursor ions. The use of various transition metals ions as charge carriers of glycopeptide and glycan might provide additional structural information and needs to be investigated.

METHODS

A 9.4 T SolariX FTICR mass spectrometer was used for collision-induced dissociation (CID) of glycopeptide and glycan. Group IIB metal ions, including Zn²⁺ , Cd²⁺ and Hg²⁺ , were used as charge carriers. Glycopeptide NLTK-M₅ G₂ and glycan G1F were used as the model systems.

RESULTS

For Zn²⁺ - and Cd²⁺ -adducted species, cross-ring cleavages, glycosidic cleavages and cleavages along the peptide backbone could be obtained. There is a high degree of similarity in their CID spectra with that of Mg²⁺ ion-adducted glycopeptide species. For Hg²⁺ -adducted species, only glycosidic cleavages were observed in high abundance. The formation of doubly-charged ions (M²⁺ ) and a series of [f-H]⁺ fragments indicated unique dissociation pathways for Hg²⁺ -adducted glycopeptide.

CONCLUSIONS

Zn²⁺ and Cd²⁺ -adducted glycopeptide species produced similar dissociation CID spectra, whereas Hg²⁺ -adducted species produced significantly different CID spectra. Similar CID dissociation features were also observed for Group IIB metal ions adducted glycan species. These results demonstrated that different metal ions might be used to tune the dissociation behaviors of glycopeptides and glycans.

w-Type ions formed by electron transfer dissociation of Cys-containing peptides investigated by infrared ion spectroscopy

In mass spectrometry-based peptide sequencing, electron transfer dissociation (ETD) and electron capture dissociation (ECD) have become well-established fragmentation methods complementary to collision-induced dissociation. The dominant fragmentation pathways during ETD and ECD primarily involve the formation of c- and z^• -type ions by cleavage of the peptide backbone at the N─C_α bond, although neutral losses from amino acid side chains have also been observed. Residue-specific neutral side chain losses provide useful information when conducting database searching and de novo sequencing. Here, we use a combination of infrared ion spectroscopy and quantum-chemical calculations to assign the structures of two ETD-generated w-type fragment ions. These ions are spontaneously formed from ETD-generated z^• -type fragments by neutral loss of 33 Da in peptides containing a cysteine residue. Analysis of the infrared ion spectra confirms that these z^• -ions expel a thiol radical (SH^• ) and that a vinyl C═C group is formed at the cleavage site. z^• -type fragments containing a Cys residue but not at the cleavage site do not spontaneously expel a thiol radical, but only upon additional collisional activation after ETD.

Electron transfer dissociation mass spectrometry of acidic phosphorylated peptides cationized with trivalent praseodymium

The lanthanide ion praseodymium, Pr(III), was employed to study metallated ion formation and electron transfer dissociation (ETD) of 27 biological and model highly acidic phosphopeptides. All phosphopeptides investigated form metallated ions by electrospray ionization (ESI) that can be studied by ETD to yield abundant sequence information. The ions formed are [M + Pr - H]²⁺ , [M + Pr]³⁺ , and [M + Pr + H]⁴⁺ . All biological phosphopeptides with a chain length of seven or more residues generate [M + Pr]³⁺ . For biological phosphopeptides, [M + Pr]³⁺ undergoes more backbone cleavage by ETD than [M + Pr - H]²⁺ and, in some cases, full sequence coverage occurs. Acidic model phosphorylated hexa-peptides and octa-peptides, composed of alanine residues and one phosphorylated residue, form exclusively [M + Pr - H]²⁺ by ESI. Limited sequence information is obtained by ETD of [M + Pr - H]²⁺ with only metallated product ions being generated. For two biological phosphopeptides, [M + Pr + H]⁴⁺ is observed and may be due to the presence of at least one residue with a highly basic side chain that facilitates the addition of an extra proton. For the model phosphopeptides, more sequence coverage occurs when the phosphorylated residue is in the middle of the sequence than at either the N- or C-terminus. ETD of the metallated precursor ions formed by ESI generates exclusively metallated and nonmetallated c- and z-ions for the biological phosphopeptides, while metallated c-ions, z-ions, and a few y-ions form for the model phosphopeptides. Most of the product ions contain the phosphorylated residue indicating that the metal ion binds predominantly at the deprotonated phosphate group. The results of this study indicate that ETD is a promising tool for sequencing highly acidic phosphorylated peptides by metal adduction with Pr (III) and, by extension, all nonradioactive lanthanide metal ions.

Influence of the metals and ligands in dinuclear complexes on phosphopeptide sequencing by electron-transfer dissociation tandem mass spectrometry

Phosphorylation is one of the most important protein modifications, and electron-transfer dissociation tandem mass spectrometry (ETD-MS/MS) is a potentially useful method for the sequencing of phosphopeptides, including determination of the phosphorylation site. Notably, ETD-MS/MS typically provides useful information when the precursor contains more than three positive charges. It is not yet used as an analysis method for large-scale phosphopeptide production due to difficulties occurring in the production of acidic phosphopeptides having more than three positive charges. To increase the charge state of phosphopeptides, we used dinuclear metal complexes, which selectively bind to the phosphate group in phosphopeptides with the addition of positive charge(s). Dinuclear copper, zinc, and gallium complexes were tested and it was found that the type of metal present in the complex strongly affected the affinity of the phosphorylated compounds and their ETD fragmentation. The dinuclear copper complex interacted weakly with the phosphate groups and ETD-induced peptide fragmentation was largely suppressed by the presence of Cu²⁺, which worked as an electron trap. The dinuclear gallium complex was strongly bound to a phosphate group. However, the ligand binding to gallium acted as an electron trap and the presence of dinuclear gallium complex in the precursor for ETD-MS/MS hampered the sequencing of the phosphopeptides, as in the case of dinuclear copper complexes. In contrast, dinuclear zinc complexes efficiently bind to phosphopeptides with an increase in the charge state, facilitating phosphopeptide sequencing by ETD-MS/MS. The fragmentation of the ligand and peptide backbone in the dinuclear zinc-phosphopeptide complex were competitively induced by ETD. These processes are influenced by the ligand structure and so the detailed ETD fragmentation pathways were investigated using density functional theory calculations.

Native electrospray mass spectrometry approaches to probe the interaction between zinc and an anti-angiogenic peptide from histidine-rich glycoprotein

Zinc modulates the biological function of histidine-rich glycoprotein (HRG) through binding to its His-rich region (HRR). The Zn2+-binding properties of a 35 amino-acid biologically-active peptide mimic of the HRR, HRGP330, were investigated using dissociative mass spectrometry approaches in addition to travelling-wave ion mobility mass spectrometry (TWIM-MS). Native mass spectrometry confirmed zinc binding to HRGP330; however, broadening of the 1H NMR resonances upon addition of Zn2+ ions precluded the attainment of structural information. A complementary approach employing TWIM-MS indicated that HRGP330 has a more compact structure in the presence of Zn2+ ions. Top-down MS/MS data supported a metal-binding-induced conformational change, as fewer fragments were observed for Zn2+-bound HRGP330. Zn2+-bound fragments of both N-terminal and C-terminal ends of the peptide were identified from collision-induced dissociation (CID) and electron transfer dissociation/proton transfer reaction (ETD/PTR) experiments, suggesting that multiple binding sites exist within this region of HRG. The combination of mass spectrometry and NMR approaches provides new insight into the highly dynamic interaction between zinc and this His-rich peptide.

Effects of acidic peptide size and sequence on trivalent praseodymium adduction and electron transfer dissociation mass spectrometry

Using the lanthanide ion praseodymium, Pr(III), metallated ion formation and electron transfer dissociation (ETD) were studied for 25 biological and model acidic peptides. For chain lengths of seven or more residues, even highly acidic peptides that can be difficult to protonate by electrospray ionization will metallate and undergo abundant ETD fragmentation. Peptides composed of predominantly acidic residues form only the deprotonated ion, [M + Pr - H]2+ ; this ion yields near complete ETD sequence coverage for larger peptides. Peptides with a mixture of acidic and neutral residues generate [M + Pr]3+ , which cleaves between every residue for many peptides. Acidic peptides that contain at least one residue with a basic side chain also produce the protonated ion, [M + Pr + H]4+ ; this ion undergoes the most extensive sequence coverage by ETD. Primarily metallated and non-metallated c- and z-ions form for all peptides investigated. Metal adducted product ions are only present when at least half of the peptide sequence can be incorporated into the ion; this suggests that the metal ion simultaneously attaches to more than one acidic site. The only site consistently lacking dissociation is at the N-terminal side of a proline residue. Increasing peptide chain length generates more backbone cleavage for metal-peptide complexes with the same charge state. For acidic peptides with the same length, increasing the precursor ion charge state from 2+ to 3+ also leads to more cleavage. The results of this study indicate that highly acidic peptides can be sequenced by ETD of complexes formed with Pr(III). Copyright © 2017 John Wiley & Sons, Ltd.

High-Confidence Sequencing of Phosphopeptides by Electron Transfer Dissociation Mass Spectrometry Using Dinuclear Zinc(II) Complex

Phosphorylation is the most abundant protein modification, and tandem mass spectrometry (MS²) with electron transfer dissociation (ETD) has proven to be a promising method for phosphoproteomic applications owing to its ability to determine phosphorylation sites on proteins. However, low precursor charge states hinder the ability to obtain useful information through peptide sequencing by ETD, and the presence of acidic phosphate groups contributes to a low charge state of peptide ions. In the present report, we used a dinuclear zinc complex, (Zn₂L)³⁺ (L = alkoxide form of 1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-ol) for electrospray ionization (ESI), followed by ETD-MS² analysis. Since (Zn₂L)³⁺ selectively bound to phosphopeptide with addition of a positive charge per phosphate group, the use of (Zn₂L)³⁺ for ESI improved the ionization yield of phosphopeptides in phosphoprotein digest. Additionally, an increase in the charge state of phosphopeptides were observed by addition of (Zn₂L)³⁺, facilitating phosphopeptide sequencing by ETD-MS². Since the binding between (Zn₂L)³⁺ and the phosphate group was retained during the ETD process, a comparison between the ETD mass spectra obtained using two dinuclear zinc complex derivatives containing different zinc isotopes, namely (⁶⁴Zn₂L)³⁺ and (⁶⁸Zn₂L)³⁺, provided information about the number of phosphate groups in each fragment ion, allowing the phosphorylation site to be unambiguously determined. The details of the fragmentation processes of the (Zn₂L)³⁺-phosphopeptide complex were investigated using a density functional theory calculation. As in the case of protonated peptides, ETD induced peptide backbone dissociation in the (Zn₂L)³⁺-phosphopeptide complex proceeded through an aminoketyl radical intermediate.

The Effects of Trivalent Lanthanide Cationization on the Electron Transfer Dissociation of Acidic Fibrinopeptide B and its Analogs

Electrospray ionization (ESI) on mixtures of acidic fibrinopeptide B and two peptide analogs with trivalent lanthanide salts generates [M + Met + H](4+), [M + Met](3+), and [M + Met -H](2+), where M = peptide and Met = metal (except radioactive promethium). These ions undergo extensive and highly efficient electron transfer dissociation (ETD) to form metallated and non-metallated c- and z-ions. All metal adducted product ions contain at least two acidic sites, which suggest attachment of the lanthanide cation at the side chains of one or more acidic residues. The three peptides undergo similar fragmentation. ETD on [M + Met + H](4+) leads to cleavage at every residue; the presence of both a metal ion and an extra proton is very effective in promoting sequence-informative fragmentation. Backbone dissociation of [M + Met](3+) is also extensive, although cleavage does not always occur between adjacent glutamic acid residues. For [M + Met - H ](2+), a more limited range of product ions form. All lanthanide metal peptide complexes display similar fragmentation except for europium (Eu). ETD on [M + Eu - H](2+) and [M + Eu](3+) yields a limited amount of peptide backbone cleavage; however, [M + Eu + H](4+) dissociates extensively with cleavage at every residue. With the exception of the results for Eu(III), metallated peptide ion formation by ESI, ETD fragmentation efficiencies, and product ion formation are unaffected by the identity of the lanthanide cation. Adduction with trivalent lanthanide metal ions is a promising tool for sequence analysis of acidic peptides by ETD. Graphical Abstract ᅟ.

Difference of Electron Capture and Transfer Dissociation Mass Spectrometry on Ni(2+)-, Cu(2+)-, and Zn(2+)-Polyhistidine Complexes in the Absence of Remote Protons

Electron capture dissociation (ECD) and electron transfer dissociation (ETD) in metal-peptide complexes are dependent on the metal cation in the complex. The divalent transition metals Ni(2+), Cu(2+), and Zn(2+) were used as charge carriers to produce metal-polyhistidine complexes in the absence of remote protons, since these metal cations strongly bind to neutral histidine residues in peptides. In the case of the ECD and ETD of Cu(2+)-polyhistidine complexes, the metal cation in the complex was reduced and the recombination energy was redistributed throughout the peptide to lead a zwitterionic peptide form having a protonated histidine residue and a deprotonated amide nitrogen. The zwitterion then underwent peptide bond cleavage, producing a and b fragment ions. In contrast, ECD and ETD induced different fragmentation processes in Zn(2+)-polyhistidine complexes. Although the N-Cα bond in the Zn(2+)-polyhistidine complex was cleaved by ETD, ECD of Zn(2+)-polyhistidine induced peptide bond cleavage accompanied with hydrogen atom release. The different fragmentation modes by ECD and ETD originated from the different electronic states of the charge-reduced complexes resulting from these processes. The details of the fragmentation processes were investigated by density functional theory. Graphical Abstract ᅟ.

Dissociation of trivalent metal ion (Al(3+), Ga(3+), In(3+) and Rh(3+))--peptide complexes under electron capture dissociation conditions

RATIONALE

The electron capture dissociation (ECD) of proteins/peptides is affected by the nature of charge carrier. It has been reported that transition metal ions could tune the ECD pathway of peptides. To further explore the charge carrier effect of metal ions, ECD of peptides adducted with trivalent transition metal ions, including group IIIB (Al(3+), Ga(3+), and In(3+) ) and Rh(3+), were investigated and compared with that of the lanthanide ion (Ln(3+)).

METHODS

Bradykinin-derived peptides were used as model peptides to probe the dissociation pathways. The ECD experiments were performed on a Bruker APEX III 4.7T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer.

RESULTS

Typical c-/z-ions with and without metal ions were observed in the ECD of peptides adducted with Group IIIB metal ions as charge carriers. Connection of non-metalated c-ions and metalated z-ions at the position of the serine residue indicated that serine is one of the binding sites of the metal ion on the model peptides. Typical slow heating ions, including metalated a-/b-ions and non-metalated y-ions, were generated in ECD of Rh(3+) -adducted peptides.

CONCLUSIONS

Based on the experimental results, it is proposed that (i) for Group IIIB metal ion-peptide complexes, the incoming electron is captured by the proton in the salt-bridge structures of precursor ions; (ii) for Rh(3+) -peptide complexes, the incoming electron is captured by the metal ion due to the formation of charge-solvated precursor ions formed through arginine residue-metal coordination. Our results indicate that the heterogeneity of precursor ions plays an important role for the ECD of metalated peptides.

N-Cα Bond Cleavage of Zinc-Polyhistidine Complexes in Electron Transfer Dissociation Mediated by Zwitterion Formation: Experimental Evidence and Theoretical Analysis of the Utah-Washington Model

Electron capture dissociation (ECD) and electron transfer dissociation (ETD) of gas-phase ions are widely used for peptide/protein sequencing by mass spectrometry. To understand the general mechanism of ECD/ETD of peptides, we focused on the ETD fragmentation of metal-peptide complexes in the absence of remote protons. Since Zn(2+) strongly binds to neutral histidine residues in peptides, Zn(2+)-polyhistidine complexation does not generate any remote protons. However, in the absence of remote protons, electron transfer to the Zn(2+)-polyhistidine complex induced the N-Cα bond cleavage. The formation pathway for the ETD products was investigated by density functional theory calculations. The calculations showed that the charge-reduced zinc-peptide radical, [M + Zn](•+), can exist in the low-energy zwitterionic amide π* states, which underwent homolytic N-Cα bond dissociation. The homolytic cleavage resulted in the donation of an electron from the N-Cα bond to the nitrogen atom, producing an iminoenol c' anion. The counterpart z(•) radical contained a radical site on the α-carbon atom. The iminoenol c' anion then abstracted a proton to presumably form the more stable amide c' fragment. The current experimental and computational joint study strongly suggested that the N-Cα bond cleavage occurred through the aminoketyl radical-anion formation for Zn(2+)-polyhistidine complexes in ETD.