Further studies on the fragmentation of protonated ions of peptides containing aspartic acid, glutamic acid, cysteine sulfinic acid, and cysteine sulfonic acid

Here we examined the fragmentation, on a quadrupole ion-trap mass spectrometer, of the protonated ions of a group of peptides containing one arginine and two different acidic amino acids, one being aspartic acid (Asp) or glutamic acid (Glu) and the other being cysteine sulfinic acid [C(SO2H)] or cysteine sulfonic acid [C(SO3H)]. Our results showed that, upon collisional activation, the cleavage of the peptide bond C-terminal to C(SO2H) is much more facile than that of the peptide bond C-terminal to Asp, Glu, or C(SO3H). There is no significant difference, however, in susceptibility to cleavage of peptide bonds that are C-terminal to Asp, Glu, and C(SO3H). To understand these experimental observations, we carried out B3LYP/6-31G* density functional theory calculations for a model cleavage reaction of GXG --> b2 + Gly, in which X is Asp, Glu, C(SO2H), or C(SO3H). Our calculation results showed that the cleavage reaction is thermodynamically more favorable when X = C(SO2H) than when X = Asp or C(SO3H). We attributed the less facile cleavage of the amide bond after Glu to that the formation of a six-membered ring b ion for Glu-bearing peptides is kinetically not as favorable as the formation of a five-membered ring b ion for peptides containing the other three acidic amino acids. The results from this study may provide useful tools for peptide sequencing.     

Interactions of mono- and divalent metal ions with aspartic and glutamic acid investigated with IR photodissociation spectroscopy and theory

The interaction of metal ions with aspartic (Asp) and glutamic (Glu) acid and the role of gas-phase acidity on zwitterionic stability were investigated using infrared photodissociation spectroscopy in the spectral range 950-1900 cm (-1) and by hybrid density functional theory. Lithium ions interact with both carbonyl oxygen atoms and the amine nitrogen for both amino acids, whereas cesium interacts with both of the oxygen atoms of the C-terminus and the carbonyl oxygen of the side chain for Asp. For Glu, this structure is competitive, but a structure in which the cesium ion interacts with just the carbonyl oxygen atoms is favored and the calculated spectrum for this structure is more consistent with the experimentally measured spectrum. In complexes with either of these metal ions, both amino acids are non-zwitterionic. In contrast, Glu*Ca (2+) and Glu*Ba (2+) both adopt structures in which Glu is zwitterionic and the metal ion interacts with both oxygens of the C-terminal carboxylate and the carbonyl oxygen in the side chain. Assignment of the zwitterionic form of Glu is strengthened by comparisons to the spectrum of the protonated form, which indicate spectral features associated with a protonated amino nitrogen. Comparisons with results for glutamine, which adopts nearly the same structures with these metal ions, indicate that the lower Delta H acid of Asp and Glu relative to other amino acids does not result in greater relative stability of the zwitterionic form, a result that is directly attributed to effects of the metal ions which disrupt the strong interaction between the carboxylic acid groups in the isolated, deprotonated forms of these amino acids.     

Electrospray ionization mass spectra of amino acid phosphoramidates of adenosine

Amino acid phosphoramidates of adenosine were synthesized and determined by positive and negative ion electrospray ionization mass spectrometry (ESI-MS) in conjunction with tandem mass spectrometry (MS/MS). The fragmentation pathways were investigated. In the positive ion mass spectra abundant characteristic fragment ions appeared, and many complementary ions were found. In the negative ion mass spectra only a few fragment ions were observed, and most of them contained phosphoryl groups. The results show that ESI-MS is a useful tool for structural determination of amino acid phosphoramidates of nucleosides.     

Mobile and localized protons: a framework for understanding peptide dissociation

Protein identification and peptide sequencing by tandem mass spectrometry requires knowledge of how peptides fragment in the gas phase, specifically which bonds are broken and where the charge(s) resides in the products. For many peptides, cleavage at the amide bonds dominate, producing a series of ions that are designated b and y. For other peptides, enhanced cleavage occurs at just one or two amino acid residues. Surface-induced dissociation, along with gas-phase collision-induced dissociation performed under a variety of conditions, has been used to refine the general 'mobile proton' model and to determine how and why enhanced cleavages occur at aspartic acid residues and protonated histidine residues. Enhanced cleavage at acidic residues occurs when the charge is unavailable to the peptide backbone or the acidic side-chain. The acidic H of the side-chain then serves to initiate cleavage at the amide bond immediately C-terminal to Asp (or Glu), producing an anhydride. In contrast, enhanced cleavage occurs at His when the His side-chain is protonated, turning His into a weak acid that can initiate backbone cleavage by transferring a proton to the backbone. This allows the nucleophilic nitrogen of the His side-chain to attack and form a cyclic structure that is different from the 'typical' backbone cleavage structures.     

Fragmentation Characteristics of Deprotonated N-linked Glycopeptides: Influences of Amino Acid Composition and Sequence

Glycopeptide structural analysis using tandem mass spectrometry is becoming a common approach for elucidating site-specific N-glycosylation. The analysis is generally performed in positive-ion mode. Therefore, fragmentation of protonated glycopeptides has been extensively investigated; however, few studies are available on deprotonated glycopeptides, despite the usefulness of negative-ion mode analysis in detecting glycopeptide signals. Here, large sets of glycopeptides derived from well-characterized glycoproteins were investigated to understand the fragmentation behavior of deprotonated N-linked glycopeptides under low-energy collision-induced dissociation (CID) conditions. The fragment ion species were found to be significantly variable depending on their amino acid sequence and could be classified into three types: (i) glycan fragment ions, (ii) glycan-lost fragment ions and their secondary cleavage products, and (iii) fragment ions with intact glycan moiety. The CID spectra of glycopeptides having a short peptide sequence were dominated by type (i) glycan fragments (e.g., ^2,4A_R, ^2,4A_R-1, D, and E ions). These fragments define detailed structural features of the glycan moiety such as branching. For glycopeptides with medium or long peptide sequences, the major fragments were type (ii) ions (e.g., [peptide + ^0,2X₀–H]^– and [peptide–NH₃–H]^–). The appearance of type (iii) ions strongly depended on the peptide sequence, and especially on the presence of Asp, Asn, and Glu. When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn–36]^–, was abundantly formed. Observed fragments are reasonably explained by a combination of existing fragmentation rules suggested for N-glycans and peptides.

Structure characterization of lipocyclopeptide antibiotics,aspartocins A,B & C,by ESI‐MSMS and ESI‐nozzle‐skimmer‐MSMS

Three lipocyclopeptide antibiotics, aspartocins A (1), B (2), and C (3), were obtained from the aspartocin complex by HPLC separation methodology. Their structures were elucidated using previously published chemical degradation results coupled with spectroscopic studies including ESI‐MS, ESI‐Nozzle Skimmer‐MSMS and NMR. All three aspartocin compounds share the same cyclic decapeptide core of cyclo [Dab2 (Asp1‐FA)‐Pip3‐MeAsp4‐Asp5‐Gly6‐Asp7‐Gly8‐Dab9‐Val10‐Pro11]. They differ only in the fatty acid side chain moiety (FA) corresponding to (Z)‐13‐methyltetradec‐3‐ene‐carbonyl, (+,Z)‐12‐methyltetradec‐3‐ene‐carbonyl and (Z)‐12‐methyltridec‐3‐ene‐carbonyl for aspartocins A (1), B (2), and C (3), respectively. All of the sequence ions were observed by ESI‐MSMS of the doubly charged parent ions. However, a number of the sequence ions observed were of low abundance. To fully sequence the lipocyclopeptide antibiotic structures, these low abundance sequence ions together with complementary sequence ions were confirmed by ESI‐Nozzle‐Skimmer‐MSMS of the singly charged linear peptide parent fragment ions H‐Asp5‐Gly6‐Asp7‐Gly8‐Dab9‐Val10‐Pro11‐Dab2¹⁺‐Asp1‐FA. Cyclization of the aspartocins was demonstrated to occur via the β‐amino group of Dab2 from ions of moderate intensity in the ESI‐MSMS spectra. As the fatty acid moieties do not undergo internal fragmentations under the experimental ESI mass spectral conditions used, the 14 Da mass difference between the fatty acid moieties of aspartocins A (1) and B (2) versus aspartocin C (3) was used as an internal mass tag to differentiate fragment ions containing fatty acid moieties and those not containing the fatty acid moieties. The most numerous and abundant fragment ions observed in the tandem mass spectra are due to the cleavage of the tertiary nitrogen amide of the pipecolic acid residue‐3 (16 fragment ions) and the proline residue‐11 (7 fragment ions). In addition, the neutral loss of ethanimine from α,β‐diaminobutyric acid residue 9 was observed for the parent molecular ion and for 7 fragment ions. Copyright © 2009 John Wiley & Sons, Ltd.     

Sequencing of anti-thyroxine monoclonal antibody fab fragment by ion trap mass spectrometry

A comprehensive mass spectrometric strategy is described for the sequencing of anti-thyroxine monoclonal antibody Fab region (48 000 Da). After reduction and S-carboxymethylation of the Fab, the modified light chain and Fd fragment were separated and subjected to multiple proteolytic digestions. The resulting digests were characterized by on-line microbore liquid chromatography/electrospray ionization ion trap mass spectrometry. Database search against published immunoglobulins (IgGs) allowed identification of all the peptides in constant domains. The homologous framework residues in the IgGs were utilized as 'sequence maps' for the sequence determination of variable domains. S-Carboxymethylation with an isotopic-enriched moiety greatly facilitated the recognition and data elucidation of cysteinyl peptides through the unique isotopic distribution patterns specific to the modified peptides. Methylation of peptide mixtures provided additional information for the interpretation of MS/MS spectra, allowing easy differentiation of Asp/Asn and Gln/Glu pairs. This study clearly demonstrates the power of mass spectrometry for the sequencing of antibodies without knowing the corresponding DNA sequences.     

Electrospray Ionization Mass Spectra of Amino Acid Methyl Ester 5′-Phosphoramidates of 2′,3′-Isopropylideneuridine

IntroductionIn recent years, nucleosides and their analogshave been extensively studied as potential anticancerand antiviral agents[1—3]. For example, several purineand pyridine bases and nucleoside analogs are used aschemotherapeutic arsenal. For their biological activity,these analogs should be intracellularly metabolized to5′-mononucleotides by kinase-mediated phosphoryla-tion[4]. To overcome the problemof drug resistance andto improve the membrane penetration, a series of aminoacid phosp…     

Electrospray Ionization Mass Spectra of Amino Acid Methyl Ester 5′-Phosphoramidates of 2′,3′-Isopropylideneuridine

Amino acid methyl ester phosphates were synthesized and determined by using positive-ion mode electrospray ionization mass spectrometry(ESIMS) in combination with multistage tandem mass spectrometry. The fragmentation pathways were investigated, and it was observed that most fragment ions contained the phosphoryl group. It was interesting to observe that the fragmentation pathways of the protonated molecule show some differences when compared with those of the sodium ion adduct. The methoxy group of amino acid methyl ester can migrate from the carbonyl group to the phosphoryl group in the sodium ion adduct.     

Electrospray Ionization Mass Spectra of Amino Acid Methyl Ester 5 ＇-Phosphoramidates of 2＇, 3＇-Isopropylideneuridine

Amino acid methyl ester phosphates were synthesized and determined by using positive-ion mode dectrospmy ionization mass spectrometry（ESIMS） in combination with multistage tandem mass spectrometry. The fragmentation pathways were investigated, and it was observed that most fragment ions contained the phosphoryl group. It was interesting to observe that the fragmentation pathways of the protonated molecule show some differences when compared with those of the sodium ion adduct. The methoxy group of amino acid methyl ester can migrate from the carbonyl group to the phosphoryl group in the sodium ion adduct.     

Atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry of sulfonic acid derivatized tryptic peptides.

Atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) and ion trap mass spectrometry have been used to study the fragmentation behavior of native peptides and peptide derivatives prepared for de novo sequencing applications. Sulfonic acid derivatized peptides were observed to fragment more extensively and up to 28 times more efficiently than the corresponding native peptides. Tandem mass spectra of native peptides containing aspartic or glutamic acids are dominated by cleavage on the C-terminal side of the acidic residues. This significantly limits the amount of sequence information that can be derived from those compounds. The MS/MS spectra of native tryptic peptides containing oxidized Met residues show extensive loss of CH(3)SOH and little sequence-specific fragmentation. On the other hand, the tandem mass spectra of derivatized peptides containing Asp, Glu and oxidized Met show much more uniform fragmentation along the peptide backbone. The AP-MALDI tandem mass spectra of some derivatized peptides were shown to be qualitatively very similar to the corresponding vacuum MALDI postsource decay mass spectra, which were obtained on a reflector time-of-flight instrument. However, the ion trap mass spectrometer offers several advantages for peptide sequencing relative to current reflector time-of-flight instruments including improved product ion mass measurement accuracy, improved precursor ion selection and MS(n). These latter capabilities were demonstrated with solution digests of model proteins and with in-gel digests of 2D-gel separated proteins.     

Mass-based classification (MBC) of peptides: Highly accurate precursor ion mass values can be used to directly recognize peptide phosphorylation

Accurate mass values as obtainable by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) were employed in a theoretical study to differentiate between nonmodified and phosphorylated peptides. It was found that for peptide masses up to 1,000 u more than 98% of all theoretical monophosphorylated peptides (all possible combinations of proteinogenic amino acids having one phosphorylation on S, T, or Y) can be distinguished from nonphosphorylated peptides directly by their mass, if mass values are determined with an accuracy of better than +/-0.1 ppm. At a peptide mass of 1,500 u still 70% of all possible monophosphorylated peptides are distinguishable from nonmodified peptides by their accurate mass alone. In contrast to established techniques of data-dependent multidimensional mass spectrometry, only the mass of the precursor ion is necessary to decide upon subsequent fragment ion analysis of a peptide for sequence analysis in an LC-MS/MS investigation of a complex sample, when using a precalculated mass distribution table of theoretical peptides. A mass distribution table of nonphosphorylated and monophosphorylated peptides with a bin width of 0.1 mu was made available via the open web site www.peptidecomposer.com.     

Radical <Emphasis Type="BoldItalic">a</Emphasis>-Ions in Electron Capture Dissociation: On the Origin of Species

Radical a* ions appear in electron capture dissociation mass spectra sporadically, but sometimes with high intensity. Mechanistically, radical a ions are hypothesized to arise due to thermodynamically disadvantaged charge solvation on the backbone nitrogen (instead of carbonyl), which upon neutralization produces a hypervalent group instantly fragmenting into a radical b* and conventional y' ion. The former species is unstable and, after releasing a CO molecule, decays to an a* ion. Here we validate this scenario by direct observation of the complementarity of a* and y' ions by interrogation of an ECD MS/MS database of >10,000 doubly and >5,000 triply charged tryptic peptides. Intriguingly, the most abundant a*/y' pairs are found to come from the cleavage of the same backbone link as the most abundant c' and z* complementary ions. This result gives strong support to the “local” N-Cα bond cleavage mechanism, in which the dissociation occurs at the site of charge solvation. However, a second strong peak is observed in the c'/z* fragment distribution four residues away from the a*/y' cleavage, which supports the indirect N-Cα bond cleavage mechanism. The size distribution of a ions from doubly (but not triply!) charged precursors shows deficit of a3 ions, and possibly a6 ions.     

A mechanism for the loss of 60 u from peptides containing an arginine residue at the C-terminus

The loss of 60 u from protonated peptide ions containing an arginine residue at the C-terminus has been investigated by means of low energy tandem mass spectrometry. The lowest energy conformation of singly charged bradykinin is thought to involve a salt-bridge structure, which may lead to the formation of two isomeric forms. It is thought that one isomer retains the ionizing proton at the C-terminal end of the peptide, leading to the formation of the [b _n?1 + H + OH]⁺ fragment ion, and the other isomer retains the charge at the N-terminus, leading to the formation of the [M + H ? 60]⁺ fragment ion. It was found that the formation of the [M + H ? 60]⁺ ion occurs only from singly charged precursor ions. In addition, the loss of 60 u occurs from peptides in which the charge is localized at the N-terminus. These results indicate that the mechanism of formation of the [M + H ? 60]⁺ ion may be driven by a charge-remote process.     

SO<Stack><Subscript>2</Subscript><Superscript>−·</Superscript></Stack> electron transfer ion/ion reactions with disulfide linked polypeptide ions

Multiply-charged peptide cations comprised of two polypeptide chains (designated A and B) bound via a disulfide linkage have been reacted with SO2-* in an electrodynamic ion trap mass spectrometer. These reactions proceed through both proton transfer (without dissociation) and electron transfer (with and without dissociation). Electron transfer reactions are shown to give rise to cleavage along the peptide backbone, loss of neutral molecules, and cleavage of the cystine bond. Disulfide bond cleavage is the preferred dissociation channel and both Chain A (or B)-S* and Chain A (or B)-SH fragment ions are observed, similar to those observed with electron capture dissociation (ECD) of disulfide-bound peptides. Electron transfer without dissociation produces [M + 2H]+* ions, which appear to be less kinetically stable than the proton transfer [M + H]+ product. When subjected to collision-induced dissociation (CID), the [M + 2H]+* ions fragment to give products that were also observed as dissociation products during the electron transfer reaction. However, not all dissociation channels noted in the electron transfer reaction were observed in the CID of the [M + 2H]+* ions. The charge state of the peptide has a significant effect on both the extent of electron transfer dissociation observed and the variety of dissociation products, with higher charge states giving more of each.     

Use of combined mass spectrometry methods for the characterization of a new variant of human hemoglobin: The double mutant hemoglobin villeparisis β77(EF1) His → Tyr, β 80 (EF4) Asn → Ser

Hemoglobin Villeparisis was found during a systematic measurement of glycated hemoglobin. Electrospray mass spectra of the globin indicate an apparently unchanged molecular weight within the error range (0.01%). The tryptic digest of the β chain shows a chromatographically abnormal βT-9 peptide. The mass-to-charge ratio value of its [M+H]⁺ ion, as measured by liquid secondary ionization mass spectrometry, is one mass unit lower than that of the normal βT-9. However, the electrospray mass spectrum of this peptide exhibits mainly a doubly charged ion, whereas the normal βT-9 gives a triply charged ion. None of the allowed single amino acid substitutions for a 1-u shift down (Glu → Gln, Asp → Asn, or Asn → Ile) can explain the suppression of one protonation site. This can be due only to the replacement of the internal histidine by a nonbasic residue. Thus at least two amino acid exchanges occur within the same peptide: one involves the internal histidine, and the sum of the mass shifts is ?1 u. Consideration of the βT-9 sequence and taking account for the genetic code rules, the only possibility was ¹¹His → Tyr (+26 mass shift) associated with ¹⁴Asn → Ser (?27 mass shift). This conclusion was consistent with the tandem mass spectrum of the [M+H]⁺ ion and was further confirmed by chemical microsequencing.     

Atmospheric-pressure Penning ionization of aliphatic hydrocarbons

A study has been made of the atmospheric-pressure Penning ionization (APPeI) of aliphatic hydrocarbons (pentane, hexane, heptane, and octane) with long-lived rare gas atoms (Rg*). The metastable rare gas atoms (He*, Ne*, Ar* and Kr*) were generated by the negative-mode corona discharge of atmospheric-pressure rare gases. In the Rg*APPeI mass spectra for aliphatic hyrocarbons, the relative abundances of fragment ions were found to increase in the order of He* --> Ne* --> Ar* --> Kr*. The order is in the opposite direction to the internal energies of the Rg*. The less fragmentation observed for He* may be because the nascent molecular ions [M(+.)]* formed by Penning ionization have lifetimes long enough for them to be collisionally deactivated in the atmospheric-pressure ion source. It was found that the relative abundances of fragment ions in Ar*APPeI increased when the sample pressure in the ion source was reduced. This is attributed to the collision of Ar* with molecular ions followed by fragmentation.     

Negative ion fragmentations of deprotonated peptides: backbone cleavages directed through both Asp and Glu

The collision-induced spectra of [M - H](-) ions of a variety of natural and synthetic amphibian peptides containing Asp and/or Glu exhibit characteristic gamma backbone cleavage ions that identify the positions of these residues in the peptide. A theoretical study suggests that the Glu cleavage involves an S(N)i reaction of the carboxylate anion from the Glu alpha side chain to form a deprotonated cyclic lactone. The presence of either Asp or Glu or other residues that effect pronounced side-chain cleavages (e.g. Ser or Thr) results in the normal alpha and beta backbone cleavages being reduced in comparison to those cleavages which originate from side chains.     

An optimized HPLC/MS/MS method for quantification of excitatory amino acids in rat hippocampus and its application in brain ischemia/reperfusion research

An optimized HPLC/MS/MS method was established to quantify glutamate (Glu) and aspartic acid (Asp) in rat hippocampus with glutamate‐d5 (Glu‐d5) as internal standard. The mass spectrometry was operated under the multiple reaction monitoring mode using electrospray ionization in the positive ion mode for Glu and negative ion mode for Asp. The retention times of Glu, Asp and Glu‐d5 were 1.53, 2.07 and 1.52 min, respectively. The linearity of calibration curves was good, with r² > 0.99 and a lower limit of quantitation of 10 ng/mL. The intra‐day precisions (relative standard deviation, RSD) of Glu and Asp were in the range of 3.61–8.17 and 4.22–10.09%, respectively; the inter‐day precisions (RSD) of Glu and Asp were in the range of 3.57–5.19 and 2.49–5.04%, respectively. The accuracies of Glu and Asp were in the range of ?2.10–6.20 and ?0.90–10.00%, respectively. The recovery rates of 10, 100 and 1000 ng/mL were found to be 0.89 ± 0.24, 1.01 ± 0.10 and 0.90 ± 0.12 for Glu and 0.99 ± 0.26, 0.93 ± 0.07 and 1.13 ± 0.13 for Asp, respectively. This optimized method was successfully applied to quantify the concentration of Glu and Asp in rat hippocampus in brain ischemia/reperfusion research. Copyright © 2014 John Wiley & Sons, Ltd.     

Generation of hydrogen radicals for reactivity studies in Fourier transform ion cyclotron resonance mass spectrometry

An efficient technique for generation of H* (D*) radicals in Fourier transform ion cyclotron resonance (FTICR) mass spectrometry is described. The method allows the probing of the reactivity of gas-phase H* radicals towards various ions isolated in the cell of an FTICR mass spectrometer. Results on interactions of H* and D* radicals with trapped positive or negative C60 fullerene ions, as well as singly charged peptide ions, are presented. Hydrogen radical addition or H/D-exchange reactions between trapped ions and free H* (D*) radicals were observed. Potential implementation of the technique for probing the gas-phase three-dimensional structures of polyatomic ions is discussed as well.