Evidence for Sequence Scrambling in Collision-Induced Dissociation of y-Type Fragment Ions

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 (¹³C₁) 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.

Mechanism of Formation of the Major Estradiol Product Ions Following Collisional Activation of the Molecular Anion in a Tandem Quadrupole Mass Spectrometer

The importance of the mass spectral product ion structure is highlighted in quantitative assays, which typically use multiple reaction monitoring (MRM), and in the discovery of novel metabolites. Estradiol is an important sex steroid whose quantitation and metabolite identification using tandem mass spectrometry has been widely employed in numerous clinical studies. Negative electrospray ionization tandem mass spectrometry of estradiol (E2) results in several product ions, including the abundant m/z 183 and 169. Although m/z 183 is one of the most abundant product ions used in many quantitative assays, the structure of m/z 183 has not been rigorously examined. We suggest a structure for m/z 183 and a mechanism of formation consistent with collision induced dissociation (CID) of E2 and several stable isotopes ([D₄]-E2, [¹³C₆]-E2, and [D₁]-E2). An additional product ion from E2, namely m/z 169, has also been examined. MS³ experiments indicated that both m/z 183 and m/z 169 originate from only E2 [M – H]^– m/z 271. These ions, m/z 183 and m/z 169, were also present in the collision induced decomposition mass spectra of other prominent estrogens, estrone (E1) and estriol (E3), indicating that these two product ions could be used to elucidate the estrogenic origin of novel metabolites. We propose two fragmentation schemes to explain the CID data and suggest a structure of m/z 183 and m/z 169 consistent with several isotopic variants and high resolution mass spectrometric measurements.      

Gas-Phase Reactivity of Peptide Thiyl (RS•), Perthiyl (RSS•), and Sulfinyl (RSO•) Radical Ions Formed from Atmospheric Pressure Ion/Radical Reactions

In this study, we demonstrated the formation of gas-phase peptide perthiyl (RSS?) and thiyl (RS?) radical ions besides sulfinyl radical (RSO?) ions from atmospheric pressure (AP) ion/radical reactions of peptides containing inter-chain disulfide bonds. The identity of perthiyl radical was verified from characteristic 65 Da (?SSH) loss in collision-induced dissociation (CID). This signature loss was further used to assess the purity of peptide perthiyl radical ions formed from AP ion/radical reactions. Ion/molecule reactions combined with CID were carried out to confirm the formation of thiyl radical. Transmission mode ion/molecule reactions in collision cell (q2) were developed as a fast means to estimate the population of peptide thiyl radical ions. The reactivity of peptide thiyl, perthiyl, and sulfinyl radical ions was evaluated based on ion/molecule reactions toward organic disulfides, allyl iodide, organic thiol, and oxygen, which followed in order of thiyl (RS?) > perthiyl (RSS?) > sulfinyl (RSO?). The gas-phase reactivity of these three types of sulfur-based radicals is consistent with literature reports from solution studies.      

Fragmentation of the metastable molecular ion of methyl lactate: The formation of oxygen-protonated methanol [CH3OH2]+ involving double hydrogen atom transfers

The spontaneous unimolecular dissociation reaction of methyl lactate (1) ionized by electron impact was investigated by a combination of mass-analyzed ion kinetic energy spectrometry and deuterium labeling. The metastable ions 1^+· decompose in a variety of ways: four fragment peaks are observed at m/z 89, 76, 61, and 45, which correspond to the losses of ?H₃, CO, CH₃?O, and ?OOCH₃, respectively. Double hydrogen atom transfer occurs in the third reaction. The source-generated m/z 61 ions decompose into oxygen-protonated methanols at m/z 33 ([CH₃OH ₂ ⁺ ]) by the loss of CO with double hydrogen atom migration. Both hydroxyl and methyne hydrogen atoms in 1 ^+· are present in the resultant protonated methanols.     

Electron ionization induced metastable decompositions of isomeric trimethylsilylmethanol, (CH3)3SiCH2OH, and methoxytrimethylsilane, (CH3)3SiOCH3

The metastable decompositions of trimethylsilylmethanol, (CH₃)₃SiCH₂OH (MW: 104, 1) and methoxytrimethylsilane, (CH₃)₃SiOCH₃ (MW: 104, 2) upon electron ionization have been investigated by use of mass-analyzed ion kinetic energy (MIKE) spectroscopy and D labeling. The metastable ions of 1 ^·+ decompose to give the fragment ions m/z 89 (CH ₃ ^· loss) and 73 (^·CH₂OH loss), whereas those of 2 ^·+ only yield the fragment ion m/z 89 (CH ₃ ^· loss). The latter fragment ion is generated by loss of a methyl radical from the trimethylsilyl group via a simple cleavage reaction as shown by D labeling. However, the fragment ions m/z 89 and 73 from 1 ^·+ are generated following an almost statistical exchange of the original methyl and methylene hydrogen atoms in the molecular ion as shown also by D labeling. This exchange indicates a complex rearrangement of the molecular ion of 1 ^·+ prior to metastable decomposition for which as key step a 1,2-trimethylsilyl group migration from carbon to oxygen is suggested. A different behavior is also found between the source-generated m/z 89 ions from 1 ^·+ which decompose in the metastable time region to give ions m/z 61 by loss of ethylene and those from 2 ^·+ which decompose in the metastable region to yield ions m/z 59 by elimination of formaldehyde.     

Probing the Complementarity of FAIMS and Strong Cation Exchange Chromatography in Shotgun Proteomics

High field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility spectrometry, coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS) offers benefits for the analysis of complex proteomics samples. Advantages include increased dynamic range, increased signal-to-noise, and reduced interference from ions of similar m/z. FAIMS also separates isomers and positional variants. An alternative, and more established, method of reducing sample complexity is prefractionation by use of strong cation exchange chromatography. Here, we have compared SCX-LC-MS/MS with LC-FAIMS-MS/MS for the identification of peptides and proteins from whole cell lysates from the breast carcinoma SUM52 cell line. Two FAIMS approaches are considered: (1) multiple compensation voltages within a single LC-MS/MS analysis (internal stepping) and (2) repeat LC-MS/MS analyses at different and fixed compensation voltages (external stepping). We also consider the consequence of the fragmentation method (electron transfer dissociation or collision-induced dissociation) on the workflow performance. The external stepping approach resulted in a greater number of protein and peptide identifications than the internal stepping approach for both ETD and CID MS/MS, suggesting that this should be the method of choice for FAIMS proteomics experiments. The overlap in protein identifications from the SCX method and the external FAIMS method was ~25 % for both ETD and CID, and for peptides was less than 20 %. The lack of overlap between FAIMS and SCX highlights the complementarity of the two techniques. Charge state analysis of the peptide assignments showed that the FAIMS approach identified a much greater proportion of triply-charged ions.      

Comparison of MS/MS Methods for Characterization of DNA/Cisplatin Adducts

The development of activation/dissociation techniques such as ultraviolet photodissociation (UVPD), infrared multiphoton dissociation (IRMPD), and electron transfer dissociation (ETD) as alternatives to collision induced dissociation (CID) has extended the range of strategies for characterizing biologically relevant molecules. Here, we describe a comprehensive comparison of CID, IRMPD, UVPD, ETD, and hybrid processes termed ETcaD and ET-IRMPD (and analogous hybrid methods in the negative mode NETcaD and NET-IRMPD) for generating sequence-specific fragment ions and allowing adduction sites to be pinpointed for DNA/cisplatin adducts. Among the six MS/MS methods, the numerous products generated by the IRMPD and UVPD techniques resulted in the most specific and extensive backbone cleavages. We conclude that IRMPD and UVPD methods generally offer the best characteristics for pinpointing the cisplatin adduction sites in the fragment-rich spectra.      

Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses,Residue-Specific Product Ions,and Comparison with Protonated Peptides

High-accuracy MS/MS spectra of deprotonated ions of 390 dipeptides and 137 peptides with three to six residues are studied. Many amino acid residues undergo neutral losses from their side chains. The most abundant is the loss of acetaldehyde from threonine. The abundance of losses from the side chains of other amino acids is estimated relative to that of threonine. While some amino acids lose the whole side chain, others lose only part of it, and some exhibit two or more different losses. Side-chain neutral losses are less abundant in the spectra of protonated peptides, being significant mainly for methionine and arginine. In addition to the neutral losses, many amino acid residues in deprotonated peptides produce specific negative ions after peptide bond cleavage. An expanded list of fragment ions from protonated peptides is also presented and compared with those of deprotonated peptides. Fragment ions are mostly different for these two cases. These lists of fragments are used to annotate peptide mass spectral libraries and to aid in the confirmation of specific amino acids in peptides.

Open image in new window

Graphical Abstract ?

     

A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation

A collision induced dissociation (CID) structure for lossless ion manipulations (SLIM) module is introduced and coupled to a quadrupole time-of-flight (QTOF) mass spectrometer. The SLIM CID module was mounted after an ion mobility (IM) drift tube to enable IM/CID/MS studies. The efficiency of CID was studied by using the model peptide leucine enkephalin. CID efficiencies (62%) compared favorably with other beam-type CID methods. Additionally, the SLIM CID module was used to fragment a mixture of nine peptides after IM separation. This work also represents the first application of SLIM in the 0.3 to 0.5 Torr pressure regime, an order of magnitude lower in pressure than previously studied.

Open image in new window

Graphical Abstract ?

     

Ground and Excited-Electronic-State Dissociations of Hydrogen-Rich and Hydrogen-Deficient Tyrosine Peptide Cation Radicals

We report a comprehensive study of collision-induced dissociation (CID) and near-UV photodissociation (UVPD) of a series of tyrosine-containing peptide cation radicals of the hydrogen-rich and hydrogen-deficient types. Stable, long-lived, hydrogen-rich peptide cation radicals, such as [AAAYR + 2H]^+● and several of its sequence and homology variants, were generated by electron transfer dissociation (ETD) of peptide-crown-ether complexes, and their CID-MS³ dissociations were found to be dramatically different from those upon ETD of the respective peptide dications. All of the hydrogen-rich peptide cation radicals contained major (77%–94%) fractions of species having radical chromophores created by ETD that underwent photodissociation at 355 nm. Analysis of the CID and UVPD spectra pointed to arginine guanidinium radicals as the major components of the hydrogen-rich peptide cation radical population. Hydrogen-deficient peptide cation radicals were generated by intramolecular electron transfer in Cu^II(2,2′:6′,2″-terpyridine) complexes and shown to contain chromophores absorbing at 355 nm and undergoing photodissociation. The CID and UVPD spectra showed major differences in fragmentation for [AAAYR]^+● that diminished as the Tyr residue was moved along the peptide chain. UVPD was found to be superior to CID in localizing C_α-radical positions in peptide cation radical intermediates.

Open image in new window

Graphical Abstract ?

     

Comparison of high- and low-energy collision-induced dissociation tandem mass spectrometry in the analysis of glycoalkaloids and their aglycons

Four aglycons (tomatidine, demissidine, solanidine, and solasodine) and three glycoalkaloids (α-tomatine, α-chaconine, and α-solanine) have been analyzed by positive ion liquid secondary ion high-energy and low-energy collision-induced dissociation (CID) tandem mass Spectrometry, performed on a four-sector (EBEB) and a hybrid (EBQQ) instrument, respectively. Both high- and low-energy collision-induced dissociation mass spectra of [M+H]⁺ ions of these compounds provided structural information that aided the characterization of the different aglycons and of the carbohydrate sequence and linkage sites in the glycoalkaloids. Low-energy CID favors charge-driven fragmentation of the aglycon rings, whilst high-energy CID spectra are more complex and contain additional ions that appear to result from charge-remote fragmentations, multiple cleavages, or complex charge-driven rearrangements. With respect to the structural characterization of the carbohydrate part, low-energy CID fragmentations of sugar residues in the glycoalkaloids generate Y _n ⁺ ions and some low intensity Z _n ⁺ ions; the high-energy spectra also exhibit strong ^1,5X _n ⁺ ions, formed by multiple cleavage of the sugar ring, and significant Z _n ⁺ ions.     

Detection of Neutral CO Lost During Ionic Dissociation Using Atmospheric Pressure Thermal Dissociation Mass Spectrometry (APTD-MS)

Elucidation of ion dissociation patterns is particularly important to structural analysis by mass spectrometry (MS). However, typically, only the charged fragments from an ion dissociation event are detected in tandem MS experiments; neutrals are not identified. In recent years, we have developed an atmospheric pressure thermal dissociation (APTD) technique that can be applied to dissociate ions at atmosphere pressure and thus provide one way to characterize neutral fragments. In this paper, we focus on the detection of neutral CO resulting from amino acid and peptide ion dissociation. In the first set of experiments, several protonated amino acids (e.g., +?1 ion of phenylalanine) were found to undergo loss of a neutral (s) of total mass 46 Da, a process leading to iminium ion formation. We successfully detected the neutral species CO by using a CO sensor, UV-Vis and MS analysis following selective CO trapping with a rhodium complex. The capture of CO from dissociation of protonated amino acids supports the assignment of the loss of 46 Da to neutral losses of CO and H₂O, rather than loss of formaldehyde or dihydroxycarbene, other possible fragmentation pathways that have been subject of debate for a long time. In a second experiment, we used the APTD method in combination with the CO detection technique, to demonstrate the formation of CO in the conversion of b ions to a ions during peptide ion dissociations. These results showed the potential of APTD in the elucidation of ion dissociation mechanisms, using simple home-built apparatus.

Open image in new window

Graphical Abstract ?

     

Liquid Injection Field Desorption Ionization Mass Spectrometry of Cyclic Metal Carbonyl Complexes with Tetra-Antimony Ligands

Reactions of (norbornadiene)Cr(CO)₄ or cis-(piperidine)₂Mo(CO)₄ with R₂Sb-SbR₂, and cyclo-(R′Sb)_n (R′ = Et, n-Pr; n = 4, 5) give the complexes cyclo-[M(CO)₄(R₂Sb-SbR′- SbR′-SbR₂)] (1: M = Cr, R = Me, R′= Et; 2: M = Mo, R = Et, R′ = Et; 3: M = Mo, R = Et, R′ = n-Pr). Not accessible to established characterization methods, the oily, extremely reactive unpurified mixture of 3 with scrambled ligands was characterized by mass spectrometry using liquid injection field desorption ionization (LIFDI).      

Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry

This study is focused on sequence analysis of peptidomimetic helical oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. After the evaluation of MS/MS spectra obtained for model compounds with either MALDI or ESI sources, we found that the MALDI-TOF-TOF instrument gave more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N′H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b, and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.      

Peptide Scrambling During Collision-Induced Dissociation is Influenced by N-terminal Residue Basicity

‘Bottom up’ proteomic studies typically use tandem mass spectrometry data to infer peptide ion sequence, enabling identification of the protein whence they derive. The majority of such studies employ collision-induced dissociation (CID) to induce fragmentation of the peptide structure giving diagnostic b-, y-, and a- ions. Recently, rearrangement processes that result in scrambling of the original peptide sequence during CID have been reported for these ions. Such processes have the potential to adversely affect ion accounting (and thus scores from automated search algorithms) in tandem mass spectra, and in extreme cases could lead to false peptide identification. Here, analysis of peptide species produced by Lys-N proteolysis of standard proteins is performed and sequences that exhibit such rearrangement processes identified. The effect of increasing the gas-phase basicity of the N-terminal lysine residue through derivatization to homoarginine toward such sequence scrambling is then assessed. The presence of a highly basic homoarginine (or arginine) residue at the N-terminus is found to disfavor/inhibit sequence scrambling with a coincident increase in the formation of b_(n-1)+H₂O product ions. Finally, further analysis of a sequence produced by Lys-C proteolysis provides evidence toward a potential mechanism for the apparent inhibition of sequence scrambling during resonance excitation CID. Graphical Abstract

?     

Collision Cross Sections and Ion Mobility Separation of Fragment Ions from Complex N-Glycans

Ion mobility mass spectrometry (IM-MS) holds great potential for structural glycobiology, in particular in its ability to resolve glycan isomers. Generally, IM-MS has largely been applied to intact glycoconjugate ions with reports focusing on the separation of different adduct types. Here, we explore IM separation and report the collision cross section (CCS) of complex type N-glycans and their fragments in negative ion mode following collision-induced dissociation (CID). CCSs of isomeric fragment ions were found, in some cases, to reveal structural details that were not present in CID spectra themselves. Many fragment ions were confirmed as possessing multiple structure, details of which could be obtained by comparing their drift time profiles to different glycans. By using fragmentation both before and after mobility separation, information was gathered on the fragmentation pathways producing some of the ions. These results help demonstrate the utility of IM and will contribute to the growing use of IM-MS for glycomics.

Open image in new window

Graphical Abstract ?

     

Gas-Phase Reactions of Dimethyl Disulfide with Aliphatic Carbanions - A Mass Spectrometry and Computational Study

Ion-molecule reactions of Me₂S₂ with a wide range of aliphatic carbanions differing by structure and proton affinity values have been studied in the gas phase using mass spectrometry techniques and DFT calculations. The analysis of the spectra shows a variety of product ions formed via different reaction mechanisms, depending on the structure and proton affinity of the carbanion. Product ions of thiophilic reaction (m/z 47), S_N2 (m/z 79), and E2 elimination – addition sequence of reactions (m/z 93) can be observed. Primary products of thiophilic reaction can undergo subsequent S_N2 and proton transfer reactions. Gibbs free energy profiles calculated for experimentally observed reactions using PBE0/6-311+G(2d,p) method show good agreement with experimental results.

Open image in new window

Graphical Abstract ?

     

Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods

Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y–46 and b+H₂O, are present in PSD, photodissociation, and charge tagging. c^?+57 and z–57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues.

Open image in new window

Graphical Abstract ?

     

On-Line Electrochemical Reduction of Disulfide Bonds: Improved FTICR-CID and -ETD Coverage of Oxytocin and Hepcidin

Particularly in the field of middle- and top-down peptide and protein analysis, disulfide bridges can severely hinder fragmentation and thus impede sequence analysis (coverage). Here we present an on-line/electrochemistry/ESI-FTICR-MS approach, which was applied to the analysis of the primary structure of oxytocin, containing one disulfide bridge, and of hepcidin, containing four disulfide bridges. The presented workflow provided up to 80 % (on-line) conversion of disulfide bonds in both peptides. With minimal sample preparation, such reduction resulted in a higher number of peptide backbone cleavages upon CID or ETD fragmentation, and thus yielded improved sequence coverage. The cycle times, including electrode recovery, were rapid and, therefore, might very well be coupled with liquid chromatography for protein or peptide separation, which has great potential for high-throughput analysis.      

Charge Transfer Dissociation (CTD) Mass Spectrometry of Peptide Cations: Study of Charge State Effects and Side-Chain Losses

1+, 2+, and 3+ precursors of substance P and bradykinin were subjected to helium cation irradiation in a 3D ion trap mass spectrometer. Charge exchange with the helium cations produces a variety of fragment ions, the number and type of which are dependent on the charge state of the precursor ions. For 1+ peptide precursors, fragmentation is generally restricted to C?CO backbone bonds (a and x ions), whereas for 2+ and 3+ peptide precursors, all three backbone bonds (C?CO, C?N, and N?Cα) are cleaved. The type of backbone bond cleavage is indicative of possible dissociation channels involved in CTD process, including high-energy, kinetic-based, and ETD-like pathways. In addition to backbone cleavages, amino acid side-chain cleavages are observed in CTD, which are consistent with other high-energy and radical-mediated techniques. The unique dissociation pattern and supplementary information available from side-chain cleavages make CTD a potentially useful activation method for the structural study of gas-phase biomolecules.

Open image in new window

Graphical Abstract ?