Fragmentation behavior of a thiourea‐based reagent for protein structure analysis by collision‐induced dissociative chemical cross‐linking

The fragmentation behavior of a novel thiourea‐based cross‐linker molecule specifically designed for collision‐induced dissociation (CID) MS/MS experiments is described. The development of this cross‐linker is part of our ongoing efforts to synthesize novel reagents, which create either characteristic fragment ions or indicative constant neutral losses (CNLs) during tandem mass spectrometry allowing a selective and sensitive analysis of cross‐linked products. The new derivatizing reagent for chemical cross‐linking solely contains a thiourea moiety that is flanked by two amine‐reactive N‐hydroxy succinimide (NHS) ester moieties for reaction with lysines or free N‐termini in proteins. The new reagent offers simple synthetic access and easy structural variation of either length or functionalities at both ends. The thiourea moiety exhibits specifically tailored CID fragmentation capabilities—a characteristic CNL of 85 u—ensuring a reliable detection of derivatized peptides by both electrospray ionization (ESI) and matrix‐assisted laser desorption/ionization (MALDI) tandem mass spectrometry and as such possesses a versatile applicability for chemical cross‐linking studies. A detailed examination of the CID behavior of the presented thiourea‐based reagent reveals that slight structural variations of the reagent will be necessary to ensure its comprehensive and efficient application for chemical cross‐linking of proteins. Copyright © 2010 John Wiley & Sons, Ltd.     

Dissociation behavior of a bifunctional tempo‐active ester reagent for peptide structure analysis by free radical initiated peptide sequencing (FRIPS) mass spectrometry

We have synthesized a homobifunctional active ester cross‐linking reagent containing a TEMPO (2,2,6,6‐tetramethylpiperidine‐1‐oxy) moiety connected to a benzyl group (Bz), termed TEMPO‐Bz‐linker. The aim for designing this novel cross‐linker was to facilitate MS analysis of cross‐linked products by free radical initiated peptide sequencing (FRIPS). The TEMPO‐Bz‐linker was reacted with all 20 proteinogenic amino acids as well as with model peptides to gain detailed insights into its fragmentation mechanism upon collision activation. The final goal of this proof‐of‐principle study was to evaluate the potential of the TEMPO‐Bz‐linker for chemical cross‐linking studies to derive 3D‐structure information of proteins. Our studies were motivated by the well documented instability of the central NO―C bond of TEMPO‐Bz reagents upon collision activation. The fragmentation of this specific bond was investigated in respect to charge states and amino acid composition of a large set of precursor ions resulting in the identification of two distinct fragmentation pathways. Molecular ions with highly basic residues are able to keep the charge carriers located, i.e. protons or sodium cations, and consequently decompose via a homolytic cleavage of the NO―C bond of the TEMPO‐Bz‐linker. This leads to the formation of complementary open‐shell peptide radical cations, while precursor ions that are protonated at the TEMPO‐Bz‐linker itself exhibit a charge‐driven formation of even‐electron product ions upon collision activation. MS³ product ion experiments provided amino acid sequence information and allowed determining the cross‐linking site. Our study fully characterizes the CID behavior of the TEMPO‐Bz‐linker and demonstrates its potential, but also its limitations for chemical cross‐linking applications utilizing the special features of open‐shell peptide ions on the basis of selective tandem MS analysis. Copyright © 2015 John Wiley & Sons, Ltd.     

A biuret‐derived,MS‐cleavable cross‐linking reagent for protein structural analysis: A proof‐of‐principle study

Chemical cross‐linking combined with mass spectrometry (XL‐MS) and computational modeling has evolved as an alternative method to derive protein 3D structures and to map protein interaction networks. Special focus has been laid recently on the development and application of cross‐linkers that are cleavable by collisional activation as they yield distinct signatures in tandem mass spectra. Building on our experiences with cross‐linkers containing an MS‐labile urea group, we now present the biuret‐based, CID‐MS/MS‐cleavable cross‐linker imidodicarbonyl diimidazole (IDDI) and demonstrate its applicability for protein cross‐linking studies based on the four model peptides angiotensin II, MRFA, substance P, and thymopentin.     

Heterobifunctional isotope‐labeled amine‐reactive photo‐cross‐linker for structural investigation of proteins by matrix‐assisted laser desorption/ionization tandem time‐of‐flight and electrospray ionization LTQ‐Orbitrap mass spectrometry

Chemical cross‐linking combined with a subsequent enzymatic digestion and mass spectrometric analysis of the created cross‐linked products presents an alternative approach to assess low‐resolution protein structures. By covalently connecting pairs of functional groups within a protein or a protein complex a set of structurally defined interactions is built up. We synthesized the heterobifunctional amine‐reactive photo‐cross‐linker N‐succinimidyl p‐benzoyldihydrocinnamate as a non‐deuterated (SBC) and doubly deuterated derivative (SBDC). Applying a 1:1 mixture of SBC and SBDC for cross‐linking experiments aided the identification of cross‐linked amino acids in the mass spectra based on the characteristic isotope patterns of fragment ions. The cross‐linker was applied to the calcium‐binding protein calmodulin with a subsequent analysis of cross‐linked products by nano‐high‐performance liquid chromatography matrix‐assisted laser desorption/ionization tandem time‐of‐flight mass spectrometry (nano‐HPLC/MALDI‐TOF/TOF‐MS) and nano‐HPLC/nano‐electrospray ionization (ESI)‐LTQ‐Orbitrap‐MS. Copyright © 2009 John Wiley & Sons, Ltd.     

Collision‐induced dissociative chemical cross‐linking reagent for protein structure characterization: applied Edman chemistry in the gas phase

Chemical cross‐linking combined with a subsequent enzymatic digestion and mass spectrometric analysis of the created cross‐linked products presents an alternative approach to assess low‐resolution protein structures and to gain insight into protein interfaces. In this contribution, we report the design of an innovative cross‐linker based on Edman degradation chemistry, which leads to the formation of indicative mass shifted fragment ions and constant neutral losses (CNLs) in electrospray ionization (ESI)‐tandem‐mass spectrometry (MS/MS) product ion mass spectra, allowing an unambiguous identification of cross‐linked peptides. Moreover, the characteristic neutral loss reactions facilitate automated analysis by multiple reaction monitoring suited for high throughput studies with good sensitivity and selectivity. The functioning of the novel cross‐linker relies on the presence of a highly nucleophilic sulfur in a thiourea moiety, safeguarding for effective intramolecular attack leading to predictive and preferred cleavage of a glycyl‐prolyl amide bond. Our innovative analytical concept and the versatile applicability of the collision‐induced dissociative chemical cross‐linking reagent are exemplified for substance P, luteinizing hormone releasing hormone LHRH and lysozyme. The novel cross‐linker is expected to have a broad range of applications for probing protein tertiary structures and for investigating protein–protein interactions. Copyright © 2009 John Wiley & Sons, Ltd.     

Poly(styrene‐co‐glycerol dimethacrylate): Synthesis,characterization, and application as a resin for gel‐phase peptide synthesis

An efficient cross‐linked polymer support for solid‐phase synthesis was prepared by introducing glycerol dimethacrylate cross‐linker to polystyrene network using free radical aqueous suspension polymerization. The support was characterized by various spectroscopic methods. Morphological feature of the resin was analyzed by microscopy. The polymerization reaction was investigated with respect to the effect of amount of cross‐linking agent, which in turn vary the swelling, loading, and the mechanical stability of the resin. The solvent uptake of the polymer was studied in relation to cross‐linking and compared with Merrifield resin. The stability of the resin was tested in different synthetic conditions used for solid‐phase peptide synthesis. Hydroxy group of the support was derivatized to chloro and then amino groups using different reagents and reaction conditions. Efficiency of the support was tested and compared with TentaGel? resin by following different steps involved in the synthesis of the 65–74 fragment of acyl carrier protein. The results showed that the poly(styrene‐co‐glycerol dimethacrylate) (GDMA‐PS) is equally efficient as TentaGel resin in peptide synthesis. The purity of the peptides was analyzed by HPLC and identities were determined by mass spectroscopy and amino acid analysis. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4382–4392, 2005     

Stereospecific control of peptide gas‐phase ion chemistry with cis and trans cyclo ornithine residues

We report non‐chiral amino acid residues cis‐ and trans‐1,4‐diaminocyclohexane‐1‐carboxylic acid (cyclo‐ornithine, cO) that exhibit unprecedented stereospecific control of backbone dissociations of singly charged peptide cations and hydrogen‐rich cation radicals produced by electron‐transfer dissociation. Upon collision‐induced dissociation (CID) in the slow heating regime, peptide cations containing trans‐cO residues undergo facile backbone cleavages of amide bonds C‐terminal to trans‐cO. By contrast, peptides with cis‐cO residues undergo dissociations at several amide bonds along the peptide ion backbone. Diastereoisomeric cO‐containing peptides thus provide remarkably distinct tandem mass spectra. The stereospecific effect in CID of the trans‐cO residue is explained by syn‐facially directed proton transfer from the 4‐ammonium group at cO to the C‐terminal amide followed by neighboring group participation in the cleavage of the CO―NH bond, analogous to the aspartic acid and ornithine effects. Backbone dissociations of diastereoisomeric cO‐containing peptide ions generate distinct [b_n]⁺‐type fragment ions that were characterized by CID‐MS³ spectra. Stereospecific control is also reported for electron‐transfer dissociation of cis‐ and trans‐cO containing doubly charged peptide ions. The stereospecific effect upon electron transfer is related to the different conformations of doubly charged peptide ions that affect the electron attachment sites and ensuing N―C_α bond dissociations.     

Understanding chemical reactivity for homo‐ and heterobifunctional protein cross‐linking agents

Chemical cross‐linking, combined with mass spectrometry, has been applied to map three‐dimensional protein structures and protein–protein interactions. Proper choice of the cross‐linking agent, including its reactive groups and spacer arm length, is of great importance. However, studies to understand the details of reactivity of the chemical cross‐linkers with proteins are quite sparse. In this study, we investigated chemical cross‐linking from the aspects of the protein structures and the cross‐linking reagents involved, by using two structurally well‐known proteins, glyceraldehyde 3‐phosohate dehydrogenase and ribonuclease S. Chemical cross‐linking reactivity was compared using a series of homo‐ and hetero‐bifunctional cross‐linkers, including bis(sulfosuccinimidyl) suberate, dissuccinimidyl suberate, bis(succinimidyl) penta (ethylene glycol), bis(succinimidyl) nona (ethylene glycol), m‐maleimidobenzoyl‐N‐hydroxysulfosuccinimide ester, 2‐pyridyldithiol‐tetraoxaoctatriacontane‐N‐hydrosuccinimide and succinimidyl‐[(N‐maleimidopropionamido)‐tetracosaethyleneglycol]ester. The protein structure itself, especially the distances between target amino acid residues, was found to be a determining factor for the cross‐linking efficiency. Moreover, the reactive groups of the chemical cross‐linker also play an important role; a higher cross‐linking reaction efficiency was found for maleimides compared to 2‐pyrimidyldithiols. The reaction between maleimides and sulfhydryl groups is more favorable than that between N‐hydroxysuccinimide esters and amine groups, although cysteine residues are less abundant in proteins compared to lysine residues. Copyright © 2013 John Wiley & Sons, Ltd.     

Synthesis of thermo‐responsive microgels in supercritical carbon dioxide using ethylene glycol dimethacrylate as a cross‐linker

Herein, we report the preparation of thermo‐responsive polymers in a green medium. The white, dry, fine powders were obtained directly from the cross‐linking polymerization of N‐isopropylacrylamide (NIPA) in supercritical carbon dioxide (scCO₂) at pressures ranging from 10 to 28 MPa utilizing ethylene glycol dimethacrylate (EGDMA) as a cross‐linker. The effects of reaction pressure, cross‐linker ratio, initiator concentration, and reaction time were investigated. In the presence of this cross‐linker (26.4% w/w), much smaller poly(N‐isopropylacrylamide) (PNIPA) microgels (<0.2 µm diameter) were formed, and it was shown that the particle size and the morphology of the polymer were strongly dependent on the cross‐linker ratio in scCO₂. Copyright © 2009 John Wiley & Sons, Ltd.     

Synthesis and Spatiotemporal Modification of Biocompatible and Stimuli‐Responsive Carboxymethyl Cellulose Hydrogels Using Thiol‐Norbornene Chemistry

Carboxymethyl cellulose (CMC) is functionalized with norbornene groups to undergo thiol‐norbornene cross‐linking reactions. Hydrogels synthesized from a single norbornene‐modified carboxymethyl cellulose (NorCMC) via a light‐initiated thiol‐ene cross‐linking reaction with a variety of dithiol cross‐linkers yield hydrogels with a tunable compression modulus ranging from 1.7 to 103 kPa. Additionally, thermoresponsiveness is spatiotemporally imparted to NorCMC hydrogels by photopatterning a dithiol‐terminated poly(N‐isopropyl acrylamide) cross‐linker, enabling swelling and topological control of the hydrogels as a function of incubation temperature. NorCMC hydrogels are cytocompatible as the viability of encapsulated human mesenchymal stem cells (hMSCs) is greater than 85% after 21 d while using a variety of cross‐linkers. Moreover, hMSCs can remodel, adhere, and spread in the NorCMC matrix cross‐linked with a matrix metalloproteinase‐degradable peptide, further demonstrating the utility of these materials as a tunable biomaterial.     

Covalent and non‐covalent binding in the ion/ion charge inversion of peptide cations with benzene‐disulfonic acid anions

Protonated angiotensin II and protonated leucine enkephalin‐based peptides, which included YGGFL, YGGFLF, YGGFLH, YGGFLK and YGGFLR, were subjected to ion/ion reactions with the doubly deprotonated reagents 4‐formyl‐1,3‐benzenedisulfonic acid (FBDSA) and 1,3‐benzenedisulfonic acid (BDSA). The major product of the ion/ion reaction is a negatively charged complex of the peptide and reagent. Following dehydration of [M + FBDSA‐H]^? via collisional‐induced dissociation (CID), angiotensin II (DRVYIHPF) showed evidence for two product populations, one in which a covalent modification has taken place and one in which an electrostatic modification has occurred (i.e. no covalent bond formation). A series of studies with model systems confirmed that strong non‐covalent binding of the FBDSA reagent can occur with subsequent ion trap CID resulting in dehydration unrelated to the adduct. Ion trap CID of the dehydration product can result in cleavage of amide bonds in competition with loss of the FBDSA adduct. This scenario is most likely for electrostatically bound complexes in which the peptide contains both an arginine residue and one or more carboxyl groups. Otherwise, loss of the reagent species from the complex, either as an anion or as a neutral species, is the dominant process for electrostatically bound complexes. The results reported here shed new light on the nature of non‐covalent interactions in gas phase complexes of peptide ions that can be used in the rationale design of reagent ions for specific ion/ion reaction applications. Copyright © 2012 John Wiley & Sons, Ltd.     

The First Zero‐Length Mass Spectrometry‐Cleavable Cross‐Linker for Protein Structure Analysis

Combining the properties of a zero‐length cross‐linker with cleavability by tandem mass spectrometry (MS/MS) poses great advantages for protein structure analysis using the cross‐linking/MS approach. These include a reliable, automated data analysis and the possibility to obtain short‐distance information of protein 3D‐structures. We introduce 1,1′‐carbonyldiimidazole (CDI) as an easy‐to‐use and commercially available, low‐cost reagent that ideally fulfils these features. CDI bridges primary amines and hydroxy groups in proteins with the lowest possible spacer length of one carbonyl unit (ca. 2.6 Å). The cross‐linking reaction can be conducted under physiological conditions in the pH range between 7.2 and 8. Urea and carbamate cross‐linked products are cleaved upon collisional activation during MS/MS experiments generating characteristic product ions, greatly improving the unambiguous identification of cross‐links. Our innovative analytical concept is exemplified and applied for bovine serum albumin (BSA), wild‐type tumor suppressor p53, an intrinsically disordered protein, and retinal guanylyl cyclase activating protein‐2 (GCAP‐2).     

Gas‐phase fragmentation study of biotin reagents using electrospray ionization tandem mass spectrometry on a quadrupole orthogonal time‐of‐flight hybrid instrument

In this study, we evaluated, by electrospray ionization mass spectrometry (ESI‐MS) and collision‐induced dissociation tandem mass spectrometry (CID‐MS/MS) using a quadrupole orthogonal time‐of‐flight (QqToF)‐MS/MS hybrid instrument, the gas‐phase fragmentations of some commercially available biotinyl reagents. The biotin reagents used were: psoralen‐BPE 1, p‐diazobenzoyl biocytin (DBB) 2, photoreactive biotin 3, biotinyl‐hexaethyleneglycol dimer 4, and the sulfo‐SBED 5. The results showed that, during ESI‐MS and CID‐MS/MS analyses, the biotin reagents followed a similar gas‐phase fragmentation pattern and the cleavages usually occurred at either end of the spacer arm of the biotin reagents. In general we have observed that the CID‐MS/MS fragmentation routes of the five precursor protonated molecules obtained from the biotin linkers 1–5 afforded a series of product ions formed essentially by similar routes. The genesis and the structural identities of all the product ions obtained from the biotin linkers 1–5 have been assigned. All the exact mass assignments of the protonated molecules and the product ions were verified by conducting separate CID‐MS/MS analysis of the deuterium‐labelled precursor ions. Copyright © 2009 John Wiley & Sons, Ltd.     

Novel organotin‐containing shell‐cross‐linked knedel and core‐cross‐linked knedel: Synthesis and application in catalysis

A series of novel organotin‐containing core‐cross‐linked knedels and shell‐cross‐linked knedels were first synthesized facilely from poly(styrene)‐b‐poly(acrylate acid) nanoparticles in different selective solvents [Tetrahydrofuran (THF)/H₂O or THF/n‐octane] by using organotin compound 1,3‐dichloro‐tetra‐n‐butyl‐distannoxane as a new cross‐linker. The formation of the 1‐chloro‐3‐carboxylato‐tetra‐n‐butyl‐distannoxane layer in our cross‐linking reaction was supported by Fourier transform infrared (FT‐IR) and inductive coupled plasma emission spectrometer (ICP) analysis of the resulting shell‐cross‐linked knedels and core‐cross‐linked knedels. Transmission electron microscopy (TEM) study showed the spherical morphology and the size of the core‐cross‐linked knedels and shell‐cross‐linked knedel. Especially, the layer structure of the core‐cross‐linked knedels was clearly displayed in TEM image. The increase of extent of cross‐linking lead to the increasing of diameter for the shell‐cross‐linked knedels, whereas there was no significant effect on the core‐cross‐linked knedels. Dynamic light scattering (DLS) measurements gave hydrodynamic diameters of the core‐cross‐linked knedels that were in agreement with the TEM diameters. Moreover, the wall thickness of the shell layer of the core‐cross‐linked knedels could be easily modified by varying the block copolymer composition. Notably, the organotin‐containing core‐cross‐linked knedel exhibited highly efficient catalytic activity for the aqueous esterification reaction under nearly neutral conditions. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

Thiol‐acrylate main‐chain liquid‐crystalline elastomers with tunable thermomechanical properties and actuation strain

The purpose of this study was to investigate the influence of cross‐linking on the thermomechanical behavior of liquid‐crystalline elastomers (LCEs). Main‐chain LCE networks were synthesized via a thiol‐acrylate Michael addition reaction. The robust nature of this reaction allowed for tailoring of the behavior of the LCEs by varying the concentration and functionality of the cross‐linker. The isotropic rubbery modulus, glass transition temperature, and strain‐to‐failure showed strong dependence on cross‐linker concentration and ranged from 0.9 MPa, 3 °C, and 105% to 3.2 MPa, 25 °C, and 853%, respectively. The isotropic transition temperature (T_i) was shown to be influenced by the functionality of the cross‐linker, ranging from 70 °C to 80 °C for tri‐ and tetra‐functional cross‐linkers. The magnitude of actuation can be tailored by controlling the amount of cross‐linker and applied stress. Actuation increased with increased applied stress and decreased with greater amounts of cross‐linking. The maximum strain actuation achieved was 296% under 100 kPa of bias stress, which resulted in work capacity of 296 kJ/m³ for the lowest cross‐linked networks. Overall, the experimental results provide a fundamental insight linking thermomechanical properties and actuation to a homogenous polydomain nematic LCE networks with order parameters of 0.80 when stretched. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 157–168     

Size and morphology controllable core cross‐linked self‐aggregates from poly(ethylene glycol‐b‐succinimide) copolymers

We developed a simple route to prepare stabilized micelles and nanovesicles in aqueous solutions. A hydrophobic poly(succinimide) (PSI) was conjugated with the hydrophilic poly(ethylene glycol) (PEG) as a new type of cross‐linkable unit. Spherical aggregates were formed when dissolving the amphiphilic PEG₆₈₂‐b‐PSI₁₃₀ copolymer in aqueous solutions directly, and polymer nanovesicles were prepared by a precipitation‐dialysis method using PEG₄₅₅‐b‐PSI₁₃₀ copolymer. Bifunctional primary amine was added to the micelle or nanovesicle solutions to prepare cross‐linked structures via aminolysis reaction of the succinimide units. The degree of cross‐linking was controlled by adjusting the molar ratio of the cross‐linker to the succinimide units. Increasing the degree of cross‐linking leads to the compaction of the micelle core thus reduced diameter. The cross‐linked polymer micelles or nanovesicles maintained their morphology in extremely diluted solutions because of their structural stability. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

Development of a tandem time‐of‐flight mass spectrometer with an electrospray ionization ion source

A new tandem time‐of‐flight mass spectrometer with an electrospray ionization ion source ‘ESI‐TOF/quadTOF’ was designed and constructed to achieve the desired aim of structural elucidation via high‐energy collision‐induced dissociation (CID), and the simultaneous detection of all fragment ions. The instrument consists of an orthogonal acceleration‐type ESI ion source, a linear TOF mass spectrometer, a collision cell, a quadratic‐field ion mirror and a microchannel plate detector. High‐energy CID spectra of doubly protonated angiotensin II and bradykinin were obtained. Several fragment ions such as a‐, d‐, v‐ and w‐type ions, characteristic of high‐energy CID, were clearly observed in these spectra. These high‐energy CID fragment ions enabled confirmation of the complete sequence, including leucine–isoleucine determinations. It was demonstrated that high‐energy CID of multiply protonated peptides could be achieved in the ESI‐TOF/quadTOF. Copyright © 2010 John Wiley & Sons, Ltd.     

A One‐Pot Cross‐Pinacol Coupling/Rearrangement Procedure

A new catalytic retro‐pinacol/cross‐pinacol reaction, followed by subsequent rearrangement or deoxygenation of the intermediately formed vicinal diols, is described. This operationally simple one‐pot protocol allows isolation of geminal α,α‐diphenyl ketones or 1,1‐diphenyl alkenes with high yields and selectivities.     

Chemical cross‐linking with a diazirine photoactivatable cross‐linker investigated by MALDI‐ and ESI‐MS/MS

Crystallography and nuclear magnetic resonance are well‐established methods to study protein tertiary structure and interactions. Despite their usefulness, such methods are not applicable to many protein systems. Chemical cross‐linking of proteins coupled with mass spectrometry allows low‐resolution characterization of proteins and protein complexes based on measuring distance constraints from cross‐links. In this work, we have investigated cross‐linking by means of a heterobifunctional cross‐linker containing a traditional N‐hydroxysuccinimide (NHS) ester and a UV photoactivatable diazirine group. Activation of the diazirine group yields a highly reactive carbene species, with potential to increase the number of cross‐links compared with homobifunctional, NHS‐based cross‐linkers. Cross‐linking reactions were performed on model systems such as synthetic peptides and equine myoglobin. After reduction of the disulfide bond, the formation of intra‐ and intermolecular cross‐links was identified and the peptides modified with both NHS and diazirine moieties characterized. Fragmentation of these modified peptides reveals the presence of a marker ion for intramolecular cross‐links, which facilitates identification. Copyright © 2010 John Wiley & Sons, Ltd.     

Comparison of CID,ETD and metastable atom‐activated dissociation (MAD) of doubly and triply charged phosphorylated tau peptides

The fragmentation behavior of the 2+ and 3+ charge states of eleven different phosphorylated tau peptides was studied using collision‐induced dissociation (CID), electron transfer dissociation (ETD) and metastable atom‐activated dissociation (MAD). The synthetic peptides studied contain up to two known phosphorylation sites on serine or threonine residues, at least two basic residues, and between four and eight potential sites of phosphorylation. CID produced mainly b‐/y‐type ions with abundant neutral losses of the phosphorylation modification. ETD produced c‐/z‐type ions in highest abundance but also showed numerous y‐type ions at a frequency about 50% that of the z‐type ions. The major peaks observed in the ETD spectra correspond to the charge‐reduced product ions and small neutral losses from the charge‐reduced peaks. ETD of the 2+ charge state of each peptide generally produced fewer backbone cleavages than the 3+ charge state, consistent with previous reports. Regardless of charge state, MAD achieved more extensive backbone cleavage than CID or ETD, while retaining the modification(s) in most cases. In all but one case, unambiguous modification site determination was achieved with MAD. MAD produced 15–20% better sequence coverage than CID and ETD for both the 2+ and 3+ charge states and very different fragmentation products indicating that the mechanism of fragmentation in MAD is unique and complementary to CID and ETD. Copyright © 2012 John Wiley & Sons, Ltd.