Surface-induced dissociation of small molecules, peptides, and non-covalent protein complexes

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250

Mass spectrometry is fast becoming a vital approach not only for the identification and quantification of proteins, but also for the study of the noncovalent assemblies they form. Approaches for ionizing, transmitting, and detecting protein complexes intact in the mass spectrometer are now well established. The challenge has therefore shifted to developing and applying mass spectrometry approaches to elucidate the structure of such species. A crucial aspect to this goal is inducing their disassembly in the gas phase to mine information as to their composition and organization. Here the consequences of collisionally activating protein complexes are illustrated through ion mobility mass spectrometry measurements and discussed in the context of the current literature. Although a consensus view of the mechanism of dissociation is starting to emerge, it is also clear that a number of aspects remain unresolved. These outstanding questions and frontier challenges must be addressed if gas-phase dissociative approaches are to reach their full potential in the study of protein assemblies. . Since that time technological and methodological developments have continued apace [2][3][4][5], such that the MS of such large species is no longer merely a technical curiosity, but rather a bona fide approach for structural biologists [6]. The many advantages that MS possesses, including speed and sensitivity of analysis [7], have made it integral to the fields of proteomics and systems biology [8,9]. The long-term challenge now is to extend the technology and methodology such that all higher levels of protein structure, from the secondary to the quinary [10], might be characterized rapidly and effectively by means of MS.Such a revolution will require the addition to, and adaptation of, the current conventional MS-based proteomic strategy. A cornerstone of this is tandem MS, wherein ions of interest are subjected to gas-phase dissociation and the fragments analyzed to provide protein sequence, and thus identity, information [11]. Recently much effort has been made to perform analogous experiments on protein complexes, whereby they are dissociated in the mass spectrometer to provide mass information on their constituents [12]. Furthermore, some evidence suggests that, aside from just providing the identity of subunits, the gas-phase dissociation process may even reveal details as to how these subunits are organized within the oligomer [13]. As such, the possibility has arisen that gas-phase dissociation coupled to MS might eventually allow the reverse engineering of protein assemblies.Over the last few years a considerable body of literature has emerged regarding the mechanism of the gas-phase dissociation of protein assemblies. A variety of activation techniques have been used [14 -18], but the most popular approach for the gas-phase dissociation of protein assemblies is currently collision-induced dissociation (CID). It is likely this is primarily attributable to its ease of implementation and its incorporation into the quadrupole t...

Section: Frontiers In Gas-phase Activation Of Protein Complexesmentioning

confidence: 99%

Section: Frontiers In Gas-phase Activation Of Protein Complexesmentioning

confidence: 99%

Collisional activation of protein complexes: Picking up the pieces

Benesch

2009

187

250

“…Melittin, kassinin, Lys [0]bradykinin, bradykinin, dynorphin-␤, GSK-␤ ␤ inhibitor, myosin kinase inhibitor, and mouse ANP [1][2][3][4][5][6][7][8][9][10][11] were purchased from American Peptide Company (Sunnyvale, CA). Polyalanine peptides were synthesized in-house using standard Fmoc coupling methodology.…”

Section: Methodsmentioning

confidence: 99%

“…here are a variety of mainstream fragmentation methodologies available for interrogating peptides, including collision-induced dissociation (CID) [1], infrared multiphoton photodissociation (IRMPD) [2], electron capture dissociation (ECD) [3], and electron-transfer dissociation (ETD) [4]. In addition, there are other methods that can be used, such as surface induced dissociation (SID) [5], black-body infrared radiative dissociation (BIRD) [6], along with various photodissociation experiments employing high-energy lasers [7][8][9][10][11]. Though none of these techniques is perfect, each has characteristic strengths and weaknesses.…”

mentioning

confidence: 99%

Rapid peptide fragmentation without electrons, collisions, infrared radiation, or native chromophores

Yeh

Sun

Meneses

et al. 2009

Ultraviolet photodissociation of peptides followed by mass analysis has several desirable advantages relative to other methods, yet it has not found widespread use due to several limitations. One shortcoming is the inefficiency with which peptides absorb in the ultraviolet. This issue has a simple solution and can be circumvented by the attachment of noncovalent adducts that contain appropriate chromophores. Subsequent photoactivation of the chromophore leads to vibrational excitation of the complex and eventually to fragmentation of the peptide. Herein, the energetics that control the efficiency of this process are examined as a function of the characteristics of both the peptide and the noncovalently attached chromophore. Fragmentation efficiency decreases with increasing peptide size and is also constrained by the binding energy of the noncovalent adduct. The optimum chromophore should have excellent absorption at the excitation wavelength and a low luminescence quantum yield. It is demonstrated that a naphthyl based 18-crown-6 adduct is ideally suited for attaching to a variety peptides and fragmenting them following absorption of 266 nm light. [7][8][9][10][11]. Though none of these techniques is perfect, each has characteristic strengths and weaknesses. For example CID is easily employed in the source region of any instrument with atmospheric pressure ionization. CID is also easily accommodated elsewhere in an instrument as long as high vacuum is not required. In contrast, IRMPD is well suited for collisionless environments. In this regard, CID and IRMPD provide complementary capabilities. Furthermore, since both methods fragment ions by the stepwise addition of small amounts of energy, the results obtained are frequently quite similar.However, CID and IRMPD are both limited by the fact that energy deposition occurs over a relatively long time scale, typically milliseconds to seconds. In contrast, ultraviolet photodissociation (UVPD) occurs on a much shorter time scale and can yield fragment ions characteristic of CID or IRMPD. However, the major limitation of UVPD is that the precursor ion must contain a suitable chromophore. For peptides, UVPD requires either short wavelength lasers (less than 200 nm) or peptides rich in tyrosine, tryptophan, and phenylalanine that can absorb at longer wavelengths. Therefore, UVPD is either limited to a small subset of all peptides or constrained by undesirable technical challenges which are encountered when working in the vacuum ultraviolet. Thus, widespread implementation of UVPD for peptide fragmentation has been to date somewhat limited.However, Brodbelt and coworkers have recently described a method to circumvent the requirement for aromatic residues or short wavelength lasers [12]. In this work, a noncovalently attached chromophore was used to absorb energy from a photon and transfer it to a peptide, causing the peptide to fragment. 18-crown-6 ether (18C6), which preferentially associates with lysine residues via the formation of three hydrogen bonds, was used for...

“…An alternative technique to CID, surface-induced dissociation (SID) [8] has been successfully used for ion fragmentation studies of small molecules [9 -14], peptides [15][16][17][18][19][20][21][22][23], and large molecules and macromolecular assemblies such as proteins and protein/protein complexes [24 -26]. Other aspects of SID have been reviewed elsewhere [27][28][29]. Compared to CID, SID has several advantages.…”

mentioning

confidence: 99%

Kinetics of Surface-Induced Dissociation of N(CH₃)₄⁺ and N(CD₃)₄⁺ Using Silicon Nanoparticle Assisted Laser Desorption/Ionization and Laser Desorption/Ionization

Yoon

Gamage

Gillig

et al. 2009

Self Cite

The implementation of surface-induced dissociation (SID) to study the fast dissociation kinetics (sub-microsecond dissociation) of peptides in a MALDI TOF instrument has been reported previously. Silicon nanoparticle assisted laser desorption/ionization (SPALDI) now allows the study of small molecule dissociation kinetics for ions formed with low initial source internal energy and without MALDI matrix interference. The dissociation kinetics of N(CH 3 ) 4 ϩ and N(CD 3 ) 4 ϩ were chosen for investigation because the dissociation mechanisms of N(CH 3 ) 4 ϩ have been studied extensively, providing well-characterized systems to investigate by collision with a surface. With changes in laboratory collision energy, changes in fragmentation timescale and dominant fragment ions were observed, verifying that these ions dissociate via unimolecular decay. At lower collision energies, methyl radical (CH 3 ) loss with a submicrosecond dissociation rate is dominant, but consecutive H loss after CH 3 loss becomes dominant at higher collision energies. These observations are consistent with the known dissociation pathways. The dissociation rate of CH 3 loss from N(CH 3 ) 4 ϩ formed by SPALDI and dissociated by an SID lab collision energy of 15 eV corresponds to log k ϭ 8.1, a value achieved by laser desorption ionization (LDI) and SID at 5 eV. The results obtained with SPALDI SID and LDI SID confirm that (1) the dissociation follows unimolecular decay as predicted by RRKM calculations; (2) the SPALDI process deposits less initial energy than LDI, which has advantages for kinetics studies; and (3) fluorinated self-assembled monolayers convert about 18% of laboratory collision energy into internal energy. SID TOF experiments combined with SPALDI and peak shape analysis enable the measurement of dissociation rates for fast dissociation of small molecules. [15][16][17][18][19][20][21][22][23], and large molecules and macromolecular assemblies such as proteins and protein/protein complexes [24 -26]. Other aspects of SID have been reviewed elsewhere [27][28][29]. Compared to CID, SID has several advantages. Most notably, SID is a single-collision process with a defined impact plane and arrival time, a very fast activation time [30], and high kinetic to internal energy conversion efficiency. Rice-Ramsperger-Kassel-Marcus (RRKM) modeling has successfully explained unimolecular decay processes by SID [18 -20]. Dynamics simulations have also been carried out to investigate ion-surface collisions [31,32].Matrix-assisted laser desorption/ionization surfaceinduced dissociation time-of-flight (MALDI SID TOF) spectra of small peptides, such as des-R 1 -bradykinin and des-R 9 -bradykinin, were reported previously [21].