Photodissociation of high molecular weight peptides and proteins in a two-stage linear time-of-flight mass spectrometer

193 nm Ultraviolet Photodissociation for the Characterization of Singly Charged Proteoforms Generated by MALDI

MALDI imaging allows for the near-cellular profiling of proteoforms directly from microbial, plant, and mammalian samples. Despite detecting hundreds of proteoforms, identification of unknowns with only intact mass information remains a distinct challenge, even with high mass resolving power and mass accuracy. To this end, many supplementary methods have been used to create experimental databases for accurate mass matching, including bulk or spatially resolved bottom-up and/or top-down proteomics. Herein, we describe the application of 193 nm ultraviolet photodissociation (UVPD) for fragmentation of quadrupole isolated singly charged ubiquitin (m/z 8565) by MALDI-UVPD on a UHMR HF Orbitrap. This platform permitted the high-resolution accurate mass measurement of not just terminal fragments but also large internal fragments. The outlined workflow demonstrates the feasibility of top-down analyses of isolated MALDI protein ions and the potential toward more comprehensive characterization of proteoforms in MALDI imaging applications.

Improvement of m/z accuracy for linear matrix-assisted laser desorption/ionization time-of-flight mass spectrometer

RATIONALE

Linear matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is widely used in analytical and biomedical applications. The use of delayed extraction increases the resolution, but the roughness of the matrix crystals and the misalignment of the target plate in the order of a few micrometers cause a substantial spread in the ion TOF values and a decrease in mass accuracy.

METHODS

The method of mass spectra correction based on the correlation of matrix fragment peaks in MALDI mass spectra was used. Experiments were performed using the MALDI-TOF instrument CMI-1600. SIMION 8.1 and MATLAB were used for ion motion simulations. Data analysis was done using the home-built custom-developed software and MATLAB.

RESULTS

It was shown that the peak position drift in the MALDI-TOF mass spectra depends linearly on the TOF in a wide mass range. While using the linear correction of the TOF scale, an increase in m/z accuracy of more than 10 times was achieved. The mass accuracy was limited by the resolution of the fast Analog-to-Digital Converter (ADC) used.

CONCLUSIONS

It is expected that the proposed method will significantly increase the dynamic range, since it becomes possible to sum up corrected individual mass spectra without a significant loss of resolution. Timescale adjusting can be used for both linear TOF instruments and reflector systems of various configurations.

193 nm Ultraviolet Photodissociation Mass Spectrometry of Tetrameric Protein Complexes Provides Insight into Quaternary and Secondary Protein Topology

Protein-protein interfaces and architecture are critical to the function of multiprotein complexes. Mass spectrometry-based techniques have emerged as powerful strategies for characterization of protein complexes, particularly for heterogeneous mixtures of structures. In the present study, activation and dissociation of three tetrameric protein complexes (streptavidin, transthyretin, and hemoglobin) in the gas phase was undertaken by 193 nm ultraviolet photodissociation (UVPD) for the characterization of higher order structure. High pulse energy UVPD resulted in the production of dimers and low charged monomers exhibiting symmetrical charge partitioning among the subunits (the so-called symmetrical dissociation pathways), consistent with the subunit organization of the complexes. In addition, UVPD promoted backbone cleavages of the monomeric subunits, the abundances of which corresponded to the more flexible loop regions of the proteins.

Formation of gas-phase peptide ions and their dissociation in MALDI: insights from kinetic and ion yield studies

Insights on mechanisms for the generation of gas-phase peptide ions and their dissociation in matrix-assisted laser desorption ionization (MALDI) gained from the kinetic and ion yield studies are presented. Even though the time-resolved photodissociation technique was initially used to determine the dissociation kinetics of peptide ions and their effective temperature, it was replaced by a simpler method utilizing dissociation yields from in-source decay (ISD) and post-source decay (PSD). The ion yields for a matrix and a peptide were measured by repeatedly irradiating a region on a sample and collecting ion signals until the sample in the region was completely depleted. Matrix- and peptide-derived gas-phase cations were found to be generated by pre-formed ion emission or by ion-pair emission followed by anion loss, but not by laser-induced ionization. The total number of ions, that is, matrix plus peptide, was found to be equal to the number of ions emitted from a pure matrix. A matrix plume was found to cool as it expanded, from around 800-1,000 K to 400-500 K. Dissociation of peptide ions along b/y channels was found to occur statistically, that is, following RRKM behavior. Small critical energy (E0  = 0.6-0.7 eV) and highly negative critical entropy (ΔS(‡)  = -30 to -25 eu) suggested that the transition structure was stabilized by multiple intramolecular interactions.

157 nm photodissociation of dipeptide ions containing N-terminal arginine

Twenty singly-charged dipeptide ions with N-terminal arginine were photodissociated using 157 nm light in both a linear ion-trap mass spectrometer and a MALDI-TOF-TOF mass spectrometer. Analogous to previous work on dipeptides containing C-terminal arginine, this set of samples enabled insights into the photofragmentation propensities associated with individual residues. In addition to familiar products such as a-, d-, and immonium ions, m2 and m2+13 ions were also observed. Certain side chains tended to cleave between their β and γ carbons without necessarily forming d- or w-type ions, and a few other ions were produced by the high-energy fragmentation of multiple bonds.

157 nm photodissociation of a complete set of dipeptide ions containing C-terminal arginine

Twenty singly-charged dipeptide ions with C-terminal arginine were photodissociated with 157 nm light and their tandem mass spectra recorded. Many of the small product ions that were observed are standard peptide fragments that have been commonly seen in VUV photodissociation studies. However, the study of a library of dipeptides containing all 20 N-terminal amino acids enabled the recognition of trends associated with the occurrence of w-, v-, and immonium ions, the observation of competition between forming N- and C-terminal fragments in dipeptide RR, and the identification of some unusual fragment ions appearing at masses of 183, 187, 196, and 197 Da. A highly accurate internal calibration of the photodissociation TOF-TOF data enabled molecular formulae for these four product ions to be derived. Their proposed structures reflect the rather high-energy nature of this fragmentation phenomenon.

Wavelength-tunable ultraviolet photodissociation (UVPD) of heparin-derived disaccharides in a linear ion trap

A set of three heparin-derived disaccharide deprotonated ions was isolated in a linear ion trap and subjected to UV laser irradiation in the 220-290 nm wavelength range. The dissociation yields of the deprotonated molecular ions were recorded as a function of laser wavelength. They revealed maximum absorption at 220 nm for the nonsulfated disaccharide, but centered at 240 nm for the sulfated species. The comparison of the fragmentation patterns between ultraviolet photodissociation (UVPD) at 240 nm and CID modes showed roughly the same distribution of fragment ions resulting from glycosidic bond cleavages. Interestingly, UVPD favored additional cross ring cleavages of A and X type ion series enabling easier sulfate group location. It also reduced small neutral losses (H(2)O).

Ultraviolet photofragmentation of biomolecular ions

Mass spectrometric identification of all types of molecules relies on the observation and interpretation of ion fragmentation patterns. Peptides, proteins, carbohydrates, and nucleic acids that are often found as components of complex biological samples represent particularly important challenges. The most common strategies for fragmenting biomolecular ions include low- and high-energy collisional activation, post-source decay, and electron capture or transfer dissociation. Each of these methods has its own idiosyncrasies and advantages but encounters problems with some types of samples. Novel fragmentation methods that can offer improvements are always desirable. One approach that has been under study for years but is not yet incorporated into a commercial instrument is ultraviolet photofragmentation. This review discusses experimental results on various biological molecules that have been generated by several research groups using different light wavelengths and mass analyzers. Work involving short-wavelength vacuum ultraviolet light is particularly emphasized. The characteristics of photofragmentation are examined and its advantages summarized.

Factors that impact the vacuum ultraviolet photofragmentation of peptide ions

Several groups have investigated the photodissociation of peptide ions with ultraviolet light. Significant differences have been reported with 157 and 193 nm excitation. Recent studies have shown that the mass analyzer can also influence the observed photofragment distribution. Comparison of experiments using different peptides, wavelengths, and mass analyzers is undesirably complicated. In the present work, several peptides are analyzed with both 157 and 193 nm photodissociation in tandem-TOF and linear ion trap mass spectrometers. The results indicate that the fragment ion distribution can be influenced by both the photodissociation wavelength and the mass analyzer. The two wavelengths generate similar spectra in an ion trap but quite different results in a tandem-TOF instrument.

Comparative studies of 193-nm photodissociation and TOF-TOFMS analysis of bradykinin analogues: the effects of charge site(s) and fragmentation timescales

The dissociation reactions of [M + H]+, [M + Na]+, and [M + Cu]+ ions of bradykinin (amino acid sequence RPPGFSPFR) and three bradykinin analogues (RPPGF, RPPGFSPF, PPGFSPFR) are examined by using 193-nm photodissociation and post-source decay (PSD) TOF-TOF-MS techniques. The photodissociation apparatus is equipped with a biased activation cell, which allows us to detect fragment ions that are formed by dissociation of short-lived (<1 mus) photo-excited ions. In our previously reported photodissociation studies, the fragment ions were formed from ions dissociating with lifetimes that exceeded 10 mus; thus these earlier photofragment ion spectra and post-source decay (PSD) spectra [composite of both metastable ion (MI) and collision-induced dissociation (CID)] were quite similar. On the other hand, short-lived photo-excited ions dissociate by simple bond cleavage reactions and other high-energy dissociation channels. We also show that product ion types and abundances vary with the location of the charge on the peptide ion. For example, H+ and Na+ cations can bind to multiple polar functional groups (basic amino acid side chains) of the peptide, whereas Cu+ ions preferentially bind to the guanidino group of the arginine side-chain and the N-terminal amine group. Furthermore, when Cu+ is the charge carrier, the abundances of non-sequence informative ions, especially loss of small neutral molecules (H2O and NH3) is decreased for both photofragment ion and PSD spectra relative to that observed for [M + H]+ and [M + Na]+ peptide ions.

Peptide sequencing by MALDI 193-nm photodissociation TOF MS

Ultraviolet photodissociation time-of-flight (TOF) mass spectrometry (MS) is described as a method for determination of peptide ion primary structure. Monoisotopic selection and bond-specific activation, combined with the rapidity of TOF MS analysis, render this technique invaluable to the rapidly expanding field of proteomics. Photofragment ion spectra of model peptides acquired using both post-source decay (PSD) focusing and TOF-TOF experimental methods are exhibited. Advantages of 193-nm photodissociation for de novo sequencing of peptide ions are discussed.

Specific photodissociation of peptides with multi-stage mass spectrometry

We report collision-induced dissociation (CID) and laser-induced dissociation (LID) performed at different wavelengths between 220 and 280 nm of the peptides leucine-enkephalin (protonated) and gramicidin A (sodiated). Hydrogen-atom losses and side-chain cleavages were observed in LID experiments. These losses depend on the laser wavelength and lead to the formation of radical ions. The fragmentations of these radicals, which are not observed in CID experiments, were investigated in multi-stage mass spectrometry experiments.

Photodissociation of singly protonated peptides at 193 nm investigated with tandem time-of-flight mass spectrometry

Photodissociation at 193 nm of some singly protonated peptides generated by matrix-assisted laser desorption/ionization was investigated using tandem time-of-flight mass spectrometry. For peptides with arginine at the C-terminus, x, upsilon, and w fragment ions were generated preferentially while a and d fragment ions dominated for peptides with arginine at the N-terminus. These are the same characteristics as photodissociation at 157 nm reported previously. Overall, the photodissociation spectra obtained at 157 and 193 nm were strikingly similar.

Photoinduced dissociation of electrospray-generated ions in an ion trap/time-of-flight mass spectrometer using a pulsed CO2 laser

An ion trap/time-of-flight (IT/TOF) mass spectrometer was developed and applied to infrared multiphoton dissociation (IRMPD) studies of ions generated by electrospray ionization. A pulsed 10.6- micro m laser beam from a CO(2) laser was used for excitation of trapped ions. Results from IRMPD of peptide ions show that this method provides useful information related to the amino acid sequence of analyzed peptides. Comparative studies show that IRMPD spectra are similar to those obtained using a 266-nm UV laser beam for excitation. However, in contrast to multiple-pulse excitation required at 266 nm, the energy of a single laser pulse in IRMPD is sufficient to induce dissociation of peptide ions. The laser power is practically an exclusive parameter that must be controlled in order to obtain IRMPD spectra that will provide the optimal structural information. It is further demonstrated that the IRMPD IT/TOF technique has the potential to probe the structural features of larger ions that cannot be readily fragmented by collision-induced dissociation (CID). A multiply charged ion of equine cytochrome c is successfully fragmented in a single laser pulse experiment. The IRMPD IT/TOF technique is also shown to be a promising tool for studying dissociation kinetics of peptide and protein ions. Unlike other methods that usually monitor the dissociation ion kinetics in a dissociation time frame of greater than milliseconds, the IT/TOF can promptly detect all product ions generated by the dissociation process, and thus monitor the dissociation process of peptides and proteins in a sub-millisecond time frame. This instrument allows us to determine the dissociation rates of cytochrome c ions using high-energy photoexcitation. It is found that the charge state of the protein ion has a significant effect on dissociation kinetics, which is consistent with that found under low-energy excitation experiments. It is shown that the increase in energy of a laser pulse from 130 to 180 mJ changes the dissociation rate constant for the +12 ion from k = 2.4 x 10(3) x s(-1) to k = 7.3 x 10(4) x s(-1). The +8 ion following excitation at 130 mJ dissociates slower with a rate constant of k = 2.6 x 10(2) x s(-1). The rate difference observed is attributed to conformational differences among the ions with different charge states.

Reactions of atomic transition-metal ions with long-chain alkanes

Understanding metal ion interactions with long-chain alkanes not only is of fundamental importance in the areas of organometallic chemistry, surface chemistry, and catalysis, but also has significant implication in mass spectrometry method development for the analysis of polyethylene. Polyethylene represents one of the most challenging classes of polymers to be analyzed by mass spectrometry. In this work, reactions of several transition-metal ions including Cr+, Mn+, Fe+, Co+, Ni+, Cu+, and Ag+ with long-chain alkanes, C28H58 and C36H74, are reported. A metal powder and the nonvolatile alkane are co-deposited onto a sample target of a laser desorption/ionization (LDI) time-of-flight mass spectrometer. The metal ions generated by LDI react with the vaporized alkane during desorption. It is found that all these metal ions can form adduct ions with the long-chain alkanes. Fe+, Co+, and Ni+ produce in-source fragment ions resulting from dehydrogenation and dealkylation of the adduct ions. The post-source decay (PSD) spectra of the metal-alkane adduct ions are recorded. It is shown that PSD of Ag+ alkane adduct ions produces bare metal ions only, suggesting weak binding between this metal ion and alkane. The PSD spectra of the Fe+, Co+, and Ni+ alkane adduct ions display extensive fragmentation. Fragment ions are also observed in the PSD spectra of Cr+, Mn+, and Cu+ alkane adduct ions. The high reactivity of Fe+, Co+, and Ni+ is consistent with that observed in small alkane systems. The unusually high reactivity of Cr+, Mn+, and Cu+ is rationalized by a reaction scheme where a long-chain alkane first forms a complex with a metal ion via ion/induced dipole interactions. If sufficient internal energy is gained during the complex formation, metal ions can be inserted into C-H and C-C bonds of the alkane, followed by fragmentation. The thermal energy of the neutral alkane is believed to be the main source of the internal energy acquired in the complex. Finally, the implication of this work on mass spectrometry method development for polyethylene analysis is discussed.

193-nm Photodissociation of ions from saturated and unsaturated aliphatic molecules

To determine the analytical utility of photodissociation as a general fragmentation technique for tandem mass spectrometry of organic ions, the ability to fragment those ions considered least likely to absorb photons efficiently was investigated. To this end, the ability to photodissociate ions of aliphatic compounds by using 193-nm photons has been studied. Three fragment ions, the C4H 9 (+) ion from n-hexane, the C4H 7 (+) ion from 2-hexene, and C4H 5 (+) from 2-hexyne, have been photodissociated. The fragmentation efficiencies for all three ions studied were between 25 and 45%. The photofragment ion spectrum for each precursor ion studied is made up of characteristic fragments. These spectra demonstrate the ability to photodissociate aliphatic ions that originate from both saturated and unsaturated molecules. This provides substantial hope that virtually all organic ions will be able to be photodissociated by using 193-nm photons.