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.

Extracting both peptide sequence and glycan structural information by 157 nm photodissociation of N-linked glycopeptides

The 157 nm photodissociation of N-linked glycopeptides was investigated in MALDI tandem time-of-flight (TOF) and linear ion trap mass spectrometers. Singly charged glycopeptides yielded abundant peptide and glycan fragments. The peptide fragments included a series of x-, y-, v-, and w- ions with the glycan remaining intact. These provide information about the peptide sequence and the glycosylation site. In addition to glycosidic fragments, abundant cross-ring glycan fragments that are not observed in low-energy CID were detected. These fragments provide insight into the glycan sequence and linkages. Doubly charged glycopeptides generated by nanospray in the linear ion trap mass spectrometer also yielded peptide and glycan fragments. However, the former were dominated by low-energy fragments such as b- and y- type ions while glycan was primarily cleaved at glycosidic bonds.

Identification of isomeric N-glycan structures by mass spectrometry with 157 nm laser-induced photofragmentation

Characterization of structural isomers has become increasingly important and extremely challenging in glycobiology. This communication demonstrates the capability of ion-trap mass spectrometry in conjunction with 157 nm photofragmentation to identify different structural isomers of permethylated N-glycans derived from ovalbumin without chromatographic separation. The results are compared with collision-induced dissociation (CID) experiments. Photodissociation generates extensive cross-ring fragment ions as well as diagnostic glycosidic product ions that are not usually observed in CID MS/MS experiments. The detection of these product ions aids in characterizing indigenous glycan isomers. The ion trap facilitates MS(n) experiments on the diagnostic glycosidic fragments and cross-ring product ions generated through photofragmentation, thus allowing unambiguous assignment of all of the isomeric structures associated with the model glycoprotein used in this study. Photofragmentation is demonstrated to be a powerful technique for the structural characterization of glycans.

Use of 157-nm photodissociation to probe structures of y- and b-type ions produced in collision-induced dissociation of peptide ions

y- and b-type fragment ions produced in the collisional dissociation of arginine-terminated peptide ions are photodissociated with 157-nm light in a linear trap. y-type ions are shown to have the same structure as that of intact peptides of the same sequence with the ionizing proton located at the most basic residue(s). For generic b-type ions, the ionizing proton is shown to be sequestered at the N-terminal arginine, which is consistent with the proposed oxazolone structure.

Analysis of methylation, acetylation, and other modifications in bacterial ribosomal proteins

A wide variety of post-translational modifications of expressed proteins are known to occur in living organisms (1). Although their presence in an organism cannot be predicted from the genome, these modifications can play critical roles in protein structure and function. The identification of post-translational modifications can be critical in understanding the functions of proteins involved in important biological pathways and mass spectrometry offers a fast, accurate method for observing them. This chapter describes the procedure for analyzing ribosomal proteins of Escherichia coli by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and Caulobacter crescentus ribosomal proteins by electrospray quadrupole time-of-flight (ESI-QTOF) mass spectrometry.

Structural analysis of leukotriene C4 isomers using collisional activation and 157 nm photodissociation

The fragmentation of 5-hydroxy-6-glutathionyl-7,9,11,14-eicosatetraenoic acid [leukotriene C4 or LTC4 (5, 6)] and its isomeric counterpart LTC4 (14, 15) were studied by low and high-energy collisional induced dissociation (CID) and 157 nm photofragmentation. For singly charged protonated LTC4 precursors, photodissociation significantly enhances the signal intensities of informative fragment ions that are very important to distinguish the two LTC4 isomers and generates a few additional fragment ions that are not usually observed in CID experiments. The ion trap enables MSn experiments on the fragment ions generated by photodissociation. Photofragmentation is found to be suitable for the structural identification and isomeric differentiation of cysteinyl leukotrienes and is more informative than low or high-energy CID. We describe for the first time the structural characterization of the LTC4 (14, 15) isomer by mass spectrometry using CID and 157 nm light activation methods.

Fast and accurate identification of semi-tryptic peptides in shotgun proteomics

MOTIVATION

One of the major problems in shotgun proteomics is the low peptide coverage when analyzing complex protein samples. Identifying more peptides, e.g. non-tryptic peptides, may increase the peptide coverage and improve protein identification and/or quantification that are based on the peptide identification results. Searching for all potential non-tryptic peptides is, however, time consuming for shotgun proteomics data from complex samples, and poses a challenge for a routine data analysis.

RESULTS

We hypothesize that non-tryptic peptides are mainly created from the truncation of regular tryptic peptides before separation. We introduce the notion of truncatability of a tryptic peptide, i.e. the probability of the peptide to be identified in its truncated form, and build a predictor to estimate a peptide's truncatability from its sequence. We show that our predictions achieve useful accuracy, with the area under the ROC curve from 76% to 87%, and can be used to filter the sequence database for identifying truncated peptides. After filtering, only a limited number of tryptic peptides with the highest truncatability are retained for non-tryptic peptide searching. By applying this method to identification of semi-tryptic peptides, we show that a significant number of such peptides can be identified within a searching time comparable to that of tryptic peptide identification.

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.

The use of bioabsorbable seamguard during laparoscopic appendectomy

The laparoscopic approach to appendectomy for acute appendicitis is becoming increasingly favored among surgeons. Endoscopic stapling remains a common approach for division of the appendix and mesoappendix, but staple line bleeding along the mesentery is commonly observed, occasionally demanding surgical control for complete hemostasis. Bioabsorbable seamguard was used as an adjunct to endoscopic stapling of the mesoappendix in 33 consecutive adult patients during laparoscopic appendectomy for acute appendicitis, with complete immediate staple line hemostasis observed by the operative surgeon in all cases. There were no intraoperative complications and no late infectious intra-abdominal complications. There were no postoperative bleeding complications. Bioabsorbable seamguard is a safe and effective adjunct to endoscopic mesoappendiceal stapling which prevents intraoperative and postoperative staple line bleeding.

Probing the structure and activity of trypsin with amidination

Trypsin reacts with S-methylisothiourea for 1 to 2 h and the number of primary amine sites at which covalent labeling occurs is determined by mass spectrometry. By digesting the amidinated trypsin and mass analyzing the proteolytic peptides the sites of reaction are determined. The addition of cytochrome c to a solution of amidinated trypsin enables the proteolytic activity and autolytic properties of the enzyme to be studied.

Effects of tryptic peptide esterification in MALDI mass spectrometry

The effect of esterification on MALDI ion yield is investigated by using alcohols having different aliphatic chain lengths. For peptides whose ionization yields increase with derivatization, more hydrophobic alcohols tend to yield greater peak enhancements. The completeness of the reaction increases from propanol to methanol. Undesired solvolysis of the amide group in the side chain of Asn or Gln leads to unexpected ester products. Ethanol is suggested as the optimal alcohol for esterification in proteomics experiments since it yields almost complete esterification without substantial solvolysis. Ethanol esterification was employed to facilitate the identification of gel-separated proteins.

Two dimensional liquid phase separations of proteins using online fractionation and concentration between chromatographic dimensions

Multi-dimensional liquid chromatography is often presented as an alternative to two-dimensional (2-D) gel electrophoresis for separating complex protein mixtures. The vast majority of analytical-scale 2-D LC systems have employed either off-line fractionation or stepped gradients in the first dimension separation. The latter severely restrict flexibility in setting up the first dimension gradient. We propose a novel two-dimensional LC system that employs online fractionation of proteins into a series of small reversed phase trapping columns. These traps effectively decouple the two separation dimensions and avoid problems associated with off-line fraction collection. Flexibility in determining the gradient programs for the two separations is thus enhanced. The reduced diameter of the trapping columns concentrates analyte between chromatographic dimensions. The apparatus is coupled with online electrospray time-of-flight mass spectrometry to characterize ribosomal proteins of Caulobacter crescentus.

Probing the structure of the Caulobacter crescentus ribosome with chemical labeling and mass spectrometry

The ribosomal proteins of Caulobacter crescentus were amidinated before and after disassembly of the organelle and the results analyzed by mass spectrometry. Comparison with structural information from previous X-ray crystal studies of other bacterial ribosomes provides insight about the C. crescentus ribosome. In total, 47 of the 54 proteins present in the ribosome of C. crescentus were detected after labeling. The extent of derivatization for each protein is strongly dependent on the solvent accessibility of its target residues. Proteins of the ribosome stalk, which are known to be largely solvent-accessible, were labeled quite extensively. In striking contrast, other proteins that are known to be highly shielded in their subunits were labeled at very few of their potential sites. Furthermore, evidence that protein L12 binds to the ribosome via its N-terminal domain is consistent with previous findings.

Persistent sciatic artery—A curious vascular anomaly

A persistent sciatic artery (PSA) is a rare vascular anomaly not extensively described in the interventional cardiology literature. Because of its vulnerable position, it is associated with a high risk of aneurysm formation, making it prone to thrombus formation with subsequent arterial insufficiency because of distal embolization. We report the case of an 80-year-old woman who was found to have bilateral PSA with unilateral aneurysm and evidence of possible distal embolization on conventional angiography.

Laser-induced photofragmentation of neutral and acidic glycans inside an ion-trap mass spectrometer

Permethylated acidic and neutral N-glycans representing different types of glycan structures, such as linear and branched sialylated structures, high-mannose type and fucosylated complex type, were photodissociated with 157 nm vacuum ultraviolet light in a linear ion trap. Cross-ring fragments corresponding to high-energy fragmentation pathways were observed in abundance for all studied structures. Some product ions appear diagnostic for a linkage of sialic acid residues and the glycan antenna to which these residues are attached. A conclusive assignment of the fucosylation site of the studied glycan structure has been facilitated through measurement of cross-ring fragmentation resulting from photodissociation.

A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus

Ribosomes from the Gram-negative alpha-proteobacterium Caulobacter crescentus were isolated using standard methods. Proteins were separated using a two-dimensional liquid chromatographic system that allowed the analysis of whole proteins by direct coupling to an ESI-QTOF mass spectrometer and of proteolytic digests by a number of mass spectrometric methods. The masses of 53 of 54 ribosomal proteins were directly measured. Protein identifications and proposed post-translational modifications were supported by proteolysis with trypsin, endoprotease Glu-C, and exoproteases carboxypeptidases Y and P. Tryptic peptide mass maps show an average sequence coverage of 62%, and carboxypeptidase C-terminal sequence tagging provided unambiguous identification of the small, highly basic proteins of the large subunit. C. crescentus presents some post-translational modifications that are similar to those of Escherichia coli (e.g., N-terminal acetylation of S9 and S18) along with some unique variations, such as a near absence of L7 and extensive modification of L11. The comprehensive description of this organism's ribosomal proteome provides a foundation for the study of ribosome structure, dependence of post-translational modifications on growth conditions, and the evolution of subcellular organelles.

Advancement in protein inference from shotgun proteomics using peptide detectability

A major challenge in shotgun proteomics has been the assignment of identified peptides to the proteins from which they originate, referred to as the protein inference problem. Redundant and homologous protein sequences present a challenge in being correctly identified, as a set of peptides may in many cases represent multiple proteins. One simple solution to this problem is the assignment of the smallest number of proteins that explains the identified peptides. However, it is not certain that a natural system should be accurately represented using this minimalist approach. In this paper, we propose a reformulation of the protein inference problem by utilizing the recently introduced concept of peptide detectability. We also propose a heuristic algorithm to solve this problem and evaluate its performance on synthetic and real proteomics data. In comparison to a greedy implementation of the minimum protein set algorithm, our solution that incorporates peptide detectability performs favorably.

A non-nephrotoxic gentamicin congener that retains antimicrobial efficacy

Aminoglycoside antibiotics, although of major clinical importance in the treatment of serious Gram- negative infections and a potential therapeutic agent in the amelioration of diseases that are characterized by premature stop mutations, are associated with a high incidence of acute renal failure. With the use of HPLC techniques, the four components (congeners) of gentamicin, the most commonly used aminoglycoside, were isolated and characterized. Described here is a congener with minimal cytotoxicity in cell culture and animal studies that retained normal bactericidal properties in both Bacillus subtilis and a multidrug-resistant form of Klebsiella pneumoniae. Furthermore, in animal studies, this congener failed to induce the functional and pathologic changes that are characteristic of gentamicin nephrotoxicity that is seen with the native compound. Finally, internalization of this non-nephrotoxic component was unaltered, but the subcellular distribution was different from native gentamicin or the other three cytotoxic congeners. These studies have identified a component of the native gentamicin congener mixture that retains its bactericidal properties with minimal or no apparent nephrotoxicity.

Structures of alpha-type ions formed in the 157 nm photodissociation of singly-charged peptide ions

One hundred fifty-seven nm photodissociation of singly-charged peptide ions induces the cleavage of alpha-carbon to carbonyl-carbon bonds along the backbone. a(n) + 1 radical ions are observed as the primary photolysis products of peptides with N-terminal arginines in a linear ion trap mass spectrometer. The radical elimination pathways undertaken by the a(n) + 1 radical ions to form more stable even-electron species are studied in hydrogen-deuterium (H/D) exchange experiments. Two types of a(n) ions along with d-type ions are observed as secondary elimination products. The relative abundance of each depends on the C-terminal residue of the radical fragment ion.

A nutrient uptake role for bacterial cell envelope extensions

Bacteria exist in a variety of morphologies, but the relationship between cellular forms and biological functions remains poorly understood. We show that stalks (prosthecae), cylindrical extensions of the Caulobacter crescentus cell envelope, can take up and hydrolyze organic phosphate molecules and contain the high-affinity phosphate-binding protein PstS, but not PstA, a protein that is required for transport of phosphate into the cytoplasm. Therefore, uptake, hydrolysis, and periplasmic binding of a phosphate source can take place in the stalk, but high-affinity import must take place in the cell body. Furthermore, by using analytical modeling, we illustrate the biophysical advantage of the stalk as a morphological adaptation to the diffusion-limited, oligotrophic environments where C. crescentus thrives. This advantage is due to the fact that a stalk is long and thin, a favorable shape for maximizing contact with diffusing nutrients while minimizing increases in both surface area and cell volume.

A computational approach toward label-free protein quantification using predicted peptide detectability

We propose here a new concept of peptide detectability which could be an important factor in explaining the relationship between a protein's quantity and the peptides identified from it in a high-throughput proteomics experiment. We define peptide detectability as the probability of observing a peptide in a standard sample analyzed by a standard proteomics routine and argue that it is an intrinsic property of the peptide sequence and neighboring regions in the parent protein. To test this hypothesis we first used publicly available data and data from our own synthetic samples in which quantities of model proteins were controlled. We then applied machine learning approaches to demonstrate that peptide detectability can be predicted from its sequence and the neighboring regions in the parent protein with satisfactory accuracy. The utility of this approach for protein quantification is demonstrated by peptides with higher detectability generally being identified at lower concentrations over those with lower detectability in the synthetic protein mixtures. These results establish a direct link between protein concentration and peptide detectability. We show that for each protein there exists a level of peptide detectability above which peptides are detected and below which peptides are not detected in an experiment. We call this level the minimum acceptable detectability for identified peptides (MDIP) which can be calibrated to predict protein concentration. Triplicate analysis of a biological sample showed that these MDIP values are consistent among the three data sets.

Probing Protein Tertiary Structure with Amidination

A chemical derivatization method, amidination, that has recently been effectively employed in peptide mass spectrometry experiments is used to covalently modify lysines in several standard proteins. Protein and peptide mass spectra identify sites at which the reaction does or does not occur. This is therefore a rapid approach to elucidate solvent-accessible regions of folded proteins.

Peptide de Novo Sequencing Facilitated by a Dual-Labeling Strategy

A novel peptide derivatization strategy based on guanidination and amidination is presented. Mass-coded labels help distinguish N- and C-terminal fragment ions produced by collision-induced dissociation and are of general utility since peptide N-termini are coded. The amidine labels also promote specific fragmentation pathways that elucidate N-terminal residues and provide valuable internal calibrants. This strategy is demonstrated with the tryptic peptides of several model proteins, including two that are phosphorylated. Additionally, interpreted peptide sequences are matched against a database of over 80,000 proteins to assess the selectivity of this sequencing approach.

Pathways of peptide ion fragmentation induced by vacuum ultraviolet light

One Hundred Fifty-Seven nm photodissociation of singly protonated peptides generates unusual distributions of fragment ions. When the charge is localized at the C-terminus of the peptide, spectra are dominated by x-, v-, and w-type fragments. When it is sequestered at the N-terminus, a- and d-type ions are overwhelmingly abundant. Evidence is presented suggesting that the fragmentation occurs via photolytic radical cleavage of the peptide backbone at the bond between the alpha- and carbonyl-carbons followed by radical elimination to form the observed daughter ions.