Size effect on fragmentation in tandem mass spectrometry

The collision energy or collision voltage necessary to obtain 50% fragmentation (characteristic collision energy/voltage, CCE or CCV) has been systematically determined for different types of molecules [poly(ethylene glycols) (PEG), poly(tetrahydrofuran) (PTHF), and peptides] over a wide mass (degrees of freedom) range. In the case of lithium-cationized PEGs a clear linear correlation (R(2) > 0.996) has been found between CCE and precursor ion mass on various instrument types up to 4.5 kDa. A similar linear correlation was observed between CCV and the mass-to-charge ratio. For singly and multiply charged polymers studied under a variety of experimental conditions and on several instruments, all data were plotted together and showed correlation coefficient R(2) = 0.991. A prerequisite to observe such a good linear correlation is that the energy and entropy of activation in a class of polymers is likely to remain constant. When compounds of different structure are compared, the CCV will depend not only on the molecular mass but the activation energy and entropy as well. This finding has both theoretical and practical importance. From a theoretical point of view it suggests fast energy randomization up to at least 4.5 kDa so that statistical rate theories are applicable in this range. These results also suggest an easy method for instrument tuning for high-throughput structural characterization through tandem MS: after a standard compound is measured, the optimum excitation voltage is in a simple proportion with the mass of any structurally similar analyte at constant experimental conditions.

Avemar (wheat germ extract) in cancer prevention and treatment

Many healthy foods are derived from wheat germ. The molecular composition of these products, however, greatly differs as shown by normal-phase HPLC-mass spectrometry analysis; thus, experimental data obtained by one of them is not necessarily true for the other. Avemar is a nontoxic wheat germ extract registered as a special nutriment for cancer patients in Hungary. It shows potent anticancer activity on cell lines by deeply interfering with glucose metabolism and affecting expressions of several kinases. In in vivo experimental models, Avemar is also effective by enhancing the activity of the immune system such as stimulating NK cell activity (by reducing MHC I molecule expression), enhancing TNF secretion of the macrophages, increasing ICAM 1 molecule expression on the vascular endothelial cells. All of these lead to apoptosis of tumor cells. The wide range of biological activity of Avemar probably cannot be explained by only one active ingredient. Since there are numerous experimental data and the clinical benefit repeatedly confirmed Avemar can be one of the most potent and best researched food supplements available for cancer patients.

Matrix/analyte ratio influencing polymer molecular weight distribution in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been used to characterize poly(L-lysine) polymers and unique oligomer peptides, like 10-, 15- and 25-mer [Lys]n oligolysine peptides. Several matrices have been tried in order to find optimal conditions, but only alpha-cyano-4-hydroxycinnamic acid gave analytically useful spectra. The synthetic oligomers and their mixtures gave good quality spectra, showing protonated and cationized molecules, including doubly charged species. The polymers, analogously, gave a wide distribution of single- and double-cationized peak series. The polymer distributions observed indicate the presence of significant suppression effects. The concentration (matrix/analyte ratio) was found to influence the results significantly; distributions shifting to higher masses when higher polymer concentrations were used. This effect was studied in detail using the synthetic ('monodisperse') oligolysine peptides. It was found that the relative intensities change by over an order of magnitude in the 0.1-10 pmol/microL concentration range (typical for most proteomic analyses). The results indicate that concentration effects need to be considered when MALDI-MS is used for quantitative purposes.

Letter: Collision energy and cone voltage optimisation for glycopeptide analysis

Instrument tuning commonly used for peptide analysis and for proteomics causes a high degree of fragmentation for glycopeptides. This results in a strongly biased glycosylation pattern. To obtain correct results for glycopeptides, both the cone voltage and the collision energy has to be reduced significantly. A suitable standard for tuning the instrument for glycopeptide analysis is aspartic acid (which fragments under similar conditions as glycopeptides); while low mass sugar fragments (for example, at 657.3 Da) are good indicators for the presence/absence of glycopeptide fragmentation.

Investigation of genetic variants of alpha-1 acid glycoprotein by ultra-performance liquid chromatography-mass spectrometry

Genetic variants of human plasma alpha-1 acid glycoprotein (AGP) have been studied in cancer, compared with a group of healthy control. AGP has four genetic variants: AGP F1, F2, and S variants correspond to the ORM1 gene whereas AGP A corresponds to the ORM2 gene. The proportion of ORM1 and ORM2 variants were studied in plasma using a novel UPLC-MS method. Plasma total AGP level was 0.5 +/- 0.2 g L(-1) and the proportions of the ORM1 and ORM2 variants were 76.3 +/- 8.2% and 23.7 +/- 8.2%, respectively. In cancer plasma AGP levels increased fourfold and the proportion of ORM1 variants increased to 88.7 +/- 6.8%. Changes in the proportion of genetic variants due to cancer were clearly significant, as shown by statistical analysis. Three different cancer types have been studied, lymphoma, melanoma, and ovarian cancer. The results did not show any difference depending on cancer type. The results indicate that, in accordance with prior expectations, the ORM1 variant is predominantly responsible for the acute-phase property of AGP.

GlycoMiner: a new software tool to elucidate glycopeptide composition

New computer software, GlycoMiner, has been developed to automatically identify tandem (MS/MS) spectra obtained in liquid chromatography/mass spectrometry (LC/MS) runs which correspond to N-glycopeptides. The program complements conventional proteomics analysis, and can be used in a high-throughput environment. The program interprets the spectra and determines the structure of the corresponding glycopeptides. GlycoMiner runs under Windows, can process spectra obtained on various instruments, and can be downloaded from our website (w3.chemres.hu/ms/glycominer). The algorithm works similarly to a human expert; evaluates the low mass oxonium ions; deduces oligosaccharide losses from the protonated molecule; and identifies the mass of the peptide residue. The program has been tested on tryptic digests of two glycopeptides: AGP (which has five different N-glycosylation sites) and transferrin (with two N-glycosylation sites). Results have been evaluated both manually and by GlycoMiner. Out of 3132 MS/MS spectra 338 were found to correspond to glycopeptides; identification by GlycoMiner showed a 0.1% false positive and 0.1% false negative rate. From these it was possible to identify 196 glycan structures manually; GlycoMiner correctly identified all of these, with no false positives. The rest were low quality spectra, not suitable for structure assignment.

Mass spectrometric and linear discriminant analysis of N-glycans of human serum alpha-1-acid glycoprotein in cancer patients and healthy individuals

N-glycan oligosaccharides of human serum alpha(1)-acid glycoprotein (AGP) samples isolated from 43 individuals (healthy individuals and patients with lymphoma and with ovarian tumor) were analyzed by MALDI-TOF mass spectrometry and a multivariate statistical method (linear discriminant analysis, LDA). 34 different glycan structures have been identified. From the glycosylation pattern determined by mass spectrometry fucosylation and branching indices have been calculated. These parameters show only small differences between the patient groups studied, but these differences are not sufficiently large to use as a potential biomarker. LDA analysis, on the other hand shows a very good separation between the three groups (with a classification of 88%). Cross-validation indicates that the method has predictive power: Identifying cancerous vs. healthy individuals shows 96% selectivity and 93% specificity; identification of lymphoma vs. the mixed group of healthy and ovarian tumor cases is also promising (72% selectivity and 84% specificity). The pilot study presented here demonstrates that mass spectrometry combined with linear discriminant analysis (LDA) may provide valuable data for identifying and studying the pathophysiology of malignant diseases.

Internal energy distribution of peptides in electrospray ionization : ESI and collision-induced dissociation spectra calculation

The internal energy of ions and the timescale play fundamental roles in mass spectrometry. The main objective of this study is to estimate and compare the internal energy distributions of different ions (different nature, degree of freedom 'DOF' and fragmentations) produced in an electrospray source (ESI) of a triple-quadrupole instrument (Quattro I Micromass). These measurements were performed using both the Survival Yield method (as proposed by De Pauw) and the MassKinetics software (kinetic model introduced by Vékey). The internal energy calibration is the preliminary step for ESI and collision-induced dissociation (CID) spectra calculation. meta-Methyl-benzylpyridinium ion and four protonated peptides (YGGFL, LDIFSDF, LDIFSDFR and RLDIFSDF) were produced using an electrospray source. These ions were used as thermometer probe compounds. Cone voltages (V(c)) were linearly correlated with the mean internal energy values (<E(int) >) carried by desolvated ions. These mean internal energy values seem to be slightly dependent on the size of the studied ion. ESI mass spectra and CID spectra were then simulated using the MassKinetics software to propose an empirical equation for the mean internal energy (<E(int) >) versus cone voltage (V(c)) for different source temperatures (T): < E(int) > = [405 x 10(-6) - 480 x 10(-9) (DOF)] V(c)T + E(therm)(T). In this equation, the E(therm)(T) parameter is the mean internal energy due to the source temperature at 0 V(c).

Analysis of complex oligosaccharides using graphitized carbon liquid chromatography/mass spectrometry

The sugar fraction of alpha-1 acid glycoprotein (AGP) was studied using porous graphitized carbon (PGC) chromatography coupled to mass spectrometry. Electrospray ionization provides efficient control over fragmentation; at low collision energy only molecular species were observed, allowing accurate oligosaccharide profiling. PGC chromatography was useful separating 18 sugars differing in monosaccharide composition. Most of these were separated into several isomeric forms; altogether 49 different oligosaccharides were found in AGP.

SORI excitation: collisional and radiative processes

Theoretical modeling of sustained off-resonance irradiation collision-induced dissociation (SORI-CID) experiments in Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry is described in the present paper. Manipulation of various analytical expressions yield the result that the average laboratory frame collision energy is equal to 2/3 of the maximum kinetic energy in SORI. Survival yields (the fraction of nondecomposed molecular ions) as a function of excitation time, collision energy, and source temperature have been considered: results of MassKinetics-type reaction kinetics modeling were compared with experimental results obtained by Guo et al. (Int. J. Mass Spectrom.2003, 225, 71-82). The results show that radiative cooling has a major influence in SORI-CID. They also suggest that collisional cooling is significant only at very low (less than 0.02 eV) center of mass collision energy; therefore it has a very small influence on the SORI process. Survival yield curves showed excellent agreement between experiments and calculations optimizing two parameters only (collisional energy-transfer efficiency and radiative cooling rate). Using leucine enkephalin as a model compound, the results indicate 0.128 +/- 0.021 energy deposition in a single collision and 7.5 +/- 0.5 s(-1) infrared cooling rate. We also present that these two physical parameters cannot be properly deconvoluted. This effect shows the importance of the parallel consideration of different physical processes.

Mass spectrometric and quantum-chemical study on the structure, stability, and chirality of protonated serine dimers

Stability and structure of homo- and heterochiral protonated serine (Ser) dimers were investigated by a combination of mass spectrometry and ab initio quantum chemical calculations. This established that the energy difference between the most stable homo- and heterochiral forms is very small: tandem mass spectrometry with Cooks' kinetic method yielded a negligible difference in Gibbs free energy (0.2+/-0.2 kJ mol(-1)). The various isomeric forms of (Ser)2 H+ and their energetics were determined by extensive electronic-structure calculations, which yielded homo- and heterochiral forms of the isomers with distinctly different relative energies. The most stable homochiral isomer is stabilized by two hydrogen bonds and is far more stable than any other homochiral isomer. The most stable heterochiral isomer has completely different features, and it is characterized by a salt-bridge structure. This clearly shows that salt-bridge structures do exist in the gas phase even in comparatively small molecules and in the absence of particularly basic or acidic functional groups.

Analysis of sterols by high-performance liquid chromatography/mass spectrometry combined with chemometrics

A newly developed high-performance liquid chromatography/mass spectrometry (HPLC/MS) method has been successfully used to analyze plasma concentrations of various phytosterols (cholestanol and beta-sitosterol) and cholesterol metabolites (desmosterol and lathosterol). This was based on an unusual solvent combination of water/methanol vs. methanol/acetone/n-hexane applied on a Purospher Star RP-18e (125 x 2 mm, 3 microm) column, which proved excellent for the separation, identification and quantification of plasma sterols. Simple solid-phase extraction preparation of plasma samples was performed, followed by the developed fast and robust HPLC separation. Results on four groups of people were compared, those with low, normal and high plasma cholesterol levels and those with high cholesterol levels on statin therapy, and the results were evaluated using linear discriminant analysis (LDA). Variable selection for LDA was achieved using backward removal selection. Highly discriminatory variables were the ratios of desmosterol to sitosterol and of lathosterol to total plasma cholesterol. The latter ratio was also excellent for distinguishing subjects on statin therapy. The success rate of classification was 100%. The present pilot study shows the potential of HPLC/MS analysis and chemometrics for studying cholesterol-related disorders and warrants future full-scale medical study.

Glycosylation site analysis of human alpha-1-acid glycoprotein (AGP) by capillary liquid chromatography-electrospray mass spectrometry

A new anionic surfactant (RapiGest SF) was successfully used for site-specific analysis of glycosylation in human alpha-1-acid glycoprotein (AGP). By means of this analytical approach combined with capillary HPLC-mass spectrometry (and tandem mass spectrometry), the N-linked glycosylation pattern of AGP was explored. On the basis of mass matching and MS/MS experiments ca 80 different AGP-derived glycopeptides were identified. Glycosylation shows a markedly different pattern for the various glycosylation sites. At sites I and II, triantennary complex-type oligosaccharides predominate and at sites III, IV and V, tetra-antennary complex-type oligosaccharides predominate. Sites IV and V show the presence of additional N-acetyl lactosamine (Gal-GlcNAc) units (even higher degree of branching and/or longer antennae are also present).

High performance liquid chromatography-mass spectrometry based chemometric characterization of olive oils

In this study the effective discrimination of extra virgin olive oils is described using HPLC-MS, combined with chemometric evaluation. The presented method is simple since the diluted oil sample is directly injected into the system, without any preliminary chemical derivatization or purification step. Separation of diacylglycerols, triacylglycerols and sterols occurs within 20 min and is achieved using an octadecyl-silica column. Detection is performed by positive APCI mass spectrometry which provided sensitivity to detect over 50 compounds in the sample. After extraction of data, stepwise discriminant function analysis is used to select the variables with the highest discriminative power. These variables are used to perform linear discriminant analysis and classify/predict the samples. One-hundred per cent classification and 99% prediction rate was achieved for olive oils obtained from Nocellara, Biancolilla and Cerausola cultivars. Reliability of prediction was tested by cross validation.

Liquid chromatographic and mass spectrometric analysis of human serum acid alpha-1-glycoprotein

Human serum acid alpha-1-glycoprotein (AGP, orosomucoid) content of healthy individuals and cancer patients was measured, isolated and purified using a protocol of fast and biocompatible sample preparation, ion exchange and dye-ligand affinity chromatographic methods. In comparison to the healthy individuals significantly higher serum AGP levels were found in a wide spectrum of cancer patients, indicating its diagnostic value in the malignant disease. Oligosaccharide content of AGP samples was separated following PNGase F enzyme digestion and analysed by RP-HPLC and MALDI-TOF mass spectrometry. RP-HPLC and MALDI-TOF mass spectrometric analysis of sugar constituents of AGP specimen originated from selected cancer patients with high serum AGP levels indicated the appearance of anomal distribution of bi-, tri- and tetra-antennary oligosaccharide structures compared to the healthy controls.

An HPLC-MS approach for analysis of very long chain fatty acids and other apolar compounds on octadecyl-silica phase using partly miscible solvents

A novel approach for analyzing underivatized very long chain fatty acids (C16-C26) and other apolar compounds such as triacylglycerols is described. It is based on reversed-phase HPLC separation followed by mass spectrometric detection. Partly miscible solvents are used for stepwise gradient elution starting with a methanol/water and ending with a methanol/n-hexane binary mixture. The developed technique does not need derivatization, and analysis is fast (fatty acids were separated in 2-min-long chromatograms) and robust. The developed method is also very sensitive; a quantitation limit in the low-picogram range was achieved for fatty acids. The separation mechanism and advantages of the suggested technique are discussed and illustrated in the case of blood analysis and plant oil characterization.

Combination of solid-phase affinity capture on magnetic beads and mass spectrometry to study non-covalent interactions: example of minor groove binding drugs

A simple and novel approach was developed to detect non-covalent interactions. It is based on combination of solid-phase affinity capture with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). One of the interacting molecules is bound to magnetic beads and is incubated with the target molecules in solution. The complex bound on the solid support is removed from the solution and transferred for MALDI analysis. Mass spectrometry is used only to detect the target compound, which is far more straightforward than detecting the intact non-covalent complex. To demonstrate the applicability of the method, an AT-rich oligonucleotide (5'-CCCCCAATTCCCCC-3') and its complementary biotinylated sequence (5'-biotin-GGGGGAATTGGGGG-3') were hybridized and immobilized to paramagnetic particles by streptavidin-biotin interaction. The immobilized duplex oligonucleotide was reacted with minor groove binding drugs, Netropsin, Distamycin A, Hoechst 33258 and 4',6-diamidino-2-phenylindole. The resulting DNA-drug complex bound to the particles was separated and analyzed by linear MALDI-TOFMS after washing. Drugs were selectively detected in the spectra. Relative binding strengths were also estimated using competitive complexation.

Amino acid cluster formation studied by electrospray ionization mass spectrometry

The association properties of natural and non-natural amino acids were studied in detail using electrospray ionization mass spectrometry. The results show a highly diverse cluster formation behavior of amino acids. There are differences regarding the degree of clustering (average cluster size), the presence or absence of one or several 'magic' clusters of special stability and the influence of chirality on cluster stability. Cluster formation does not show a good correlation with simple physico-chemical properties (such as solubility), indicating that it is a specific process and not only a simple aggregation during evaporation/ionization. A systematic study of cluster formation of serine derivatives reveals that all functional groups play a prominent role in the binding of the magic octamer. The results support the idea of the zwitterionic character of the octamer. Electrospray ionization of the side-chain acetylated serine shows the formation of a very stable tetramer with a strong preference for homochirality. The results suggest that Ser8 is made up of two tetramer subunits, held together by hydrogen bonds of the side-chain.

Internal energy distribution in electrospray ionization

Internal energies and energy distributions were studied using the 'survival yield' method developed previously. In addition to conventional benzylpyridinium salts, protonated esters (fragmenting by rearrangement) and protonated leucine enkephalin were also used, extending the validity of the technique. Fragmentation processes were studied in the cone voltage region and modeled by the RRKM-based MassKinetics program. The results show that the shapes of the energy distributions are similar to thermal distributions. The mean internal energies are very similar for all compound classes studied, and show a linear increase with collision energy in the 10-50 eV region.

Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of Human α-1-Acid Glycoprotein

The ultrahigh resolution and sensitivity of electrospray ionization Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometry have for the first time been exploited for the characterization of highly sialylated glycoproteins, using human alpha-1-acid glycoprotein as the model compound. An alternative approach to the widely used high-performance liquid chromatography (HPLC) and matrix-assisted laser desorption/ionization (MALDI) assays is described. This new method does not require any enzymatic or chemical digestion (removal of sialyl groups or deglycosylation), chemical derivatization (introduction of chromophore groups), or preliminary chromatographic separation (HPLC or electrophoresis). Following ESI and accumulation of ions in a hexapole ion guide, ions are injected into the ICR cell. A selected mass window from the overall ion population is isolated and axialized prior to detection. After acquisition and Fourier transform of the transient signal the resulted spectrum is evaluated in order to determine the charge state of the detected ions and the isotope pattern of the measured protein glycoform. The presence of ions from the same glycoform with different charge states was confirmed. The advantages and limitations of the technique are discussed. Future prospects and possible applications are indicated.

Accuracy of enthalpy and entropy determination using the kinetic method: are we approaching a consensus?

There is an emerging consensus regarding the applicability of the kinetic method. All parties acknowledge that it is an approximate quantitative technique, capable of yielding not only enthalpy, but also entropy values. Opinions differ mainly on the accuracy of the results but it is agreed that the energy (effective temperature) dependence of kinetic method plots needs to be checked in all but the simplest of cases. When the 'apparent basicity' is found to depend on collision energy (and hence effective temperature), the extended kinetic method must be used. We have performed a large-scale modeling study, involving thousands of randomly selected molecular systems and a variety of experimental conditions, using exact calculations and realistic data sets. The results show that when the measured entropy difference between the two competing reaction channels is less than approximately 35 J mol(-1) K(-1), overall errors (standard deviations) of DeltaH(298) determined by the kinetic method are +/-5 kJ mol(-1); those of DeltaS(298) are +/-10 J mol(-1) K(-1). These include not only inherent errors of the kinetic method, but also errors in ion abundance measurement (5%) and inaccurate knowledge of reference compound thermochemistry (+/-2 kJ mol(-1), on average). We recommend, in general, that these errors be reported in kinetic method studies. When the measured entropy difference between the two competing fragmentation channels is large (>35 J mol(-1) K(-1)), it is likely to be significantly underestimated and errors of the kinetic method increase significantly.