Liquid chromatography and electron-capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry

Liquid separation methods in combination with electrospray mass spectrometry as well as the recently introduced fragmentation method electron capture dissociation (ECD) have become powerful tools in proteomics research. This paper presents the results of the first successful attempts to combine liquid chromatography (LC) and Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) with ECD in the analysis of a mixture of standard peptides and of a bovine serum albumin tryptic digest. A novel electron injection system provided conditions for ECD sufficient to yield extensive sequence information for the most abundant peptides in the mixtures on the time-scale of the chromatographic separation. The results suggest that LC/ECD-FTICRMS can be employed in the characterization of peptides in enzymatic digests of proteins or protein mixtures and identify and localize posttranslational modifications.     

Automatic internal calibration in liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry of protein digests

Accurately measured peptide masses can be used for large-scale protein identification from bacterial whole-cell digests as an alternative to tandem mass spectrometry (MS/MS) provided mass measurement errors of a few parts-per-million (ppm) are obtained. Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) routinely achieves such mass accuracy either with internal calibration or by regulating the charge in the analyzer cell. We have developed a novel and automated method for internal calibration of liquid chromatography (LC)/FTICR data from whole-cell digests using peptides in the sample identified by concurrent MS/MS together with ambient polydimethylcyclosiloxanes as internal calibrants in the mass spectra. The method reduced mass measurement error from 4.3 +/- 3.7 ppm to 0.3 +/- 2.3 ppm in an E. coli LC/FTICR dataset of 1000 MS and MS/MS spectra and is applicable to all analyses of complex protein digests by FTICRMS.     

Nano-high-performance liquid chromatography in combination with nano-electrospray ionization Fourier transform ion-cyclotron resonance mass spectrometry for proteome analysis

Fourier transform ion-cyclotron resonance (FTICR) mass spectrometry offers several advantages for the analysis of biological samples, including excellent mass resolution, ultra-high mass measurement accuracy, high sensitivity, and wide mass range. We report the application of a nano-HPLC system coupled to an FTICR mass spectrometer equipped with nanoelectrospray source (nano-HPLC/nano-ESI-FTICRMS) for proteome analysis. Protein identification in proteomics is usually conducted by accurately determining peptide masses resulting from enzymatic protein digests and comparing them with theoretically digested protein sequences from databases. A tryptic in-solution digest of bovine serum albumin was used to optimize experimental conditions and data processing. Spots from Coomassie Blue and silver-stained two-dimensional (2D) gels of human thyroid tissue were excised, in-gel digested with trypsin, and subsequently analyzed by nano-HPLC/nano-ESI-FTICRMS. Additionally, we analyzed 1D-gel bands of membrane preparations of COS-6 cells from African green monkey kidney as an example of more complex protein mixtures. Nano-HPLC was performed using 1-mm reverse-phase C-18 columns for pre-concentration of the samples and reverse-phase C-18 capillary columns for separation, applying water/acetonitrile gradient elution conditions at flow rates of 200 nL/min. Mass measurement accuracies smaller than 3 ppm were routinely obtained. Different methods for processing the raw data were compared in order to identify a maximum number of peptides with the highest possible degree of automation. Parallel identification of proteins from complex mixtures down to low-femtomole levels makes nano-HPLC/nano-ESI-FTICRMS an attractive approach for proteome analysis.     

Suppression correction and characteristic study in liquid chromatography/Fourier transform mass spectrometry measurements

Analysis of peptide profiles from liquid chromatography/Fourier transform mass spectrometry (LC/FTMS) reveals a nonlinear distortion in intensity. Investigation of the measured C(13)/C(12) ratios comparing with theoretical ones shows that the nonlinearity can be attributed to signal suppression of low abundance peptide peaks. We find that the suppression is homogenous for different isotopes of identical peptides but non-homogenous for different peptides. We develop an iterative correction algorithm that corrects the intensity distortions for peptides with relatively high abundance. This algorithm can be applied in a wide range of applications using LC/FTMS. We also analyze the distortion characteristics of the instrument for lower abundance peptides, which should be considered when interpreting quantification results of LC/FTMS.     

Combined infrared multiphoton dissociation and electron-capture dissociation using co-linear and overlapping beams in Fourier transform ion cyclotron resonance mass spectrometry

A novel set-up for Fourier transform ion cyclotron resonance mass spectrometry (FTICR) is reported for simultaneous infrared multiphoton dissociation (IRMPD) and electron-capture dissociation (ECD). An unmodified electron gun ensures complete, on-axis overlap between the electron and the photon beams. The instrumentation, design and implementation of this novel approach are described. In this configuration the IR beam is directed into the ICR cell using a pneumatically actuated mirror inserted into the ion-optical path. Concept validation was made using different combinations of IRMPD and ECD irradiation events on two standard peptides. The ability to perform efficient IRMPD, ECD and especially simultaneous IRMPD and ECD using lower irradiation times is demonstrated. The increase in primary sequence coverage, with the combined IRMPD and ECD set-up, also increases the confidence in peptide and protein assignments.     

Tailored noise waveform/collision-induced dissociation of ions stored in a linear ion trap combined with liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry

A new collision-induced dissociation (CID) technique based on broadband tailored noise waveform (TNW) excitation of ions stored in a linear ion trap has been developed. In comparison with the conventional sustained off-resonance irradiation (SORI) CID method commonly used in Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), this MS/MS technique increases throughput by eliminating the long pump-down delay associated with gas introduction into the high vacuum ICR cell region. In addition, the TNW-CID method speeds spectrum acquisition since it does not require Fourier transformation, calculation of resonant frequencies and generation of the excitation waveforms. We demonstrate TNW-CID coupled with on-line capillary reverse-phase liquid chromatography separations for the identification of peptides. The experimental results are compared with data obtained using conventional quadrupole ion trap MS/MS and SORI-CID MS/MS in an ICR cell.     

Hydrophilic interaction chromatography with Fourier transform mass spectrometry of monosaccharide anhydrides

A fast, selective, and sensitive method for the determination of three monosaccharide anhydrides (galactosan, mannosan, levoglucosan), based on hydrophilic interaction chromatography and Fourier transform mass spectrometry, was successfully developed. The simple experimental stationary phase and mass spectrometry performance screening allowed the selection of the best available chromatographic and mass spectrometry conditions. Thus, the chromatographic separation was performed on a highly selective stationary phase containing a zwitterionic phosphorylcholine group and the monosaccharide anhydrides were detected as [M+HCOO]^? adduct in the negative mode. The method showed accuracy in the range of 84–111 and 89–102% with interbatch precision expressed as relative standard deviations of 5.6–15.4 and 5.0–9.0% for the aerosol extract and snow samples, respectively. The limit of quantification in absolute values ranged from 10 to 30 pg, the limit of quantification, expressed as concentration, ranged was 0.3–0.9 ng/m³ for aerosol and 10–20 ng/mL for snow samples. The method was successfully applied for the determination of monosaccharide anhydrides in aerosol and snow samples.     

Negative electron transfer dissociation Fourier transform mass spectrometry of glycosaminoglycan carbohydrates

Electron transfer through gas phase ion-ion reactions has led to the widespread application of electron- based techniques once only capable in ion trapping mass spectrometers. Although any mass analyzer can in theory be coupled to an ion-ion reaction device (typically a 3-D ion trap), some systems of interest exceed the capabilities of most mass spectrometers. This case is particularly true in the structural characterization of glycosaminoglycan (GAG) oligosaccharides. To adequately characterize highly sulfated GAGs or oligosaccharides above the tetrasaccharide level, a high resolution mass analyzer is required. To extend previous efforts on an ion trap mass spectrometer, negative electron transfer dissociation coupled with a Fourier transform ion cyclotron resonance mass spectrometer has been applied to increasingly sulfated heparan sulfate and heparin tetrasaccharides as well as a dermatan sulfate octasaccharide. Results similar to those obtained by electron detachment dissociation are observed.     

Development and evaluation of on-line nanoliter flow analysis of protein digests by pneumatic-splitter electrospray liquid chromatography mass spectrometry

We have developed a novel approach to characterize protein digests by pneumatic-splitter electrospray ionization liquid chromatography mass spectrometry (PSESI-LCMS). This technique involves an interfacing of a pneumatic splitter that can dynamically generate and control a steady split flow rate of nanoliters per minute. An average PSESI-LCMS analysis, depending on the desired split ratio, consumes less than 200 femtomoles of sample. A tryptic digest map of a glycoprotein, fetuin, and a Lys-C digest map of a recombinant neurotrophin protein, neurotrophin-3, are reported here for this investigation.     

The determination of glycopeptides by liquid chromatography/mass spectrometry with collision-induced dissociation

Glycopeptides derived from ribonuclease B and ovomucoid have been subjected to collision-induced dissociation (CID) in the second quadrupole of a triple quadrupole mass spectrometer. Doubly charged parent ions gave predictable fragmentation that yielded partial sequence information of the attached oligosaccharide as Hex and HexNAc units. Common oxonium ions are observed in the product ion mass spectra of the glycopeptides that correspond to HexNAc⁺ (m/z 204) and HexHexNAc⁺ (m/z 366). A strategy for locating the glycopeptides in the proteolytic digest mixtures of glycoproteins by ions spray liquid chromatography mass spectrometry (LC/MS) is described by utilizing CID in the declustering region of the atmospheric pressure ionization mass spectrometer to produce these characteristic oxonium ions. This LC/CID/MS approach is used to identify glycopeptides in proteolytic digest mixtures of ovomucoid, asialofetuin, and fetuin. LC/CID/MS in the selected ion monitoring mode may be used to identify putative glycopeptides from the proteolytic digest of fetuin.     

Pressure limited sustained off-resonance irradiation for collision-activated dissociation in Fourier transform mass spectrometry

A theoretical evaluation of the sustained off-resonance irradiation of ions (SORI) in the presence of a collisional buffer gas in a Fourier transform ion cyclotron resonance mass spectrometer is presented. It is shown that there is an optimal pressure for a given set of irradiation parameters corresponding to the most effective dissociation. Theoretical predictions are compared with experimental results for the dissociation of electrosprayed biopolymer ions and with previously accepted view of the SORI process.     

Quantitative liquid chromatography/mass spectrometry for the analysis of microdialysates

Microdialysis (MD) is an in vivo sampling technique used to investigate biochemical events in the extracellular fluid of animal and human tissues. MD produces protein- and cell-free, aqueous samples which can be analyzed without further sample clean-up. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is a sensitive and selective analysis technique which is suitable to quantify low concentrated target analytes in microdialysates. This paper reviews the LC-MS/MS methods which are described for the quantification of endogenous molecules, such as neurotransmitters and peptides, and of exogenous molecules, such as drugs, in microdialysates. Since miniaturization of the LC-MS/MS methods is the key to obtain maximal sensitivity of the analytical technique, this feature is discussed in the paper. In addition, critical issues related to the quantification of low concentrated molecules in microdialysates are described such as the presence of matrix effects, the low MD efficiency and the sticking of, for instance, neuropeptides.     

Characterization of imazamox degradation by-products by using liquid chromatography mass spectrometry and high-resolution Fourier transform ion cyclotron resonance mass spectrometry

The photodecomposition of imazamox, a herbicide of the imidazolinone family, was investigated in pure water. The main photoproducts from the photolysis were followed over time by liquid chromatography mass spectrometry and structures were proposed from exact mass determinations obtained by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The method comprised exact mass determination with better than 0.2 ppm mass accuracy and a corresponding structural visualization taking care of respective isotopes with an adapted van Krevelen diagram that enabled a systematic approach to the characterisation of the elementary composition of each photoproduct. By taking advantage of the high resolving power of FT-ICR MS to make precise formula assignments, the derived 2D van Krevelen diagram (O/C; H/C; m/z) enabled one to structurally differentiate the formed photoproducts and to propose a degradation pathway for imazamox. Figure Overview of applied method to analyse the photolysis process of imazamox herbicide     

Peptide and protein characterization by high-rate electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry

The analytical utility of the electron capture dissociation (ECD) technique, developed by McLafferty and co-workers, has substantially improved peptide and protein characterization using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). The limitations of the first ECD implementations on commercial instruments were eliminated by the employment of low-energy electron-injection systems based on indirectly heated dispenser cathodes. In particular, the ECD rate and reliability were greatly increased, enabling the combination of ECD/FTICR-MS with on-line liquid separation techniques. Further technique development allowed the combination of two rapid fragmentation techniques, high-rate ECD and infrared multiphoton dissociation (IRMPD), in a single experimental configuration. Simultaneous and consecutive irradiations of trapped ions with electrons and photons extended the possibilities for ion activation/dissociation and led to improved peptide and protein characterization. The application of high-rate ECD/FTICR-MS has demonstrated its power and unique capabilities in top-down sequencing of peptides and proteins, including characterization of post-translational modifications, improved sequencing of peptides with multiple disulfide bridges and secondary fragmentation (w-ion formation). Analysis of peptide mixtures has been accomplished using high-rate ECD in bottom-up mass spectrometry based on mixture separation by liquid chromatography and capillary electrophoresis. This paper summarizes the current impact of high-rate ECD/FTICR-MS for top-down and bottom-up mass spectrometry of peptides and proteins.     

Microcolumn liquid chromatography/Fourier transform infrared spectrometry interface using a potassium bromide disk

Summary A redesigned interface is reported for use in the detection of microcolumn liquid chromatographic effluents with a Fourier transform infrared spectrometer. The solutes eluting from the column are continuously deposited onto a 50mm diameter KBr disk as a “buffer-memory”. The disk is rotated by a stepper motor with a controlling electronics. After the chromatographic run, the disk is simply transferred to the spectrometer and the transmission spectra are measured as the disk rotates. The use of such a large KBr disk as a substrate permits to obtain spectra of the components having a large capacity factor.     

Alkaline liquid chromatography/electrospray ionization skimmer collision-induced dissociation mass spectrometry for phosphopeptide screening.

A rapid on-line method for the identification of phosphorylated peptides in enzymatic protein digests by specific marker ion signals is described. In our study we investigated the use of alkaline conditions together with a previously described method for selective and sensitive detection of phosphopeptide ions combining high-performance capillary liquid chromatography (LC) and electrospray ionization mass spectrometry (ESI-MS). Phosphorylation-specific marker ions (m/z 79, PO(3)(-), and m/z 97, H(2)PO(4)(-)) were generated by skimmer collision-induced dissociation (sCID) in the negative-ion mode. The method was evaluated and validated for mono-phosphorylated synthetic peptides using different alkaline pH values and CID offsets. Alkaline conditions (pH 10.5) enhance the generation of phosphopeptide-specific fragment ions from serine- and tyrosine-phosphorylated peptides, and enable the use of m/z 79 (PO(3)(-)) and m/z 97 (H(2)PO(4)(-)) as phosphorylation-specific marker traces. Note that HPLC separation in trifluoroacetic acid containing solvents impairs the use of m/z 97 (C(2)F(3)O(-) fragment ion at m/z 97) as a phosphorylation-specific marker. The optimized method was applied for the detection of phosphorylated peptides in a tryptic beta-casein digest. The expected mono- and tetra-phosphorylated peptides were detected and rapidly identified by (mu)LC/ESI-sCID-MS and (mu)LC/ESI-MS analysis.     

Liquid chromatography electron capture dissociation tandem mass spectrometry (LC-ECD-MS/MS) versus liquid chromatography collision-induced dissociation tandem mass spectrometry (LC-CID-MS/MS) for the identification of proteins

Electron capture dissociation (ECD) offers many advantages over the more traditional fragmentation techniques for the analysis of peptides and proteins, although the question remains: How suitable is ECD for incorporation within proteomic strategies for the identification of proteins? Here, we compare LC-ECD-MS/MS and LC-CID-MS/MS as techniques for the identification of proteins. Experiments were performed on a hybrid linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer. Replicate analyses of a six-protein (bovine serum albumin, apo-transferrin, lysozyme, cytochrome c, alcohol dehydrogenase, and β-galactosidase) tryptic digest were performed and the results analyzed on the basis of overall protein sequence coverage and sequence tag lengths within individual peptides. The results show that although protein coverage was lower for LC-ECD-MS/MS than for LC-CID-MS/MS, LC-ECD-MS/MS resulted in longer peptide sequence tags, providing greater confidence in protein assignment.     

Deamidation and transamidation of substance P by tissue transglutaminase revealed by electron-capture dissociation fourier transform mass spectrometry

Tissue transglutaminase (tTGase) catalyzes both deamidation and transamidation of peptides and proteins by using a peptidyl glutamine as primary substrate. A precise consensus sequence for the enzyme is unknown and the ratio between deamidated and transamidated (or cross‐linked) reaction products is highly substrate‐dependent. Due to its overlapping body distribution with tTGase and ease of manipulation with tandem mass spectrometry, we used the neuropeptide substance P as a model to investigate the associated enzymatic kinetics and reaction products. Online liquid‐chromatography Fourier‐transform ion‐cyclotron‐resonance mass spectrometry (FT‐ICR MS) combined with electron‐capture dissociation (ECD) was employed to study the tTGase‐induced modifications of substance P. A particular strength of ECD for peptide‐enzyme reaction product monitoring is its ability to distinguish isomeric amino acids, for example, Glu and iso‐Glu, by signature product ions. Our studies show that the primary reaction observed is deamidation, with the two consecutive glutamine residues converted sequentially into glutamate: first Gln₅, and subsequently Gln₆. We then applied ECD FT‐ICR MS to identify the transamidation site on an enzymatically cross‐linked peptide, which turned out to correspond to Gln₅. Three populations of substance‐P dimers were detected that differed by the number of deamidated Gln residues. The higher reactivity of Gln₅ over Gln₆ was further confirmed by cross‐linking SP with monodansylcadaverine (MDC). Overall, our approach described herein is of a general importance for mapping both enzymatically induced post‐translational protein modifications and cross‐linking. Finally, in vitro Ca‐signaling assays revealed that the main tTGase reaction product, the singly deamidated SP (RPKPEQFFGLM‐NH₂), has increased agonist potency towards its natural receptor, thus confirming the biologically relevant role of deamidation.