Nano electrospray combined with a quadrupole ion trap for the analysis of peptides and protein digests

An integrated experimental and theoretical reaction path search: analyses of the multistage reaction of an ionized diethylether dimer involving isomerization, proton transfer, and dissociation

A multistage reaction involving isomerization, proton transfer, and dissociation of an ionized diethylether dimer is studied by combination of infrared spectroscopy, tandem mass spectrometry, and a theoretical reaction path search.

Corona Discharge Suppression in Negative Ion Mode Nanoelectrospray Ionization via Trifluoroethanol Addition

Negative ion mode nanoelectrospray ionization (nESI) is often utilized to analyze acidic compounds, from small molecules to proteins, with mass spectrometry (MS). Under high aqueous solvent conditions, corona discharge is commonly observed at emitter tips, resulting in low ion abundances and reduced nESI needle lifetimes. We have successfully reduced corona discharge in negative ion mode by trace addition of trifluoroethanol (TFE) to aqueous samples. The addition of as little as 0.2% TFE increases aqueous spray stability not only in nESI direct infusion, but also in nanoflow liquid chromatography (nLC)/MS experiments. Negative ion mode spray stability with 0.2% TFE is approximately 6× higher than for strictly aqueous samples. Upon addition of 0.2% TFE to the mobile phase of nLC/MS experiments, tryptic peptide identifications increased from 93 to 111 peptides, resulting in an average protein sequence coverage increase of 18%.

Determination of Sulfonamides in Chicken Muscle by Pulsed Direct Current Electrospray Ionization Tandem Mass Spectrometry

A simple and rapid approach for the simultaneous detection of trace amounts of six sulfonamides in chicken muscle was developed using pulsed direct current electrospray ionization tandem mass spectrometry (pulsed-dc ESI-MS/MS). The pretreatment of chicken muscle samples consisted of two steps: acetonitrile extraction and n-hexane delipidation. Sulfonamides do not need to be derivatized or chromatographed prior to pulsed-dc ESI-MS/MS. The factors affecting the performance of pulsed-dc ESI-MS/MS were studied. Under optimum conditions, the quantitative performance of pulsed-dc ESI-MS/MS was validated according to European Union Decision 2002/657/EC, and the sensitivity of pulsed-dc ESI-MS/MS was 3 times higher than that of ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The limits of detection obtained by pulsed-dc ESI-MS/MS were in the range of 0.07-0.11 μg/kg. The proposed method was simple, rapid, and sensitive, and was successfully used for quantitation and rapid screening of sulfonamides in real chicken muscle samples.

Matrix effect management in liquid chromatography mass spectrometry: the internal standard normalized matrix effect

LC-MS is becoming a standard for many applications, thanks to high sensitivity and selectivity; nevertheless, some issues are still present, particularly due to matrix effect (ME). Considering this, the use of optimal internal standards (ISs, usually stable-isotope labeled) is important, but not always possible because of cost or availability. Therefore, a deep investigation of the inter-lot variability of the ME and of the correcting power of the chosen IS (isotope-labeled or not) is mandatory. While the adoption of isotopically labeled ISs considered as a 'gold standard' to mitigate ME impact on analytical results, there is not consensus about the standard technique to evaluate it during method validation. In this paper, currently available techniques to evaluate, reduce or counterbalance ME are presented and discussed. Finally, these techniques were summarized in a flowchart for a robust management of ME, particularly considering the concept of 'internal standard normalized ME'.

Mass spectral similarity for untargeted metabolomics data analysis of complex mixtures

While in nucleotide sequencing, the analysis of DNA from complex mixtures of organisms is common, this is not yet true for mass spectrometric data analysis of complex mixtures. The comparative analyses of mass spectrometry data of microbial communities at the molecular level is difficult to perform, especially in the context of a host. The challenge does not lie in generating the mass spectrometry data, rather much of the difficulty falls in the realm of how to derive relevant information from this data. The informatics based techniques to visualize and organize datasets are well established for metagenome sequencing; however, due to the scarcity of informatics strategies in mass spectrometry, it is currently difficult to cross correlate two very different mass spectrometry data sets from microbial communities and their hosts. We highlight that molecular networking can be used as an organizational tool of tandem mass spectrometry data, automated database search for rapid identification of metabolites, and as a workflow to manage and compare mass spectrometry data from complex mixtures of organisms. To demonstrate this platform, we show data analysis from hard corals and a human lung associated with cystic fibrosis.

Fragmentation follows structure: top-down mass spectrometry elucidates the topology of engineered cystine-knot miniproteins

Over the last decades the field of pharmaceutically relevant peptides has enormously expanded. Among them, several peptide families exist that contain three or more disulfide bonds. In this context, elucidation of the disulfide patterns is extremely important as these motifs are often prerequisites for folding, stability, and activity. An example of this structure-determining pattern is a cystine knot which comprises three constrained disulfide bonds and represents a core element in a vast number of mechanically interlocked peptidic structures possessing different biological activities. Herein, we present our studies on disulfide pattern determination and structure elucidation of cystine-knot miniproteins derived from Momordica cochinchinensis peptide MCoTI-II, which act as potent inhibitors of human matriptase-1. A top-down mass spectrometric analysis of the oxidised and bioactive peptides is described. Following the detailed sequencing of the peptide backbone, interpretation of the MS(3) spectra allowed for the verification of the knotted topology of the examined miniproteins. Moreover, we found that the fragmentation pattern depends on the knottin's folding state, hence, tertiary structure, which to our knowledge has not been described for a top-down MS approach before.

Practical aspects of in vivo detection of neuropeptides by microdialysis coupled off-line to capillary LC with multistage MS

A method using capillary liquid chromatography-triple-stage mass spectrometry (LC-MS(3)) to determine endogenous opioid peptides in microdialysis samples collected in vivo was developed, validated, and applied to measurements in the rat striatum. Peptides in dialysate rapidly degraded when stored at room temperature or -80 degrees C. Adding acetic acid to a final concentration of 5% stabilized the peptides for 5 days allowing storage of fractions and off-line measurements which proved more convenient and reliable than previously used on-line methods. Study of the effect of dialysis flow rate from 0.2 to 2 microL/min and column inner diameter (i.d.) from 25 to 75 microm on the relative signal obtained for peptides revealed that lowest flow rates and smallest column i.d. gave the highest relative signal. The method was tested for 10 different neuropeptides and limits of detection (LODs) were from 0.5 to 60 pM (4 microL samples) for most. beta-Endorphin had an LOD of 5 nM when detected directly, but it could be quantitatively determined by detecting a characteristic peptide produced by tryptic digestion with an LOD of 3 pM. This approach may prove useful for other large neuropeptides as well. The method was used to determine met-enkephalin, leu-enkephalin, dynorphin A(1-8), and beta-endorphin in vivo. Endomorphin 1 and 2 were below the detection limit of the method in vivo. Quantitative determination of leu-enkephalin using external calibration was verified by standard addition experiments. The improvements over previous approaches using capillary LC-MS(n) make in vivo neuropeptide monitoring more practical and feasible for a variety of neuropeptides.

Pulsed Nano-Electrospray Ionization: Characterization of Temporal Response and Implementation with a Flared Inlet Capillary

The temporal response of pulsed nano-electrospray ionization mass spectrometry (nano-ESI-MS) was studied and its influence on ion formation and detection was characterized. Rise and decay times for the mass resolved ion current were determined to be 20 ± 3 msec and 61 ± 5 msec, respectively, which led to a maximum pulse rate of 12 Hz. Pulsed nano-ESI operation was demonstrated from a multi-sprayer source controlled by a high voltage pulsing circuit constructed in-house. The desired source mode of operation (e.g. pulsing or continuous) can be realized solely by controlling the voltage applied to each sprayer.

Multidimensional liquid phase separations for mass spectrometry

Large part of the current research in biology, medicine, and biotechnology depends on the analysis of DNA (genomics), proteins (proteomics), or metabolites (metabolomics). The advances in biotechnology also command development of adequate analytical instrumentation capable to analyze minute amounts of samples. The analysis of the content of single cells may serve as an example of ultimate analytical applications. Most of the separation techniques have been developed in the last three decades and alternative approaches are being investigated. At present, the main protocols for analyses of complex mixtures include 2-DE (IEF) followed by electrophoresis in SDS polyacrylamide gel (SDS-PAGE) and chromatographic techniques. Information-rich techniques such as MS and NMR are essential for the identification and structure analysis of the analyzed compounds. High resolution separation of the individual sample components is often a prerequisite for success. High resolution proteomic analysis in the majority of laboratories still relies on the time consuming and laborious offline methods. This review highlights some of the important aspects of 2-D separations including microfluidics.

Effect of decreasing column inner diameter and use of off-line two-dimensional chromatography on metabolite detection in complex mixtures

Capillary liquid chromatography coupled with electrospray ionization to a quadrupole ion trap mass spectrometer was explored as a method for the analysis of polar anionic compounds in complex metabolome mixtures. A ternary mobile phase gradient, consisting of aqueous acidic, aqueous neutral and organic phases in combination with an aqueous compatible reversed-phase stationary phase allowed metabolites with a wide range of polarities to be resolved and detected. Detection limits in the full scan mode for glycolysis and tricarboxylic acid cycle intermediates were from 0.9 to 36fmol. Using this system, 111+/-9 (n=3) metabolites were detected in Escherichia coli lysate samples. Reducing column I.D. from 50 to 25microm increased the number of metabolites detected to 156+/-17 (n=3). The improvement in number of metabolites detected was attributed to an increase in separation efficiency, an increase in sensitivity, and a decrease in adduct formation. Implementation of a second separation mode, strong anion exchange, to fractionate the sample prior to capillary RPLC increased the number of metabolites detected to 244+/-21 (n=3). This improvement was attributed to the increased peak capacity which decreased co-elution of molecules enabling more sensitive detection by mass spectrometry. This system was also applied to islets of Langerhans where more significant improvements in metabolite detection were observed. In islets, 391+/-33 small molecules were detected using the two-dimensional separation. The results demonstrate that column miniaturization and use of two-dimensional separations can yield a significant improvement in the coverage of the metabolome.

Mass spectrometric contributions to the practice of phosphorylation site mapping through 2003: a literature review

Reversible phosphorylation of proteins is among the most important post-translational modifications, and elucidation of sites of phosphorylation is essential to understanding the regulation of key cellular processes such as signal transduction. Unfortunately phosphorylation site mapping is as technically challenging as it is important. Limitations in the traditional method of Edman degradation of (32)P-labeled phosphoproteins have spurred the development of mass spectrometric methods for phosphopeptide identification and sequencing. To assess the practical contributions of the various technologies we conducted a literature search of publications using mass spectrometry to discover previously unknown phosphorylation sites. 1281 such phosphorylation sites were reported in 203 publications between 1992 and 2003. This review examines and catalogs those methods, identifies the trends that have emerged in the past decade, and presents representative examples from among these methods.

Linear ion traps in mass spectrometry

Linear ion traps are finding new applications in many areas of mass spectrometry. In a linear ion trap, ions are confined radially by a two-dimensional (2D) radio frequency (RF) field, and axially by stopping potentials applied to end electrodes. This review focuses on linear ion trap instrumentation. Potentials and ion motion in linear multipole fields and methods of ion trapping, cooling, excitation, and isolation are described. This is followed by a description of various mass discrimination effects that have been reported with linear ion traps. Linear ion traps combined in various ways with three-dimensional (3D) traps, time-of-flight (TOF) mass analyzers, and Fourier transform ion cyclotron resonance mass spectrometers are then given. Linear ion traps can be used as stand alone mass analyzers, and their use for mass analysis by Fourier transforming image currents, by mass selective radial ejection, and by mass selective axial ejection are reviewed.

Proteomics in experimental gerontology

The first gerontological studies using two-dimensional gel electrophoresis (2DGE) were frustrating since it was very difficult, when not impossible, to identify the proteins for which an age-related change in expression level was suspected. Reproducibility was also a main pitfall. Accumulated progress in 2DGE and especially the development of mass spectrometry of proteins and peptides gave accessibility to the routine identification of differentially expressed proteins. A new paradigm was born: proteomics. In addition to expression changes, post-translational modifications are included in proteomics, and will be more and more studied using mass spectrometry. After a review of the current developments of 2DGE and mass spectrometry, we shall discuss how the technologies currently available in proteomics could give fresh impetus to experimental gerontology, complementary to more recent approaches based on wide expression analysis tools such as DNA and protein arrays.

Polymer microspray with an integrated thick-film microelectrode

A microfabrication process leading to a sheathless electrospray interface for mass spectrometry analysis is described. Photoablation is performed on a polymer substrate, allowing the integration of a thick-film conductive track in a sealed microchannel. High voltage is supplied close to the outlet, through an embedded microelectrode. The microspray is generated directly from the edge of the substrate without any tip addition. The flexibility of this technology provides a wide range of dimensions for the probe and the microelectrode design, including location, shape, and conductive material used. Thanks to the thick-film microelectrode and the hydrophobicity of the polymer, which avoids solution spreading at the outlet, the device has been found to be an efficient ionization source providing a stable MS signal through time. Moreover, the same device can be used several times without failure. The performance of the microspray has been studied in simple infusion mode for proteins and reserpine MS analyses. The detection limit of reserpine was found to be at the picomolar level in full-scan MS mode. It implies also that approximately 500 zmol was read consumed during 3 min of infusion. A dynamic range from pico- to millimolar level is also underlined.

Reduced enzymatic activity of glucokinase after affinity labeling: results from spectrophotometry and electrospray ionization mass spectrometry

Glucokinase catalyzes phosphoryl group transfer from ATP to glucose to form glucose-6-phosphate in the first step of cellular metabolism. While the location of the ATP-binding site of glucokinase was proposed recently, limited information exists on its conformation or the key amino acids involved in substrate binding. Affinity labeling with phenylglyoxal is used to probe possible Arg residues involved in ATP binding. Electrospray ionization mass spectrometry indicates that reaction of purified glucokinase with phenylglyoxal results in as many as six or seven sites of modification, suggesting nonspecific modification. However, preincubation of glucokinase with glucose followed by reaction with phenylglyoxal reveals only two sites of modification. Glucokinase activity assays show that enzyme preincubated with glucose possesses residual activity corresponding to the fraction of unmodified enzyme observed by mass spectrometry, strongly suggesting that glucokinase preincubated with glucose is specifically labeled and inactivated upon modification by phenylglyoxal. The data support the existing conformational model of glucokinase.

An interface with a linear quadrupole ion guide for an electrospray-ion trap mass spectrometer system

A new ion sampling interface for an electrospray ionization 3D ion trap mass spectrometer system is described. The interface uses linear rf quadrupoles as ion guides and ion traps to enhance the performance of the 3D trap. Trapping ions in the linear quadrupoles is demonstrated to improve the duty cycle of the system. Dipolar excitation of ions trapped in a linear quadrupole is used to eject unwanted ions. A resolution of ejection of up to 254 is demonstrated for protonated reserpine ions (m/z 609.3). A composite waveform with a notch in frequency space is used to eject a wide range of matrix ions and to isolate trace analyte ions in a linear quadrupole before ions are injected into the 3D trap. This is useful to overcome space charge problems in the 3D trap caused by excess matrix ions. For trace reserpine in a 500-fold molar excess of poly(propylene glycol) (PPG), it is demonstrated that the resolution and sensitivity of the 3D trap can be increased dramatically with ejection of the excess PPG matrix ions. In comparison to ejection of matrix ions in the 3D trap with a similar broad-band waveform, a 5-fold increase in sensitivity with a 7 times shorter acquisition time was achieved.

Identification of phosphorylation sites in proteins by nanospray quadrupole ion trap mass spectrometry

A method is described for identifying serine phosphorylation sites in proteins, based on conventional (32)P labeling followed by electrophoretic separation, 'in-gel' digestion with a protease, peptide extraction, reversed-phase high-performance liquid chromatographic separation and collection and off-line analysis of the radioactive fractions by nanospray ion trap mass spectrometry. The method was successfully applied to the identification of three phosphorylation sites in two proteins which were subjected to in vitro phosphorylation under physiological conditions. Different combinations of the various scanning modes of the ion trap, including high-resolution, multiple subfragmentation (or MS(n)) and fast scan analysis, were employed to identify the phosphopeptides, determine their sequence and localize the exact site of phosphorylation. 'Blind' fragmentation using fast scans was used to analyze a phosphopeptide which was undetectable in other scanning modes. The sequence, phosphorylation site and double cysteine modification of the potassium adduct of a peptide containing 35 residues were also determined by multiple fragmentation. The results not only support the validity of the proposed method for routine identification of phosphorylation sites, but also demonstrate the exceptional capability of off-line ion trap mass spectrometry in combination with nanospray ionization for performing very detailed studies on the structure of peptides.

Identification of factor C protein from Streptomyces griseus by microelectrospray mass spectrometry

Factor C, an extracellular signal protein of cellular differentiation, was studied and significant homology was found to several zinc finger-type regulatory proteins. The complete amino acid sequence, deduced from the gene, that encodes the protein, did not support the hypothesis that this protein might be a zinc finger-type regulatory protein. However, a theoretical single nucleotide insertion in the gene can result in another similarly sized protein containing about 20 His residues, which would be responsible for the high zinc affinity of factor C. The protein sample was reduced, alkylated and then in-gel digested with trypsin. The peptide fragments were then separated by capillary chromatography and identified by microelectrospray mass spectrometry. Peaks of higher intensity were sequenced by tandem mass spectrometry. The identified peptide fragments and the measured molecular mass of factor C protein also confirmed the original sequence of protein, as there was no shift in the open reading frame.

Narrow-band collisional activation technique for ion trap mass spectrometers

Narrow-bandwidth signals were applied to the end caps of an ion trap mass spectrometer to excite ions during collisional activation. Excitation waveforms were created from a single-frequency component and a random noise component using a multiplier circuit. Tandem and higher order mass spectrometry experiments (MS3) can be performed without optimization of the supplemental frequency applied to the end cap electrodes. The usefulness of this method of ion excitation is demonstrated using singly and multiply protonated peptide ions as well as sodium-cationized carbohydrates.

A novel nonmetallized tip for electrospray mass spectrometry at nanoliter flow rate

We report the fabrication of a durable nonmetallized nanospray tip. This nanospray tip does not require complex preparation procedures such as chemical treatment, deposition of gold or SiOx vapor. It was fabricated by pulling a heated glass capillary of 1.1 mm internal diameter to produce a fine tip with an orifice of 10-15 microns in diameter. A 10 microns gold-plated tungsten wire was inserted through the capillary tip. This tungsten wire played a central role in the operation of this durable nanospray tip by providing electrical contact. This type of nanospray tip could withstand electrical discharges and sustained spraying of solution at nanoliter flow rate for more than 3 h. Using insulin (35 microM) and myoglobin (1 microM) solutions, useful mass spectrum could be acquired with low fmol sensitivity.

Ion trap collisional activation of disulfide linkage intact and reduced multiply protonated polypeptides

The presence of disulfide linkages in multiply charged polypeptide ions tends to inhibit the formation of structurally informative product ions under conventional quadrupole ion trap collisional activation conditions. In particular, fragmentation that requires two cleavages (i.e., cleavage of a disulfide linkage and a peptide linkage) is strongly suppressed. Reduction of the disulfide linkage(s) by use of dithiothreitol yields parent ions upon electrospray without this complication. Far richer structural information is revealed by ion trap collisional activation of the disulfide-reduced species than from the native species. These observations are illustrated with doubly protonated native and reduced somatosin, the [M + 5H](5+) ion of native bovine insulin and the [M + 4H](4+) and [M + 3H](3+) ions of the B-chain of bovine insulin produced by reduction of the disulfide linkages in insulin, and the [M + 11H](11+) ion of native chicken lysozyme and the [M + 11H](11+) and [M + 14H](14+) ions of reduced lysozyme. In each case, the product ions produced by ion trap collisional activation were subjected to ion/ion proton transfer reactions to facilitate interpretation of the product ion spectra. These studies clearly suggest that the identification of polypeptides with one or more disulfide linkages via application of ion trap collisional activation to the multiply charged parent ions formed directly by electrospray could be problematic. Means for cleaving the disulfide linkage, such as reduction by dithiothreitol prior to electrospray, are therefore desirable in these cases.

High-sensitivity analysis and sequencing of peptides and proteins by quadrupole ion trap mass spectrometry

This paper describes experience with the commercially available LCQ quadrupole ion trap mass spectrometer applied to the off-line analysis of peptides and proteins. The standard front end of the electrospray probe was replaced with a micromanipulator which, with the aid of a magnifying device, allowed the use of a variety of miniaturized spraying interfaces. The low sample consumption and extended analysis times of these devices were ideally suitable to obtain improved results in terms of sensitivity and mass accuracy. This needed a careful optimization of the number of ions stored inside the trap (ion target parameter) and required spectrum averaging of many scans. A method is presented for the mathematical fitting of ZoomScan spectra to theoretical isotopic distributions, which allowed the mass determination of large peptides with more accuracy than that achieved by conventional deconvolution algorithms. A very simple on-line desalting configuration is also described which needed no external micro-high-performance liquid chromatographic pumps, and can be easily mounted using the built-in syringe delivery system of the LCQ. This set-up allowed extended analysis times of 'in-gel' protein digests in subpicomole amounts. Finally, the multiple fragmentation capabilities of the ion trap were found to be extremely useful for the analysis of peptide modifications such as phosphorylation and for sequencing individual peptides from highly complex MHC-bound peptide pools.

Optimization of solid phase microextraction - capillary zone electrophoresis - mass spectrometry for high sensitivity protein identification

We have previously described the use of a solid phase extraction (SPE) - capillary zone electrophoresis (CZE) - tandem mass spectrometry (MS/MS) system for protein analysis at the low femtomole to subfemtomole level. Here we describe the systematic optimization of a number of parameters which facilitate the use of the SPE-CZE-MS/MS system and further enhance its performance. Specifically, we describe a robust SPE cartridge design which can be assembled without the use of glue, the evaluation of procedures to chemically modify the inner wall of the fused-silica capillaries used in the system to improve separation and reproducibility, and the comparison of different reverse-phase (RP) resins used for the SPE cartridge. We also explored the effects of transient isotachophoresis with respect to system performance and compatibility with different fused-silica surface coatings, the RP resins used, and MS/MS. The enhanced performance of the optimized system is demonstrated by the analysis of calibrated tryptic digests of bovine serum albumin (BSA).

Separation and identification of positively charged and neutral nucleoside adducts by capillary electrochromatography-microelectrospray mass spectrometry

Capillary electrochromatography (CEC) is shown to be capable of separating mixtures containing both positively charged and neutral styrene oxide-adenosine adducts. In a study of the mechanism of deamination of positively charged 1-(2-hydroxy-1-phenylethyl) adenosine using 18O-labeled water, possible contamination of the chromatographically purified deamination product, 1-(2-hydroxy-1-phenylethyl) inosine, with the positively charged 1-(2-hydroxy-1-phenylethyl) adenosine was observed. Because the deamination product and the presumed contamination have the same molecular weights and similar structures, CEC-microelectrospray mass spectrometry (CEC-microESI/MS) was used to confirm the presence and identity of the suspected impurity. A trace amount of the positively charged 1-(2-hydroxy-1-phenylethyl) adenosine, which could not be observed by either HPLC-UV or CEC-UV, was detected by CEC-microESI/MS. This discriminatory ability of CEC-microESI/MS is attributed to the fact that positive ion mode ESI-MS is a more sensitive detector for a positively charged compound than a UV detector, and that the combination of electroosmotic and electrophoretic flows and hydrophobic interactions with the stationary phase contributes to the separation of the positively charged compound. As a result, the positively charged compound was observed to elute much earlier and with much sharper peaks than the neutral compounds for which electroosmotic flow is the only "pumping" force for the solvent.

Detection and identification of carcinogen-peptide adducts by nanoelectrospray tandem mass spectrometry

Nanoelectrospray (nanoES) tandem mass spectrometry was used to examine covalently modified peptides in crude enzymatic digests of human serum albumin (HSA) that had been exposed to either benzo[a]pyrene diol epoxide (B[a]PDE, 1), chrysene diol epoxide (CDE, 2), 5-methylchrysene diol epoxide (5MeCDE, 3), or benzo[g]chrysene diol epoxide (B[g]CDE, 4). The low flow rates of nanoES (approximately 20 nL/min) allowed several MS/MS experiments to be optimized and performed on a single sample with very little sample consumption (approximately 30 min analysis time/microL sample). Initially, nanoES was compared with conventional LC/MS/MS analysis of carcinogen-peptide adducts. For example, nanoES analysis of an unseparated digest of B[a]PDE-treated serum albumin revealed the same peptides (RRHPY and RRHPY-FYAPE) that were previously shown, by LC/MS/MS, to be adducted with B[a]PDE. In addition, nanoES could detect unstable peptide adducts that might not otherwise have been directly observable. Finally, nanoES was shown to be an effective way to screen mixtures of modified and unmodified peptides for which no chromatographic information is available.

Analysis of DNA adducts by capillary methods coupled to mass spectrometry: a perspective

The analysis of DNA adducts, important molecular biomarkers indicative of potential cellular damage by covalent attachment to DNA, is discussed. The paper focusses on a discussion of the current status in the analysis of DNA adducts via the use of capillary high-performance liquid chromatographic and capillary electrophoretic methods coupled to tandem mass spectrometry.

Peptides adsorbed on reverse-phase chromatographic beads as targets for femtomole sequencing by post-source decay matrix assisted laser desorption ionization-reflectron time of flight mass spectrometry (MALDI-RETOF-MS)

We here describe a procedure for concentrating peptides from solutions by adsorbing them onto reverse-phase beads that were added to these solutions. The beads are then transferred to the target disc of the matrix assisted laser desorption ionization-reflectron time of flight (MALDI-RETOF) mass spectrometer. Because of their hydrophobic nature, these beads cluster in a very small area on the target disc assuring an important concentration step. After drying, peptides are desorbed from the beads by adding a small volume of 50% acetonitrile in 0.1% trifluroacetic acid in water containing the matrix components. Hereby we focus the original amount of peptide material on the target disc on a very small surface, producing highly concentrated peptide-matrix mixtures. This permits high yield identification and sequence tagging by post-source-decay analysis on peptides derived from proteins only available in the femtomole range from one-dimensional (1-D) or two-dimensional (2-D) gels. The procedure is illustrated by the identification of 38 proteins from human thrombocyte membrane skeletons.

Mass spectrometry at low and high mass

The introduction of novel methods as well as expanding applications to diverse areas highlight truly impressive progress in mass spectrometry. These developments are illustrated here by two seemingly different areas of research: new methods designed for the determination of isotopic enrichment and novel ionization methods; and mass analyzers which have enabled the precise determination of the molecular weight of proteins and large oligonucleotides.

A microfabricated device for rapid protein identification by microelectrospray ion trap mass spectrometry

Nanoelectrospray mass spectrometry, the infusion at low flow rates of unseparated peptide mixtures representing protein proteolytic digests into an electrospray ionization mass spectrometer (MS), has been shown to be a suitable method for the analysis of small amounts of proteins. However, the current technique is time consuming, tedious, and difficult to automate. We used microfabrication technologies to construct a device for the sequential infusion of different peptide samples into an electrospray ionization MS without the need for sample manipulation. In this device, etched sample and buffer reservoirs are connected via etched channels to microelectrospray ion source. Peptide samples, typically unseparated tryptic digests of proteins, are applied to different reservoirs. A flow of liquid originating from a specific reservoir is generated and selectively directed toward the microsprayer and the MS by electroosmotic pumping. The analyte proteins are identified by searching sequence databases with the information contained in the collision-induced spectra of selected peptides. With this system, we have achieved a limit of detection in the low femtomoles per microliter range for peptide standards. We also show that samples deposited in different reservoirs can be sequentially mobilized without cross-contamination and that proteins can be conclusively identified at the low femtomoles per microliter level. The successful coupling online of microfabricated devices to an electrospray ionization MS represents an essential step toward the construction of automated, high-throughput, and high-sensitivity analytical systems.

Mass spectrometry in protein studies from genome to function

The demands for highly sensitive and specific analytical techniques in biochemistry, molecular biology and biotechnology are met by new developments in mass spectrometry. Femto- to attomole sensitivity and mass accuracy in a low parts per million range can now be routinely obtained. Mass spectrometry, already accepted for studies of protein secondary modifications, must, in the future, be expected to be an important tool in protein studies on all levels, ranging from proteome analysis to studies of protein higher order structures and protein interaction.

Long-lived metallized tips for nanoliter electrospray mass spectrometry

Sheathless electrospray at nL/min flow rates combined with Fourier-transform mass spectrometry has made possible high resolving power (>50,000) mass spectra of subattomole samples of >8 kDa proteins separated by capillary electrophoresis (Valaskovic, G. A.; Kelleher, N. L.; McLafferty, F. W. Science, 1996, 273, 1199-1202). However, for this new method the mechanical stability of the thin (35 to 100 nm) gold film electrodes has limited tip lifetime to 15 to 30 min. A technique for SiO x coating of the gold is described that provides a steady ion current (±10 pA) for 1 to 2 h, even with arcs or interruptions of the electrospray voltage.

Use of infrared multiphoton photodissociation with SWIFT for electrospray ionization and laser desorption applications in a quadrupole ion trap mass spectrometer

Infrared multiphoton photodissociation (IRMPD) is combined with stored wave form inverse Fourier transforms (SWIFT) to effect dissociation and ion ejection in a quadrupole ion trap mass spectrometer. The application of IRMPD to the structural characterization of biochemical ions generated by chemical ionization and electrospray ionization and the feasibility of utilizing infrared photons for the activation of laser-desorbed metal ion-crown ether complexes was examined. The effect of helium pressure on the dissociation efficiency and relative dissociation rate constants for systems with well-known thermochemistry was evaluated. The helium pressure is not detrimental to the IRMPD experiment when nominal pressures lower than 2 x 10(-5) Torr are used. At pressures close to nominally 8 x 10(-5) Torr of helium, collisonal deactivation dominates. Results show conventional CAD is a more selective dissociation technique; however, the amount of fragment ion information generated depends highly on the qz value. IRMPD, on the other hand, is independent of the value of qz such that low rf storage values can be utilized during the irradiation period. Thus, under these conditions, informative lower mass fragment ions are trapped and detected. A larger number of structurally informative fragments is generated upon irradiation with infrared photons relative to the CAD method because of the further excitation of primary fragment ions upon photoabsorption. SWIFT wave forms are successfully utilized to determine the extent of excitation of primary fragment ions as well as prove/disprove dissociation pathways of a variety of ions such as macrolide antibiotics and hydrogen-bonded complexes.