The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer

A new matrix-assisted laser desorption/ionization (MALDI) time-of-flight/time-of-flight (TOF/TOF) high-resolution tandem mass spectrometer is described for sequencing peptides. This instrument combines the advantages of high sensitivity for peptide analysis associated with MALDI and comprehensive fragmentation information provided by high-energy collision-induced dissociation (CID). Unlike the postsource decay technique that is widely used with MALDI-TOF instruments and typically combines as many as 10 separate spectra of different mass regions, this instrument allows complete fragment ion spectra to be obtained in a single acquisition at a fixed reflectron voltage. To achieve optimum resolution and focusing over the whole mass range, it may be desirable to acquire and combine three separate sections. Different combinations of MALDI matrix and collision gas determine the amount of internal energy deposited by the MALDI process and the CID process, which provide control over the extent and nature of the fragment ions observed. Examples of peptide sequencing are presented that identify sequence-dependent features and demonstrate the value of modifying the ionization and collision conditions to optimize the spectral information.     

Imaging MS methodology for more chemical information in less data acquisition time utilizing a hybrid linear ion trap-orbitrap mass spectrometer

A novel mass spectrometric imaging method is developed to reduce the data acquisition time and provide rich chemical information using a hybrid linear ion trap-orbitrap mass spectrometer. In this method, the linear ion trap and orbitrap are used in tandem to reduce the acquisition time by incorporating multiple linear ion trap scans during an orbitrap scan utilizing a spiral raster step plate movement. The data acquisition time was decreased by 43-49% in the current experiment compared to that of orbitrap-only scans; however, 75% or more time could be saved for higher mass resolution and with a higher repetition rate laser. Using this approach, a high spatial resolution of 10 μm was maintained at ion trap imaging, while orbitrap spectra were acquired at a lower spatial resolution, 20-40 μm, all with far less data acquisition time. Furthermore, various MS imaging methods were developed by interspersing MS/MS and MS(n) ion trap scans during orbitrap scans to provide more analytical information on the sample. This method was applied to differentiate and localize structural isomers of several flavonol glycosides from an Arabidopsis flower petal in which MS/MS, MS(n), ion trap, and orbitrap images were all acquired in a single data acquisition.     

Demonstration of proton-transfer reaction time-of-flight mass spectrometry for real-time analysis of trace volatile organic compounds

A proton-transfer reaction mass spectrometer based on time-of-flight mass spectrometry is described. This instrument couples a radioactive ion source and drift tube with a reflectron time-of-flight mass spectrometer. Volatile organic compounds in the gas phase with concentrations at the parts per billion by volume level can be detected in a matter of seconds, and crucially, the multichannel data acquisition in TOF-MS means that this detection sensitivity is available in all mass channels simultaneously. The typical mass resolution (m/Deltam) is in excess of 1000. The performance of the instrument is demonstrated using urban air measurements and a linear response/calibration test.     

Aerosol MALDI with a Reflectron Time-of-Flight Mass Spectrometer

Aerosol matrix-assisted laser desorption/ionization (MALDI) has been combined with a reflectron time-of-flight mass spectrometer for improved mass resolution. A methanol solution of matrix and analyte was sprayed directly into a reflectron time-of-flight mass spectrometer, and the aerosol particles were irradiated and ionized with a frequency-tripled Nd:YAG laser at 355 nm. Mass resolution of over 300 was observed for the peptides bradykinin, angiotensin II, and gramicidin D and for vitamin B(12). This represents a resolution enhancement of approximately 10-fold over that previously reported for aerosol MALDI with a linear time-of-flight instrument.     

T3-sequencing: targeted characterization of the N- and C-termini of undigested proteins by mass spectrometry

A novel extension of the "top-down" approach is introduced for the selective characterization of protein termini that does not involve proteolytic digestion steps. N- and C-terminal peptides were generated from intact proteins in the mass spectrometer and further analyzed by MS/MS-an approach referred to as T(3)-sequencing. N-terminal and C-terminal fragment ion series were obtained by the pseudo-MS/MS technique in-source decay (ISD) on a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS). These ions provided near-terminal sequence tags from the undigested protein in the ISD spectrum acquired in reflector mode and allowed to screen for the proper processing state of the terminus with respect to a reference sequence. In the second step of T(3)-sequencing, the precursor ions, which have been generated by ISD and which included the N- or C-terminal sequence, were selected in the timed ion gate of a MALDI-TOF/TOF mass spectrometer for MS/MS analysis. These spectra allowed identification of the protein, the proper definition of both termini, and allowed confirmation of suspected terminal modifications. T(3)-Sequencing appears to be an alternative to classical Edman sequencing, which is fast and even permits the analysis of N-terminally blocked proteins and their C-terminus.     

An averaging mode time-to-amplitude converter with picosecondresolution

A time-to-amplitude converter (TAC) meant to be employed in pulsed time-of-flight (TOF) laser rangefinding and capable of operating at a very high pulse repetition rate (PRR) is described. It is based on a precise time interval between the emitted light pulses and measures the phase difference of the logic-level pulse trains formed by timing pulses derived from the transmitted and received light pulses. The fast part of the TAC is constructed by means of ECL 100 K circuits. Test results indicate that the TAC is well suited for fast, millimeter-level resolution applications, and a full width at half maximum (FWHM) resolution of 1.0 ps is achieved with a 5-MHz pulse repetition rate and 0.1-Hz-10-kHz measurement bandwidth     

Arrayed time-of-flight mass spectrometry for time-critical detection of hazardous agents

The design and operation of an arrayed time-of-flight (TOF) mass spectrometer for simultaneous data acquisition from multiple samples is described. Versions of the instrument employ sets of two or four linear or reflectron mass analyzers. They are housed in the same vacuum chamber and utilize the same laser for ion desorption. Instrument performance is illustrated in the example of a two-linear-mass-analyzer array using MALDI-MS for mixtures of commercially available proteins as well as intact microorganisms. We also describe the properties of a novel short delay time (<170 ns) pulsed extraction method for linear TOF analyzers. This configuration allows uniform resolution improvements to be achieved in a wide m/z range. In addition, we present multiplexed sample preparation methods, using different reagents prior to mass analysis in the arrayed system, to increase the overall sensitivity of the MS method and to allow wider and more efficient detection across the entire range of potentially hazardous agents. In addition to the multifold increase in data collection rates, arrayed TOF-MS configurations provide a high degree of redundancy, critical for rapid, high confidence agent identification as well as for reduction in false alarm rates.     

Trace Element Microanalysis in Iron Meteorites by Laser Ablation ICPMS

A laser ablation microanalysis system has been developed that can analyze trace elements with a sensitivity in the ppb range, using a CETAC LSX-200 laser ablation system with a Finnigan Element. This capability has been applied to a set of iron meteorites to demonstrate the laser microprobe's analytical capability for the determination of platinum group elements (PGEs) with a spatial resolution of ～20 μm, comparable to that of dynamic secondary ion mass spectrometry (SIMS). The laser is shown to provide an accurate means of solid sampling for magnetic sector inductively coupled plasma mass spectrometry (ICPMS), allowing the determination of bulk metal composition, chemical zoning within the sample, and depth profiling. Recovery of the chemical zoning in taenite lamellae was achieved for Ru, Rh, and Pd, which was not previously possible using SIMS. The methods presented here show that magnetic sector ICPMS can be successfully coupled to a laser ablation system, providing the advantages of higher sensitivity of the sector instrument, low background count rates (<0.1 counts/s), and flat-topped spectral peaks, while minimizing tradeoff against the speed of data acquisition required to handle the transient signals from the laser ablation system.     

Coupling high-pressure MALDI with ion mobility/orthogonal time-of-flight mass spectrometry

A new ion mobility/time-of-flight mass spectrometer employing a high-pressure MALDI source has been designed and tested. The prototype instrument operates at a source/drift cell pressure of 1-10 Torr helium, resulting in a mobility resolution of approximately 25. A small time-of-flight mass spectrometer (20 cm) with a mass resolution of up to 200 has been attached to the drift cell to identify (in terms of mass-to-charge ratio) the separated ions. A simple tripeptide mixture has been separated in the drift tube and mass identified as singly protonated species. The ability to separate peptide mixtures, e.g., tryptic digest of a protein, is illustrated and compared to results obtained on a high-vacuum time-of-flight instrument.     

Towards nanoscale molecular analysis at atmospheric pressure by a near-field laser ablation ion trap/time-of-flight mass spectrometer

An instrument that combines near-field laser ablation at atmospheric pressure with an ion trap/time-of-flight mass spectrometer was developed. By coupling a UV laser into a fiber tip of a scanning near-field optical microscope, ablation craters much smaller than achievable with conventional laser optics can in principle be obtained. Laser ablation was performed on samples such as DHB, anthracene, and pyrene. Desorbed neutral analytes are transferred from atmospheric pressure to an ion trap, ionized, and stored. After 10 ms, the ions are extracted into a sensitive time-of-flight spectrometer. We demonstrate the feasibility of this unique SNOM-MS instrument for chemical analysis with unprecedented lateral resolution at atmospheric pressure. Spatially resolved molecular analysis with a lateral resolution of 5 microm (fwhm) and a sensitivity of approximately 60 fmol of solid anthracene is demonstrated, along with topographical analysis with the same instrument. No other technique available today offers this lateral resolution in combination with soft mass spectrometry and the capability of sampling fragile specimens at atmospheric pressure.     

Sum-Frequency Generation of Femtosecond Pulses in CsLiB(6)O(10) Down to 175 nm

Using a 150-mum-thick CsLiB(6)O(10) crystal, we produced 100-fs, >200-nJ light pulses tunable between 175 and 180 nm by sum-frequency generation at a 1-kHz repetition rate with an all-solid-state laser system mixing the fourth harmonic of a femtosecond Ti:sapphire regenerative amplifier and the idler pulse from a traveling-wave optical parametric amplifier.     

Improving the performance of MALDI-TOF in oligonucleotide analysis using a new SDIFA technology

A new technology termed SDIFA is developed to improve the mass resolution of linear matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in oligonucleotide analysis. Unlike the currently used delayed extraction method, SDIFA allows electrical isolation of the sample holder from ion extraction/acceleration and selectively samples part of the desorbed ions, thereby reducing the initial velocity distribution and improving resolution. In addition, a method was introduced to improve the space focusing of TOF. Isotope-limited mass resolution was obtained for oligonucleotides of up to 62 mer, and the true instrumental resolution reaches to 1,800 at 19.2 kDa. It was also demonstrated that excellent resolution was obtained across a large mass range using a single setting of acquisition parameters. This feature allows unambiguous identification of multiple A/T heterozygote samples in a mass range of 5,200-7,800 Da. Moreover, compared with DE, the performance of SDIFA was more stable, reproducible, and less dependent on the experimental conditions including the laser power, sample spots, sample substrates, delayed time, and extraction field strength. This enhanced ease of data acquisition is the key to automated spectrum acquisition.     

Miniature cylindrical ion trap mass spectrometer

A miniature cylindrical ion trap mass spectrometer is described, and preliminary data are presented. Functionality and performance of laboratory-scale instruments have been maintained to the extent possible in this battery-operated mass spectrometer. Capabilities include tandem mass spectrometry experiments. Custom-designed electronic components include the RF scanning and amplification system, data acquisition components, and lens power supplies, as well as a custom-software application. Direct leak and membrane introduction inlet systems are used for sample introduction. A mass/charge range of approximately 250 Th with unit mass resolution has been demonstrated.     

Development of a broadband picosecond infrared spectrometer and its incorporation into an existing ultrafast time-resolved resonance Raman, UV/visible, and fluorescence spectroscopic apparatus

We have constructed a broadband ultrafast time-resolved infrared (TRIR) spectrometer and incorporated it into our existing time-resolved spectroscopy apparatus, thus creating a single instrument capable of performing the complementary techniques of femto-/picosecond time-resolved resonance Raman (TR3), fluorescence, and UV/visible/infrared transient absorption spectroscopy. The TRIR spectrometer employs broadband (150 fs, approximately 150 cm(-1) FWHM) mid-infrared probe and reference pulses (generated by difference frequency mixing of near-infrared pulses in type I AgGaS2), which are dispersed over two 64-element linear infrared array detectors (HgCdTe). These are coupled via custom-built data acquisition electronics to a personal computer for data processing. This data acquisition system performs signal handling on a shot-by-shot basis at the 1 kHz repetition rate of the pulsed laser system. The combination of real-time signal processing and the ability to normalize each probe and reference pulse has enabled us to achieve a high sensitivity on the order of deltaOD approximately 10(-4) - 10(-5) with 1 min of acquisition time. We present preliminary picosecond TRIR studies using this spectrometer and also demonstrate how a combination of TRIR and TR3 spectroscopy can provide key information for the full elucidation of a photochemical process.     

Mass analysis of biological macromolecules at atmospheric pressure using nonresonant femtosecond laser vaporization and electrospray ionization

A nonresonant femtosecond laser pulse, with an intensity of 10(13) Wcm(-2), vaporizes proteins and biomolecules intact, regardless of molecular structure, size or electronic structure for subsequent electrospray ionization and transfer into a mass spectrometer. Rapid, direct analysis from dried sample, aqueous solution and cellular material is demonstrated at atmospheric pressure using laser electrospray mass spectrometry (LEMS). Measurements are presented for lysozyme (14.3 kDa), hemoglobin from human blood, ovalbumin (45 kDa) from hen egg white and phospholipids from hen egg yolk. Mass analysis of biological material is performed without dilution, extraction or sample preparation, other than placing the biological material onto the sample plate.     

Automatic identification of proteins with a MALDI-quadrupole ion trap mass spectrometer.

A matrix-assisted laser desorption/ionization (MALDI) ion trap mass spectrometer of new design is described. The instrument is based on a commercial Finnegan LCQ ion trap mass spectrometer to which we have added a MALDI ion source that incorporates a sample stage constructed from a compact disk and a new ion transmission interface. The ion interface contains a quadrupole ion guide installed between the skimmer and the octapoles of the original instrument configuration, allowing for operation in both MALDI and electrospray ionization modes. The instrument has femtomole sensitivity for peptides and is capable of collecting a large number of MALDI MS and MALDI MS/MS spectra within a short period of time. The MALDI source produces reproducible signals for 10(4)-10(5) laser pulses, enabling us to collect MS/MS spectra from all the discernible singly charged ions detected in a MS peptide map. We describe the different modes of the instrument operation and algorithms for data processing as applied to challenging protein identification problems.     

Surface-induced dissociation in a Fourier transform ion cyclotron resonance mass spectrometer: instrument design and evaluation

A new Fourier transform ion cyclotron resonance mass spectrometer (FTICR MS) has been constructed in our laboratory. The instrument employs surface-induced dissociation (SID) as an activation method for obtaining structural information on biomolecules in the gas phase. Tandem SID mass spectra can be acquired using either a continuous or a pulsed mode of operation. Collision energy of precursor ion is controlled by a dc offset of the ICR cell. This approach eliminates defocusing of the ion beam by the ion-transfer optics as a function of ion kinetic energy and constitutes a significant improvement over our previous experimental setup. Furthermore, it can be easily implemented on any FTICR mass spectrometer. Very high signal-to-noise ratios of 200-500 were obtained in single-scan SID mass spectra of model peptides with acquisition time less than 1.1 s. Reasonable SID signal was detected in single-scan spectra with total acquisition time of only 0.3 s. The high signal-to-noise ratio and the fast acquisition time point on a potential application of SID for high-throughput studies in FTICR MS.     

Single cell matrix-assisted laser desorption/ionization mass spectrometry imaging

Application of mass spectrometry imaging (MS imaging) analysis to single cells was so far restricted either by spatial resolution in the case of matrix-assisted laser desorption/ionization (MALDI) or by mass resolution/mass range in the case of secondary ion mass spectrometry (SIMS). In this study we demonstrate for the first time the combination of high spatial resolution (7 μm pixel), high mass accuracy (<3 ppm rms), and high mass resolution (R = 100?000 at m/z = 200) in the same MS imaging measurement of single cells. HeLa cells were grown directly on indium tin oxide (ITO) coated glass slides. A dedicated sample preparation protocol was developed including fixation with glutaraldehyde and matrix coating with a pneumatic spraying device. Mass spectrometry imaging measurements with 7 μm pixel size were performed with a high resolution atmospheric-pressure matrix-assisted laser desorption/ionization (AP-MALDI) imaging source attached to an Exactive Orbitrap mass spectrometer. Selected ion images were generated with a bin width of Δm/z = ±0.005. Selected ion images and optical fluorescence images of HeLa cells showed excellent correlation. Examples demonstrate that a lower mass resolution and a lower spatial resolution would result in a significant loss of information. High mass accuracy measurements of better than 3 ppm (root-mean-square) under imaging conditions provide confident identification of imaged compounds. Numerous compounds including small metabolites such as adenine, guanine, and cholesterol as well as different lipid classes such as phosphatidylcholine, sphingomyelin, diglycerides, and triglycerides were detected and identified based on a mass spectrum acquired from an individual spot of 7 μm in diameter. These measurements provide molecularly specific images of larger metabolites (phospholipids) in native single cells. The developed method can be used for a wide range of detailed investigations of metabolic changes in single cells.     

On-line multicomponent trace-gas analysis with a broadly tunable pulsed difference-frequency laser spectrometer

The design and application of a novel automated room-temperature laser spectrometer are reported. The compact instrument is based on difference-frequency generation in bulk LiNbO(3). The instrument employs a tunable cw external-cavity diode laser (795-825 nm) and a pulsed diode-pumped Nd:YAG laser (1064 nm). The generated mid-IR nanosecond pulses of 50-muW peak power and 6.5-kHz repetition rate, continuously tunable from 3.16 to 3.67 mum, are coupled into a 36-m multipass cell for spectroscopic studies. On-line measurements of methane are performed at concentrations between 200 ppb (parts in 10(9) by mole fraction) and approximately 1%, demonstrating a large dynamic range of 7 orders of magnitude. Furthermore computer-controlled multicomponent analysis of a mixture containing five trace gases and water vapor with an overall response time of 90 s at an averaging time of only approximately 30 s is reported. A minimum detectable absorption coefficient of 1.1 x 10(-7) cm(-1) has been achieved in an averaging time of 60 s, enabling detection limits in the ppb range for many important trace gases, such as CH(4), C(2)H(6), H(2)CO, NO(2), N(2)O, HCl, HBr, CO, and OCS.     

Simple nanosecond to minutes transient absorption spectrophotometer

We built a transient absorption spectrophotometer that can determine transient absorption spectral changes that occur at times as fast as approximately 200 ns and as slow as a minute. The transient absorption can be induced by a temperature-jump (T-jump) or by optical pumping from the deep ultraviolet (UV) to the infrared (IR) by use of single ns Nd:YAG laser pulses. Our use of a fiber-optic spectrometer coupled to a XeF flashlamp makes the collection of transient spectra easy and convenient in the spectral range from the near IR (1700 nm) down to the deep UV (200 nm), with high signal-to-noise (S/N) ratios. The spectral resolution is determined by the specific configuration of the fiber-optic spectrometer (grating groove density, fiber diameter, slit width) and varies between 0.3 and 10 nm. The utility of this spectrometer was demonstrated by measuring the rate at which a polymerized crystalline colloidal array (PCCA) of poly(N-isopropylacrylamide) nanogel particles optically switch light due to a T-jump induced by nanosecond 1.9 microm laser pulses. In addition, we measured the rate of optical switching induced by a 3 ns 355 nm pump pulse in PCCA functionalized with azobenzene.