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High magnetic field Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry provides the highest mass resolving power and mass measurement accuracy for detailed characterization of complex chemical mixtures. Here, we report the coupling of online liquid chromatography of complex mixtures with a 21 tesla FT-ICR mass spectrometer. The high magnetic field enables large ion populations to be analyzed for each spectrum for a high dynamic range, with 3.2 million mass resolving power at m/z 400 (6.2 s transient duration) or 1.6 million (3.1 s transient duration) while maintaining high mass accuracy for molecular formula assignment (root-mean-square assignment error < 0.150 ppm). Thousands of unique elemental compositions are assigned per mass spectrum, which can be grouped by the heteroatom class, double bond equivalents (the number of rings and double bonds to carbon), and carbon number. Figures of merit are discussed, as well as characterization of an Arabian heavy vacuum gas oil in terms of the ring number, compound class, double bond equivalents, and ion type. Consideration of elemental composition and retention order provides additional structural information.

Proton transfer reactions (PTR) have emerged as a powerful tool for the study of intact proteins. When coupled with m/z-selective kinetic excitation, such as parallel ion parking (PIP), one can exert exquisite control over rates of reaction with a high degree of specificity. This allows one to “concentrate”, in the gas-phase, nearly all the signal from an intact protein charge state envelope into a single charge state improving signal-to-noise by 10x or more. While this approach has been previously reported, here we show that implementing these technologies on a 21 T FT-ICR MS provides tremendous advantage for intact protein analysis. Advanced strategies for performing PTR with PIP were developed to complement this unique instrument, including subjecting all analyte ions entering the mass spectrometer to PTR and PIP. This experiment, which we call “PTR-MS(1)-PIP”, generates a pseudo-MS(1) spectrum derived from ions that are exposed to PTR reagent and PIP waveforms, but have not undergone any prior true mass filtering or ion isolation. The result is an extremely rapid and significant improvement in spectral signal-to-noise (S:N) of intact proteins. This permits observation of many more proteoforms and reduces ion injection periods for subsequent tandem mass spectrometry characterization. Additionally, the product ion parking waveform has been optimized to enhance the proton transfer reaction rate without compromise to parking efficiency. We demonstrate that this process, called “rapid park”, can improve reaction rates by 5–10x and explore critical factors discovered to influence this process. Finally, we demonstrate how coupling PTR-MS(1) and rapid park provides a ten-fold reduction in ion injection time, improving the rate of tandem MS sequencing.

Detailed characterization of complex biological surfaces by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) requires instrumentation that is capable of high mass resolving power, mass accuracy, and dynamic range. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) offers the highest mass spectral performance for MALDI MSI experiments, and often reveals molecular features that are unresolved on lower performance instrumentation. Higher magnetic field strength improves all performance characteristics of FT-ICR; mass resolving power improves linearly, while mass accuracy and dynamic range improve quadratically with magnetic field strength. Here, MALDI MSI at 21T is demonstrated for the first time: mass resolving power in excess of 1 600 000 (at m/z 400), root-mean-square mass measurement accuracy below 100 ppb, and dynamic range per pixel over 500:1 were obtained from the direct analysis of biological tissue sections. Molecular features with m/z differences as small as 1.79 mDa were resolved and identified with high mass accuracy. These features allow for the separation and identification of lipids to the underlying structures of tissues. The unique molecular detail, accuracy, sensitivity, and dynamic range combined in a 21T MALDI FT-ICR MSI experiment enable researchers to visualize molecular structures in complex tissues that have remained hidden until now. The instrument described allows for future innovative, such as high-end studies to unravel the complexity of biological, geological, and engineered organic material surfaces with an unsurpassed detail.

Fourier transform mass spectrometers routinely provide high mass resolution, mass measurement accuracy, and mass spectral dynamic range. In this work, we utilize 21 T Fourier transform ion cyclotron resonance (FT-ICR) to analyze product ions derived from the application of multiple dissociation techniques and/or multiple precursor ions within a single transient acquisition. This ion loading technique, which we call, "chimeric ion loading", saves valuable acquisition time, decreases sample consumption, and improves top-down protein sequence coverage. In the analysis of MCF7 cell lysate, we show collision-induced dissociation (CID) and electron-transfer dissociation (ETD) on each precursor on a liquid chromatography-mass spectrometry (LC-MS) timescale and improve mean sequence coverage dramatically (CID-only 15% vs chimeric 33%), even during discovery-based acquisition. This approach can also be utilized to multiplex the acquisition of product ion spectra of multiple charge states from a single protein precursor or multiple ETD/proton-transfer reactions (PTR) reaction periods. The analytical utility of chimeric ion loading is demonstrated for top-down proteomics, but it is also likely to be impactful for tandem mass spectrometry applications in other areas.

We describe complex organic mixture analysis by 21 tesla (T) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Ultrahigh mass-resolving power (m/Δm50% > 2 700 000 at m/z 400) and mass accuracy (80 ppb rms) enable resolution and confident identification of tens of thousands of unique elemental compositions. We demonstrate 2.2-fold higher mass-resolving power, 2.6-fold better mass measurement accuracy, and 1.3-fold more assigned molecular formulas compared to our custom-built, state-of-the-art 9.4 T FT-ICR mass spectrometer for petroleum and dissolved organic matter (DOM) analyses. Analysis of a heavy petroleum distillate exemplifies the need for ultrahigh-performance mass spectrometry (49 040 assigned molecular formulas for 21 T versus 29 012 for 9.4 T) and extends the identification of previously unresolved Oo, SsOo, and NOo classes. Mass selective ion accumulation (20 Thompson isolation) of an asphalt volcano sample yields 462 resolved mass spectral peaks at m/z 677 and reveals pre...

Stored waveform inverse Fourier transform (SWIFT) is a versatile method to generate complex isolation/ejection waveforms for precursor isolation prior to tandem mass spectrometry experiments. Here, we report ultrahigh resolving power ion isolation by SWIFT on a 21 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Individual histone proteoforms are isolated (0.6 m/z isolation window) with near 100% efficiency using a 52 ms SWIFT isolation, followed by in-cell fragmentation by ultraviolet photodissociation (UVPD). Ion isolation resolving power of 175 000 (m/Δm) is demonstrated by isolation of individual peaks at a spacing of 0.0034 Da at m/z 597 from a complex mixture of Canadian bitumen. An individual m/z ion, which corresponds to a single elemental composition, from a complex mixture is isolated and fragmented by infrared multiphoton dissociation (IRMPD). Theoretical and experimental considerations that limit achievable ion isolation resolving power are discussed.

The current five-year survival rate for systemic AL amyloidosis or multiple myeloma is ∼51%, indicating the urgent need for better diagnosis methods and treatment plans. Here, we describe highly specific and sensitive top-down and middle-down MS/MS methods owning the advantages of fast sample preparation, ultrahigh mass accuracy, and extensive residue cleavages with 21 telsa FT-ICR MS/MS. Unlike genomic testing, which requires bone marrow aspiration and may fail to identify all monoclonal immunoglobulins produced by the body, the present method requires only a blood draw. In addition, circulating monoclonal immunoglobulins spanning the entire population are analyzed and reflect the selection of germline sequence by B cells. The monoclonal immunoglobulin light chain FR2-CDR2-FR3 was sequenced by database-aided de novo MS/MS and 100% matched the gene sequencing result, except for two amino acids with isomeric counterparts, enabling accurate germline sequence classification. The monoclonal immunoglobulin heavy chains were also classified into specific germline sequences based on the present method. This work represents the first application of top/middle-down MS/MS sequencing of endogenous human monoclonal immunoglobulins with polyclonal immunoglobulins background.

We present laser desorption atmospheric pressure photochemical ionization mass spectrometry (LD/APPCI MS) for rapid throughput analysis of complex organic mixtures, without the need for matrix, electric discharge, secondary electrospray, or solvents/vaporizers. Analytes dried on a microscope slide are vaporized in transmission geometry by a laser beam aligned with the atmospheric pressure inlet of the mass spectrometer. The laser beam initiates a cascade of reactions in the region between the glass slide and MS inlet, leading to generation of reagent ions for chemical ionization of vaporized analyte. Positive analyte ions are generated predominantly by proton transfer, charge exchange, and hydride abstraction, whereas negative ions are generated by electron capture or proton transfer reactions, enabling simultaneous analysis of saturated, unsaturated, and heteroatom-containing hydrocarbons. The absence of matrix interference renders LD/APPCI MS particularly useful for analysis of small molecules (2000 Da) such as those present in petroleum crude oil and petroleum deposits. [M + H](+) and M(+•) dominate the positive-ion mass spectra for olefins and polyaromatic hydrocarbons, whereas saturated hydrocarbons are observed mainly as [M - H](+) and/or M(+•). Heteroatom-containing hydrocarbons are observed predominantly as [M + H](+). [M - H](-) and M(-•) are the dominant negative ions observed for analytes of lower gas-phase basicity or higher electron affinity than O2. The source was coupled with a 9.4 T Fourier transform ion cyclotron resonance mass spectrometer (FTICR MS) to resolve and identify thousands of peaks from Athabasca bitumen heavy vacuum gas oil distillates (400-425 and 500-538 °C), enabling simultaneous characterization of their polar and nonpolar composition. We also applied LD/APPCI FTICR MS for rapid analysis of sodium and calcium naphthenate deposits with little to no sample pretreatment to provide mass spectral fingerprints that enable reliable compositional characterization.

Top-down electron capture dissociation (ECD) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry was performed for structural analysis of an intact monoclonal antibody (IgG1kappa (κ) isotype, ~148 kDa). Simultaneous ECD for all charge states (42+ to 58+) generates more extensive cleavages than ECD for an isolated single charge state. The cleavages are mainly localized in the variable domains of both heavy and light chains, the respective regions between the variable and constant domains in both chains, the region between heavy-chain constant domains CH2 and CH3, and the disulfide bond (S-S)-linked heavy-chain constant domain CH3. The light chain yields mainly N-terminal fragment ions due to the protection of the interchain disulfide bond between light and heavy chain, and limited cleavage sites are observed in the variable domains for each chain, where the S-S spans the polypeptide backbone. Only a few cleavages in the S-S-linked light-chain constant domain, hinge region, and heavy-chain constant domains CH1 and CH2 are observed, leaving glycosylation uncharacterized. Top-down ECD with a custom-built 9.4 T FTICR mass spectrometer provides more extensive sequence coverage for structural characterization of IgG1κ than does top-down collision-induced dissociation (CID) and electron transfer dissociation (ETD) with hybrid quadrupole time-of-flight instruments and comparable sequence coverage for top-down ETD with orbitrap mass analyzers.

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) typically utilizes an m/z-independent excitation magnitude to excite all ions to the same cyclotron radius, so that the detected signal magnitude is directly proportional to the relative ion abundance. However, deleterious space charge interaction between ion clouds is maximized for clouds of equal radius. To minimize ion cloud interactions, we induce an m/z-dependent ion radius distribution (30%-45% of the maximum cell radius) that results in a 3-fold increase in mass spectral dynamic range for complex mixtures, consistent with increased ion cloud lifetime for less-abundant ion clouds. Further, broadband frequency-sweep (chirp) excitation that contains the second and/or third harmonic frequency of an excited ion cloud swept from low-to-high frequency produces systematic variations in accurate mass measurement not observed when the sweep direction is reversed. The ion cyclotron radius distribution induces an m/z-dependent frequency shift that can be corrected to provide a root-mean-square (rms) mass measurement error of

We present atmospheric pressure laser-induced acoustic desorption chemical ionization (AP/LIAD-CI) with O(2) carrier/reagent gas as a powerful new approach for the analysis of saturated hydrocarbon mixtures. Nonthermal sample vaporization with subsequent chemical ionization generates abundant ion signals for straight-chain, branched, and cycloalkanes with minimal or no fragmentation. [M - H](+) is the dominant species for straight-chain and branched alkanes. For cycloalkanes, M(+•) species dominate the mass spectrum at lower capillary temperature (100 °C) and [M - H](+) at higher temperature (200 °C). The mass spectrum for a straight-chain alkane mixture (C(21)-C(40)) shows comparable ionization efficiency for all components. AP/LIAD-CI produces molecular weight distributions similar to those for gel permeation chromatography for polyethylene polymers, Polywax 500 and Polywax 655. Coupling of the technique to Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for the analysis of complex hydrocarbon mixtures provides unparalleled mass resolution and accuracy to facilitate unambiguous elemental composition assignments, e.g., 1754 peaks (rms error = 175 ppb) corresponding to a paraffin series (C(12)-C(49), double-bond equivalents, DBE = 0) and higher DBE series corresponding to cycloparaffins containing one to eight rings. Isoabundance-contoured plots of DBE versus carbon number highlight steranes (DBE = 4) of carbon number C(27)-C(30) and hopanes of C(29)-C(35) (DBE = 5), with sterane-to-hopane ratio in good agreement with field ionization (FI) mass spectrometry analysis, but performed at atmospheric pressure. The overall speciation of nonpolar, aliphatic hydrocarbon base oil species offers a promising diagnostic probe to characterize crude oil and its products.

Current high-throughput top-down proteomic platforms provide routine identification of proteins less than 25 kDa with 4-D separations. This short communication reports the application of technological developments over the past few years that improve protein identification and characterization for masses greater than 25 kDa. Advances in separation science have allowed increased numbers of proteins to be identified, especially by nanoliquid chromatography (nLC) prior to mass spectrometry (MS) analysis. Further, a goal of high-throughput top-down proteomics is to extend the mass range for routine nLC MS analysis up to 80 kDa because gene sequence analysis predicts that ~70% of the human proteome is transcribed to be less than 80 kDa. Normally, large proteins greater than 50 kDa are identified and characterized by top-down proteomics through fraction collection and direct infusion at relatively low throughput. Further, other MS-based techniques provide top-down protein characterization, however at low resolution for intact mass measurement. Here, we present analysis of standard (up to 78 kDa) and whole cell lysate proteins by Fourier transform ion cyclotron resonance mass spectrometry (nLC electrospray ionization (ESI) FTICR MS). The separation platform reduced the complexity of the protein matrix so that, at 14.5 T, proteins from whole cell lysate up to 72 kDa are baseline mass resolved on a nano-LC chromatographic time scale. Further, the results document routine identification of proteins at improved throughput based on accurate mass measurement (less than 10 ppm mass error) of precursor and fragment ions for proteins up to 50 kDa.

Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) provides the highest mass resolving power and mass measurement accuracy for unambiguous identification of biomolecules. Previously, the highest-mass protein for which FTICR unit mass resolution had been obtained was 115 kDa at 7 T. Here, we present baseline resolution for an intact 147.7 kDa monoclonal antibody (mAb), by prior dissociation of noncovalent adducts, optimization of detected total ion number, and optimization of ICR cell parameters to minimize space charge shifts, peak coalescence, and destructive ion cloud Coulombic interactions. The resultant long ICR transient lifetime (as high as 20 s) results in magnitude-mode mass resolving power of ∼420 000 at m/z 2 593 for the 57+ charge state (the highest mass for which baseline unit mass resolution has been achieved), auguring for future characterization of even larger intact proteins and protein complexes by FTICR MS. We also demonstrate up to 80% higher resolving power by phase...

Valence parity provides a way to distinguish between N-terminal and C-terminal electron capture dissociation/electron transfer dissociation (ECD/ETD) product ions based on their number of hydrogen plus nitrogen atoms determined by accurate mass measurement and forms a basis for de novo peptide sequencing. The effect of mass accuracy (0.1-1 ppm error) on c'/z(•) overlap and unique elemental composition overlap is evaluated for a database of c'/z(•) product ions each based on all possible amino acid combinations and four subset databases containing the same c' ions but with z(•) ions determined by in silico digestion with trypsin, Glu-C, Lys-C, or chymotrypsin. High mass accuracy reduces both c'/z(•) overlap and unique elemental composition overlap. Of the four proteases, trypsin offers slightly better discrimination between N- and C-terminal ECD/ETD peptides. Interestingly, unique elemental composition overlap curves for c'/c' and z(•)/z(•) peptide ions exhibit discontinuities at certain nominal masses for 0.1-1.0 ppm mass error. Also, as noted in the companion article (Polfer et al. Anal. Chem.2011, DOI: 10.1021/ac201624t), the number of ECD/ETD product ion amino acid compositions as a function of nominal mass increases exponentially with mass but with a superimposed modulation due to higher prevalence of certain elemental compositions.

It has been known for 35 years that phase correction of FTICR data can in principle produce an absorption-mode spectrum with mass resolving power as much as a factor of 2 higher than conventional magnitude-mode display, an improvement otherwise requiring a (much more expensive) increase in magnetic field strength. However, temporally dispersed excitation followed by time-delayed detection results in steep quadratic variation of signal phase with frequency. Here, we present a robust, rapid, automated method to enable accurate broadband phase correction for all peaks in the mass spectrum. Low-pass digital filtering effectively eliminates the accompanying baseline roll. Experimental FTICR absorption-mode mass spectra exhibit at least 40% higher resolving power (and thus an increased number of resolved peaks) as well as higher mass accuracy relative to magnitude mode spectra, for more complete and more reliable elemental composition assignments for mixtures as complex as petroleum.

We describe the design and current performance of a 14.5 T hybrid linear quadrupole ion trap Fourier transform ion cyclotron resonance mass spectrometer. Ion masses are routinely determined at 4-fold better mass accuracy and 2-fold higher resolving power than similar 7 T systems at the same scan rate. The combination of high magnetic field and strict control of the number of trapped ions results in external calibration broadband mass accuracy typically less than 300 ppb rms, and a resolving power of 200,000 (m/Delta m50% at m/z 400) is achieved at greater than 1 mass spectrum per second. Novel ion storage optics and methodology increase the maximum number of ions that can be delivered to the FTICR cell, thereby improving dynamic range for tandem mass spectrometry and complex mixture applications.

We present a method to distinguish N-terminal from C-terminal product ions in electron capture dissociation (ECD) MS/MS due to the change in relative abundances of even-electron (prime) and odd-electron (radical) product ions produced in consecutive ECD and activated ion-ECD mass spectra. The method is based on the rate and direction of hydrogen atom transfer between N-terminal and C-terminal ECD products and its dependence on ion internal energy. We demonstrate that increasing ion internal energy by vibrational activation prior to ECD results in decreased ratio of radical/prime N-terminal product ions (c*/c' ratio), but increased ratio of radical/prime C-terminal product ions (z*/z' ratio) in many cases. The combination of AI-ECD and ECD promises to increase the confidence of mass spectrometry-based peptide sequencing and protein identification.

Applying an inverted voltage to the "sidekick" electrodes during ion cyclotron resonance detection improves both Fourier transform ion cyclotron resonance (FT-ICR) mass spectral signal-to-noise ratio (at fixed resolving power) and resolving power (at fixed signal-to-noise ratio). The time-domain signal duration increases by up to a factor of 2. The method has been applied to 7-T FT-ICR MS of electrosprayed positive ions from substance P and human growth hormone protein ( approximately 22 000 Da, m/Deltam50% 200 000), without the need for pulsed cooling gas inside the ICR trap. The modification can be easily adapted to any FT-ICR instrument equipped with sidekick electrodes. The present effects are shown to be comparable to electron field modification by injection of an electron beam during ICR detection, reported by Kaiser and Bruce (Kaiser, N. K.; Bruce, J. E. Anal. Chem. 2005, 77, 5973-5981.). Although the exact mechanism is not fully understood, computer simulations show that a flattening of the radial potential gradient along the magnetic field direction in the ICR trap may contribute to the effects. This study not only provides a way to enhance the quality of FT-ICR mass spectra but also offers insight into understanding of ion motions inside an ICR ion trap.

Amide hydrogen/deuterium exchange is a powerful biophysical technique for probing changes in protein dynamics induced by ligand interaction. The inherent low throughput of the technology has limited its impact on drug screening and lead optimization. Automation increases the throughput of H/D exchange to make it compatible with drug discovery efforts. Here we describe the first fully automated H/D exchange system that provides highly reproducible H/D exchange kinetics from 130 ms to 24 h. Throughput is maximized by parallel sample processing, and the system can run H/D exchange assays in triplicate without user intervention. We demonstrate the utility of this system to differentiate structural perturbations in the ligand-binding domain (LBD) of the nuclear receptor PPARgamma induced upon binding a full agonist and a partial agonist. PPARgamma is the target of glitazones, drugs used for treatment of insulin resistance associated with type II diabetes. Recently it has been shown that partial agonists of PPARgamma have insulin sensitization properties while lacking several adverse effects associated with full agonist drugs. To further examine the mechanism of partial agonist activation of PPARgamma, we extended our studies to the analysis of ligand interactions with the heterodimeric complex of PPARgamma/RXRalpha LBDs. To facilitate analysis of H/D exchange of large protein complexes, we performed the experiment with a 14.5-T Fourier transform ion cyclotron resonance mass spectrometer capable of measuring mass with accuracy in the ppb range.

Here we describe a mass spectrometry (MS) approach for biomarker discovery and structural characterization, based on both top-down and bottom-up analyses. Capillary electrophoresis (CE) coupled to electrospray ionization (ESI) time-of-flight (TOF) MS serves to separate and mass-measure the thousands of polypeptides contained in human urine. Statistical analysis of the differences between healthy control samples and patients with focal-segmental glomerulosclerosis, membranous glomerulonephritis, minimal change disease, IgA nephropathy, and diabetic nephropathy validates multiple biomarkers for the control and each of the diseases. To identify those biomarkers, we employ preparative CE, enabling direct infusion ESI MS analysis, followed by sample manipulation and reanalysis where necessary. We show how tandem Fourier transform ion cyclotron resonance (FT-ICR) MS identifies these sometimes large (8 kDa) biomarkers. Critically, we maintain connectivity between the CE TOF MS data and the ICR data used for biomarker identification.

13C, 15N doubly depleted 32-ribonucleotide was synthesized enzymatically by in vitro transcription from nucleoside triphosphates isolated from E. coli grown in a minimal medium containing 12C, 14N-enriched glucose and ammonium sulfate. Following purification and desalting by reversed-phase HPLC, buffer exchange with Microcon YM-3, and ethanol precipitation, electrospray ionization Fourier transform ion cyclotron resonance mass spectra revealed greatly enhanced abundance of monoisotopic ions (by a factor of approximately 100) and a narrower isotopic distribution with higher signal-to-noise ratio. The abrupt onset and high magnitude of the monoisotopic species promise to facilitate accurate mass measurement of RNA's.

We report the first field desorption ionization broadband high-resolution (m/Deltam(50%) approximately 65 000) mass spectra. We have interfaced a field ionization/field desorption source to a home-built 9.4-T FT-ICR mass spectrometer. The instrumental configuration employs convenient sample introduction (in-source liquid injection) and external ion accumulation. We demonstrate the utility of this configuration by generating high-resolution positive-ion mass spectra of C(60) and a midboiling crude oil distillate. The latter contains species not accessible by common soft-ionization methods, for example, low-voltage electron ionization, electrospray ionization, and matrix-assisted laser desorption/ionization. The present work demonstrates significant advantages of FI/FD FT-ICR MS for analysis of nonpolar molecules in complex mixtures.

Electron capture dissociation (ECD) has previously been shown by other research groups to result in greater peptide sequence coverage than other ion dissociation techniques and to localize labile posttranslational modifications. Here, ECD has been achieved for 10-13-mer peptides microelectrosprayed from 10 nM (10 fmol/microL) solutions and for tryptic peptides from a 50 nM unfractionated digest of a 28-kDa protein. Tandem Fourier transform ion cyclotron resonance (FTICR) mass spectra contain fragment ions corresponding to cleavages at all possible peptide backbone amine bonds, except on the N-terminal side of proline, for substance P and neurotensin. For luteinizing hormone-releasing hormone, all but two expected backbone amine bond cleavages are observed. The tandem FTICR mass spectra of the tryptic peptides contain fragment ions corresponding to cleavages at 6 of 12 (1545.7-Da peptide) and 8 of 21 (2944.5-Da peptide) expected backbone amine bonds. The present sensitivity is 200-2000 times higher than previously reported. These results show promise for ECD as a tool to produce sequence tags for identification of peptides in complex mixtures available only in limited amounts, as in proteomics.

Modifications to a 7 T nano-LC micro-ESI FT-ICR mass spectrometer, including a shorter octopole, approximately 100% duty cycle, improved nano-LC micro-ESI emitter tips, and reverse-phase HPLC resins that require no ion-pairing agent, combine to achieve attomole detection limit. Three peptides in a mixture totaling 500 attomoles (amol) each in water (10 microL, 50 amol/microL) are separated and detected, demonstrating detection from a mixture at low endogenous biological concentration. Two peptides in a mixture totaling 500 amol each in artificial cerebrospinal fluid (1 microL, 500 amol/microL) are separated and detected, demonstrating detection from a mixture at a biological concentration in a biological solvent. The highest sensitivity is attained with arg8-vasotocin, in which a total of 300 amol is detected in artificial cerebrospinal fluid (1 microL, 300 amol/microL) and a total of 100 amol in water (1 microL, 100 amol/microL). Arg8-vasotocin isolated from the pineal gland of rainbow trout is detected, demonstrating the ability of FT-ICR to detect and identify a true endogenous biological analyte.

The pursuit of ever higher mass-resolving power in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has driven a demand for higher magnetic field strength and longer time-domain ICR signal lifetime, with proportionate increase in data set size in direct-mode detection. Heterodyne-mode detection thus becomes increasingly important for achieving ultrahigh-mass resolution from a fixed maximum-size data set. Unfortunately, as conventionally performed (i.e., analog single phase), heterodyne detection reduces the S/N ratio by a factor of 21/2 relative to direct-mode detection. Here, we restore the factor of 21/2 by use of quadrature heterodyne detection. In addition, replacement of analog by digital heterodyning eliminates analog circuitry (and its associated noise). Finally, digital filtering of the time-domain discrete ICR signal not only eliminates the need for a bank of analog low-pass filters but also ensures that the Nyquist bandwidth and filter bandwidth are always matched, for opt...

Elemental compositional analysis of processed and unprocessed diesel fuels is obtained with a 5.6-T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer coupled to an all-glass heated inlet system (AGHIS). High-resolution mass spectra of electron-ionized diesel fuel samples are obtained from as little as a 500-nL septum injection into the AGHIS, to yield ∼500 peaks over a range 90 < m/z < 300, with as many as seven peaks present at the same nominal mass. Molecular formulas (elemental compositions) are assigned from accurate mass measurement with an average error less than ±0.5 ppm. Comparison of the raw and processed diesel spectra shows complete removal of the sulfur-containing species except for dimethyldibenzothiophene and higher alkyl-substituted dibenzothiophenes. These results confirm prior reports of the resistance of these species to hydrotreatment due to steric hindrance of catalytic desulfurization arising from 4,6 dimethyl substitution. A simple liquid chromatographic separation...

Glycidyl methacrylate (GMA) and butyl methacrylate (BMA) have the same nominal mass (142 Da) but differ in exact mass by 0.036 Da (CH(4) vs O). Therefore, copolymers formed from the two isobaric monomers exhibit a characteristic isobaric distribution due to different monomer compositions. Here, we show that electrospray ionization FT-ICR mass spectrometry at 9.4 T resolves the isobaric components of copolymers as large as 7000 Da with a resolving power (m/Δm(50%)) of ∼500 000 in a gel permeation chromatography fractionated polymer sample. That resolution provides for complete and unequivocal component analysis of such copolymers of the size used for high solid content automobile coatings. All five possible copolymer products predicted by the polymerization mechanism are resolved and identified in the mass spectrum. Two of those polymer series (each with saturated end group) were previously unresolved by mass spectrometry because they differ in mass from the two other unsaturated products by only 0.0089 Da. Finally, analysis of the asymmetrical isobaric distribution for the copolymer n-mers, (GMA)(m)(BMA)(n)(-)(m), 0≤ m ≤ n, in which species with adjacent values of m differ from each other in mass by 36 mDa (i.e., the mass difference, CH(4) vs O, between GMA and BMA) proves that GMA is less reactive than BMA in the polymerization process.

Quadrupolar axialization is implemented on a high-field electrospray ionization Fourier transform ion cyclotron resonance mass spectrometer. The method is utilized to perform highly efficient remeasurement of small proteins which were not previously amenable to the remeasurement process. For example, 100 consecutive remeasurements of the same population of melittin ions (MW 2845) yield the theoretical 10-fold improvement in signal-to-noise ratio compared to the first measurement. The efficiency of the cooling process is evaluated as a function of excitation radius and ion mass, and the results are compared to instrumental performance prior to the implementation of quadrupolar axialization. The maximum achievable excitation radius for efficient remeasurement is increased from 18% to 52% of the trapped ion cell radius. The application of quadrupolar axialization during the electrospray ion accumulation event results in a factor of 3 improvement in sensitivity when acquiring bovine insulin (MW 5734) spectra under high-resolution conditions. The mass selectivity of the technique is used to isolate a single charge state of horse myoglobin (MW 16 951)

■ CONTENTS Mass Resolution, Mass Resolving Power 708 Mass Resolution and Accuracy 708 Time-of-Flight Mass Analyzers 708 Orthogonal Acceleration (see ref 13) 709 Reflectron/Multipass TOF 709 Recent Advances in TOF Mass Analyzers 709 Selected Applications 710 Fourier Transform Mass Analyzers 710 Common Features of Fourier Transform Mass Analyzers 710 Ion Accumulation and Detection 711 Advances in Fourier Transform Mass Analyzers 711 Selected Applications 713 Author Information 715 Corresponding Author 715 Biographies 715 Acknowledgments 715 References 715

We present a novel nonresonant laser-based matrix-free atmospheric pressure ionization technique, atmospheric pressure laser-induced acoustic desorption chemical ionization (AP/LIAD-CI). The technique decouples analyte desorption from subsequent ionization by reagent ions generated from a corona discharge initiated in ambient air or in the presence of vaporized toluene as a CI dopant at room temperature. Analyte desorption is initiated by a shock wave induced in a titanium foil coated with electrosprayed sample, irradiated from the rear side by high-energy laser pulses. The technique enables facile and independent optimization of the analyte desorption, ionization, and sampling events, for coupling to any mass analyzer with an AP interface. Moreover, the generated analyte ions are efficiently thermalized by collisions with atmospheric gases, thereby reducing fragmentation. We have coupled AP/LIAD-CI to ultrahigh-resolution FT-ICR MS to generate predominantly [M + H](+) or M(+•) ions to resolve and identify thousands of elemental compositions from organic mixtures as complex as petroleum crude oil distillates. Finally, we have optimized the AP/LIAD CI process and investigated ionization mechanisms by systematic variation of placement of the sample, placement of the corona discharge needle, discharge current, gas flow rate, and inclusion of toluene as a dopant.

Ion cyclotron resonance frequency, f, is conventionally converted to ion mass-to-charge ratio, m/z (mass "calibration") by fitting experimental data spanning the entire detected m/z range to the relation, m/z = A/f + B/f(2), to yield rms mass error as low as ~200 ppb for ~10,000 resolved components of a petroleum crude oil. Analysis of residual error versus m/z and peak abundance reveals that systematic errors limit mass accuracy and thus the confidence in elemental composition assignments. Here, we present a calibration procedure in which the spectrum is divided into dozens of adjoining segments, and a separate calibration is applied to each, thereby eliminating systematic error with respect to m/z. Further, incorporation of a third term in the calibration equation that is proportional to the magnitude of each detected peak minimizes systematic error with respect to ion abundance. Finally, absorption-mode data analysis increases mass measurement accuracy only after minimization of systematic errors. We are able to increase the number of assigned peaks by as much as 25%, while reducing the rms mass error by as much as 3-fold, for significantly improved confidence in elemental composition assignment.

Atmospheric pressure photoionization (APPI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has significantly contributed to the molecular speciation of petroleum. However, a typical APPI source operates at 50 microL/min flow rate and thus causes a considerable mass load to the mass spectrometer. The recently introduced microchip APPI (microAPPI) operates at much lower flow rates (0.05-10 microL/min) providing decreased mass load and therefore decreased contamination in analysis of petroleum by FT-ICR MS. In spite of the 25 times lower flow rate, the signal response with microAPPI was only 40% lower than with a conventional APPI source. It was also shown that microAPPI provides very efficient vaporization of higher molecular weight components in petroleum analysis.

We describe automation of liquid injection field desorption/ionization (LIFDI) for reproducible sample application, improved spectral quality, and high-throughput analyses. A commercial autosampler provides reproducible and unattended sample application. A custom-built field desorption (FD) controller allows data station or front panel control of source parameters including high-voltage limit/ramp rate, emitter heating current limit/ramp rate, and feedback control of emitter heating current based on ion current measurement. Automated LIFDI facilitates ensemble averaging of hundreds of Fourier transform ion cyclotron resonance mass spectra for increased dynamic range, mass accuracy, and S/N ratio relative to single-application FD experiments, as shown here for a South American crude oil. This configuration can be adapted to any mass spectrometer with an LIFDI probe.

We have coupled atmospheric pressure photoionization (APPI) to a home-built 9.4-T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Analysis of naphtho[2,3-a]pyrene and crude oil mass spectra reveals that protonated molecules, deprotonated molecules, and radical molecular ions are formed simultaneously in the ion source, thereby complicating the spectra (>12 000 peaks per mass spectrum and up to 63 peaks of the same nominal mass), and eliminating the "nitrogen rule" for nominal mass determination of number of nitrogens. Nevertheless, the ultrahigh mass resolving power and mass accuracy of FT-ICR MS enable definitive elemental composition assignments, even for doublets as closely spaced as 1.1 mDa (SH3(13)C vs (12)C4). APPI efficiently ionizes nonpolar compounds that are unobservable by electrospray and allows nonpolar sulfur speciation of petrochemical mixtures.

In typical Fourier transform ion cyclotron resonance (FT-ICR) mass spectra, temporally dispersed excitation and the delay between excitation and detection result in continuous variation of signal phase with frequency in the detected time-domain ion signal. The complex frequency-domain spectrum of such a signal is a linear combination of absorption- and dispersion-mode spectral components with corresponding asymmetric peaks. For this reason, magnitude-mode spectral display is usually employed to yield a phase-independent uniform and symmetrical peak shape at the expense of spectral resolution. In this work, we implement simultaneous excitation and detection to enable Fourier deconvolution to recover absorption-mode spectra for both low- and high-field FT-ICR instruments. These spectra yield resolving power improvement factors approaching the maximum theoretical limit of 2.0, as well as reduction in frequency assignment errors relative to conventional magnitude-mode spectra. The Fourier deconvolution procedure has the additional benefit of correcting for spectral variation resulting from nonuniform power distribution over the excitation bandwidth and the potential benefit of providing useful diagnostic information for interpretation of experimental performance.

We have implemented efficient and rapid collisionally activated dissociation (CAD) external to an ICR cell by use of a novel axial electric potential gradient mounted in an external ion accumulation octopole. The gradient is produced by eight tilted (in the axial direction) wires mounted between the rods of the octopole. Rapid switching of the wire potential between a positive and negative value drives the ion axial motion back and forth and, in the presence of nitrogen gas at suitable pressure, induces dissociation. A fragmentation period on the order of tens of milliseconds is typical. Precursor ion isolation is achieved in a quadrupole mass filter mounted between the electrospray source and the accumulation octopole. A scan rate of1 Hz is possible with resolving power and mass accuracy equivalent to direct infusion experiments (for equivalent detection period for 1 scan). The method is thus sufficiently rapid for MS/MS with on-line LC sample introduction. Moreover, compared to CAD in the ICR cell, external CAD improves mass accuracy, producing thermal on-axis fragment ions for detection.

We have mounted a permanent on-axis dispenser cathode electron source inside the magnet bore of a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer. This configuration allows electron capture dissociation (ECD) to be performed reliably on a millisecond time scale. We have also implemented an off-axis laser geometry that enables simultaneous access to ECD and infrared multiphoton dissociation (IRMPD). Optimum performance of both fragmentation techniques is maintained. The analytical utility of performing either ECD or IRMPD on a given precursor ion population is demonstrated by structural characterization of several posttranslationally modified peptides: IRMPD of phosphorylated peptides results in few backbone (b- and y-type) cleavages, and product ion spectra are dominated by neutral loss of H3PO4. In contrast, ECD provides significantly more backbone (c- and z*-type) cleavages without loss of H3PO4. For N-glycosylated tryptic peptides, IRMPD causes extensive cleavage of the glycosidic bonds, providing structural information about the glycans. ECD cleaves all backbone bonds (except the N-terminal side of proline) in a 3-kDa glycopeptide with no saccharide loss. However, only a charge-reduced radical species and some side chain losses are observed following ECD of a 5-kDa glycopeptide from the same protein. An MS3 experiment involving IR laser irradiation of the charge-reduced species formed by electron capture results in extensive dissociation into c- and z-type fragment ions. Mass-selective external ion accumulation is essential for the structural characterization of these low-abundance (modified) peptides.

Commercial explosives are complex mixtures that contain not only the active explosive agent(s) but also a host of other organic and inorganic compounds. The ultrahigh mass resolving power (m/delta m50%200,000) and mass accuracy (1 ppm) of electrospray ionization Fourier transform ion cyclotron resonance (ESI FTICR) mass spectrometry allow for definitive identification of various species in TNT, RDX, and HMX. We are thereby able to correct prior misassignments of the elemental compositions of the most abundant negative ions from electrospray of RDX and HMX. Although the (known) active agents of many explosives may be identified by low-resolution MS or MS/MS, it is the other characteristic components (indigenous or artificial additives) whose presence and elemental composition can potentially identify the source of the product. ESI FTICR mass spectrometry of smokeless powder, TNT, and Powermite resolves and identifies numerous nonactive ingredients, many of which are recovered in a postblast residue. In contrast, the residue recovered from an explosion of military C4 yielded several species derived from RDX but virtually none from other ingredients.

At currently achievable Fourier transform ion cyclotron resonance broadband mass spectrometry resolving power (m/deltam50%350,000 for 200m/z1,000), it would be necessary to spread out a conventional mass spectrum over approximately 200 m in order to provide visual resolution of the most closely resolved peaks. Fortunately, there are natural gaps in a typical mass spectrum, spaced 1 Da apart, because virtually no commonly encountered elemental compositions yield masses at those values. Thus, it is possible to break a broadband mass spectrum into 1-Da segments, rotate each segment by 90 degrees, scale each segment according to its mass defect (i.e., difference between exact and nominal mass), and then compress the spacing between the segments to yield a compact display. For hydrocarbon systems, conversion from IUPAC mass to "Kendrick" mass (i.e., multiplying each mass by 14.00000/14.01565) further simplifies the display by rectilinearizing the peak patterns. The resulting display preserves not only the "coarse" spacings (e.g., approximately 1 Da between odd and even masses, corresponding to either even vs odd number of nitrogens or 12C(c) vs 12C(c-1)13C1 elemental compositions of the same molecule; approximately 2-Da separations, corresponding to a double bond or ring; approximately 14 Da separations, corresponding to one CH2 group) but also the "fine structure" (i.e., different mass defects for different elemental compositions) across each 1-Da segment. The method is illustrated for experimental electrospray ionization FTICR ultrahigh-resolution mass spectra of a petroleum crude oil. Several thousand elemental compositions may be resolved visually in a single one-page two-dimensional display, and various compound families-class (NnOoSs), type (Z in C(c)H2(c+z)NnOoSs), and alkylation series-may be identified visually as well.

Baseline resolution of two peptides, RVMRGMR and RSHRGHR, of neutral monoisotopic mass, approximately 904 Da, has been achieved by microelectrospray ionization Fourier transform ion cyclotron resonance mass spectrometry at a mass resolving power of approximately 3 300 000. The elemental compositions of these molecules differ by N40 vs. S2H8 (0.000 45 Da), which is less than one electron's mass (0.000 55 Da)! This result establishes a new record for the smallest resolved mass difference between any two molecules. This achievement is made possible by a combination of high magnetic field (9.4 T), large-diameter (4-in.) Penning trap, and low ion density. The implications for proteomics based on accurate mass measurements are discussed briefly.

Here we propose a novel method for rapidly identifying proteins in complex mixtures. A list of candidate proteins (including provision for posttranslational modifications) is obtained by database searching, within a specified mass range about the accurately measured mass (e.g., +/- 0.1 Da at 10 kDa) of the intact protein, by capillary liquid chromatography electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (LC ESI FT-ICR MS). On alternate scans, LC ESI infrared multiphoton dissociation (IRMPD) FT-ICR MS yields mostly b and y fragment ions for each protein, from which the correct candidate is identified as the one with the highest "hit" score (i.e., most b and y fragments matching the candidate database protein amino acid sequence masses) and sequence "tag" score (based on a series of fragment sequences differing in mass by 1 or 2 amino acids). The method succeeds in uniquely identifying each of a mixture of five proteins treated as unknowns (melittin, ubiquitin, GroES, myoglobin, carbonic anhydrase II), from more than 1000 possible database candidates within a +/- 500 Da mass window. We are also able to identify posttranslational modifications of two of the proteins (mellitin and GroES). The method is simple, rapid, and definitive and is extendable to a mixture of affinity-selected proteins, to identify proteins with a common biological function.