Gas chromatography-electron ionization and chemical ionization mass spectrometric analysis of urinary phenmetrazine after derivatization with 4-carbethoxyhexafluorobutyryl chloride--a new derivative

Phenmetrazine is a central nervous system stimulant currently used as an anorectic agent. The drug is abused and is reported to cause death from overdose. We describe a new derivatization method for phenmetrazine using 4-carbethoxyhexafluorobutyryl chloride. Quantitation of urinary phenmetrazine can be easily achieved by using N-ethyl amphetamine as an internal standard. The electron ionization mass spectrum of 4-carbethoxyhexafluorobutyryl derivative of phenmetrazine showed a molecular ion at m/z 427 and a base peak at m/z 70. In the methane chemical ionization mass spectrum, the base peak was observed at m/z 428 (protonated molecular ion). In the electron ionization mass spectrum of 4-carbethoxyhexafluorobutyryl derivative of the internal standard, N-ethyl amphetamine we did not observe a molecular ion. However, in the chemical ionization mass spectrum, the protonated molecular ion at m/z 414 was the base peak. The retention time of derivatized phenmetrazine (8.4 min) was substantially longer than the retention time of the underivatized molecule. Moreover, underivatized phenmetrazine showed poor peak shape (substantial tailing) while derivatized phenmetrazine had excellent chromatographic properties. The within-run and between-run precisions of the assay were 2.6% and 3.1% respectively at a urinary phenmetrazine concentration of 10 micrograms/mL. The assay was linear for urinary phenmetrazine concentration of 1 to 100 micrograms/mL with a detection limit of 0.2 microgram/mL.     

Rapid peptide mapping by reversed-phase liquid chromatography on nonporous silica with on-line electrospray time-of-flight mass spectrometry

Reversed-phase liquid chromatography (LC) using a nonporous silica support has been combined with electrospray (ES) time-of-flight (TOF) mass spectrometry (MS) for the fast separation and mass detection of peptides. Using this LC method, the resolution of a peptide mixture can be completed is less than 35 s. The resulting chromatographic peak widths are less than 1 s wide. Because of the unique nature of a TOF mass analyzer, complete mass spectra can be acquired at a rate which is sufficient to sample these narrow peaks. When compared with conventional LC, the same separation takes nearly 20 min to complete, and the signal-to-noise ratio observed in the total ion chromatogram is dramatically lower due to the influence of increased background noise in the mass spectra. The limit of detection for a low molecular weight peptide, Val-Pro-Leu, was found to be 6 pmol with the total ion chromatogram and 500 fmol with the reconstructed ion chromatogram. A peptide map of horse heart myoglobin, completed in 3.5 min, is shown as an example of the results which can be obtained from combining this fast LC method with fast ES/TOF/MS detection capability.     

Characteristics of mass fragmentation of steroids by atmospheric pressure chemical ionization-mass spectrometry

The characteristics of the mass spectra of sixty steroids were investigated using atmospheric pressure chemical ionization-mass spectrometry (APCI-MS). In APCI-MS, the drift voltage and nebulizer temperature affected the appearance of molecular ions. Solvent adducted ions [M+H+CH3CN]+ and [M+H+H2O]+ were decreased with an increase in drift voltage. The optimum drift voltage differed slightly for each steroid. These sixty steroids were divided into two groups according to their mass spectra profiles: one having a carbonyl group at position 3 together with a double bond at position 4 (group A) and the other bearing a hydroxyl group at the 3 position (group B). In group A, the predominant peak observed corresponded to the protonated molecular ion [M+H]+. The fragment ion corresponding to the elimination of CH2OH, COCH3 and/or COCH2OH from the steroid skeleton appeared as a base peak in some steroids of group A. In group B, predominantly [M+H-H2O]+ and/or [M+H-2H2O]+ ion(s), originating from the loss of water molecules, were observed. Other major ions in this group were the protonated molecular ions. Like other chemical ionization mass spectrometry, the mass spectrum of each steroid was very simple. These results suggest that APCI-MS is a suitable tool for the determination of the mass number of polar, nonvolatile and thermolabile steroids without derivatization.     

Electrospray mass spectrometry studies of non-heme iron-containing proteins

The oligomeric state and the metal atom stoichiometry of a series of non-heme iron-containing, multimeric proteins have been measured using electrospray ionization (ESI) in a time-of-flight (TOF) mass spectrometer. The proteins were obtained both from natural sources and by overexpression of recombinant DNA in Escherichia coli. ESI-TOF mass spectra of the metalloproteins present in nondenaturing solutions exhibit peaks corresponding to the multimeric forms of the holoproteins containing the expected number of metal atoms. Capillary-skimmer dissociation of the holoproteins produces a series of ions, which allows an exact count of the number of metal atoms present in each subunit, and also provides an indication of the oxidation state of the metal atoms. Two recombinant proteins, Phascolopsis gouldii hemerythrin (Pg-Hr) and Desulfovibrio vulgaris rubrerythrin (Dv-Rr), have been examined as well as hemerythrin isolated from Lingula reevii (Lr-Hr). ESI-TOF measurements of the aqueous solution of Pg-Hr at pH 6 yields ions of mass 108,783 Da, in close agreement with the calculated average molecular mass of an intact octameric holoprotein. Capillary-skimmer dissociation of the ions of the holoprotein produces a mass spectrum that contains peaks corresponding to a low m/z monomer and a high m/z heptamer. The masses of the monomer ions produced in this manner are assigned to the aposubunit, [subunit + Fe - 3H]+, and [subunit + 2Fe - 6 H]+. Naturally occurring Lr-Hr is composed of two subunits with average molecular masses measured under denaturing conditions by ESI-TOF to be 13,877.0 Da for the alpha-subunit and 13,517.5 Da for the beta-subunit. Under nondenaturing conditions, a multimeric species with a molecular weight of 110,663 Da is measured by ESI-TOF, corresponding to an alpha 4 beta 4 octamer. Capillary-skimmer dissociation of the alpha 4 beta 4 oligomer produces ions corresponding to both types of monomers (alpha and beta) and the corresponding heptamers (alpha 3 beta 4 and alpha 4 beta 3). In ESI-TOF measurements of recombinant rubrerythrin Dv-Rr using nondenaturing conditions, the principal ion observed corresponds to a homotetramer with an average molecular mass of 86,844 Da. Capillary-skimmer dissociation of the rubrerythrin tetramer leads to formation of a series of peaks corresponding to the subunit of the apoprotein and to subunits containing from one to three specifically bound iron atoms.     

Identification of pollutants in a municipal well using high resolution mass spectrometry

An elevated incidence of childhood cancer was observed near a contaminated site. Trace amounts of several isomeric compounds were detected by gas chromatography/mass spectrometry (GC/MS) in a concentrated extract of municipal well water. No matching library mass spectra were found and Fourier transform IR and NMR analyses were not feasible due to the low concentration of the compounds. Mass peak profiling from selected-ion-recording data (MPPSIRD) provided the sensitivity and scan speed necessary to acquire mass peak profiles at mass resolutions of 10,000 to 20,000 for the molecular ion (M+) and 10 fragment ions as capillary GC peaks eluted. Using a profile generation model (PGM), the elemental composition of the molecular ion was determined from the exact masses and abundances of the M, M + 1 and M + 2 profiles. Fragment ion compositions were determined from their exact masses based on the elements in the molecular ion. Exact mass differences between the molecular and fragment ions corresponded to unique combinations of atoms for the neutral losses. Consequent reduction of the number of possible structures for the fragment ions simplified mass spectral interpretation. After inspecting library mass spectra for smaller molecules, isomeric structures were hypothesized with cyano and alkylcyano groups attached to tetralin. A literature search found such isomers produced by an industrial polymer synthesis. Three isomers in a standard form polymerization of styrene and acrylonitrile provided the same mass spectra and GC retention times as isomers in the extract.     

Analysis of isomeric mixtures using blackbody infrared radiative dissociation: determining isomeric purity and obtaining individual tandem mass spectra simultaneously

A new method that makes possible, for the first time, simultaneous acquisition of individual dissociation mass spectra of isomeric ions in mixtures is presented. This method exploits the exquisite sensitivity of blackbody infrared radiative dissociation kinetics to minor differences in ion structure. Instead of separating precursor ions based on mass (isomers have identical mass), fragment ions are related to their original precursor ions on the basis of rate constants for dissociation. Mixtures of the peptide isomers des-R1 and des-R9 bradykinin are dissociated simultaneously at several temperatures. By fitting the kinetic data to double-exponential functions, the dissociation rate constant and abundance of each isomer in the mixture are obtained. To overcome the difficulty of fitting double-exponential functions, a novel global analysis method is used in which several dissociation data sets collected at different temperatures are simultaneously fit. The kinetic data measured at multiple temperatures are modeled with the preexponentials (corresponding to the abundance of each isomer) as "global" parameters which are constant for all data sets and the exponentials (rate constants) as "local" variables which differ for each data set. The use of global parameters significantly improves the accuracy with which abundances and dissociation rate constants of each individual compound can be obtained from the mixture data. Fragment ions produced from a mixture of these two isomers are related back to their respective precursor ions from the kinetic data. Thus, not only can the composition of the isomeric mixture be determined but an individual tandem mass spectrum of each component in the mixture can be obtained.     

Counting individual sulfur atoms in a protein by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry: experimental resolution of isotopic fine structure in proteins

A typical molecular ion mass spectrum consists of a sum of signals from species of various possible isotopic compositions. Only the monoisotopic peak (e.g., all carbons are 12C; all nitrogens are 14N, etc.) has a unique elemental composition. Every other isotope peak at approximately integer multiples of approximately 1 Da higher in nominal mass represents a sum of contributions from isotope combinations differing by a few mDa (e.g., two 13C vs. two 15N vs. one 13C and one 15N vs. 34S, vs. 18O, etc., at approximately 2 Da higher in mass than the monoisotopic mass). At sufficiently high mass resolving power, each of these nominal-mass peaks resolves into its isotopic fine structure. Here, we report resolution of the isotopic fine structure of proteins up to 15.8 kDa (isotopic 13C,15N doubly depleted tumor suppressor protein, p16), made possible by electrospray ionization followed by ultrahigh-resolution Fourier transform ion cyclotron resonance mass analysis at 9.4 tesla. Further, a resolving power of m/Deltam50% approximately 8,000,000 has been achieved on bovine ubiquitin (8.6 kDa). These results represent a 10-fold increase in the highest mass at which isotopic fine structure previously had been observed. Finally, because isotopic fine structure reveals elemental composition directly, it can be used to confirm or determine molecular formula. For p16, for example, we were able to determine (5.1 +/- 0.3) the correct number (five) of sulfur atoms solely from the abundance ratio of the resolved 34S peak to the monoisotopic peak.     

Characterization of bacterial phospholipids by electrospray ionization tandem mass spectrometry

A negative ion electrospray ionization tandem mass spectrometric technique was developed for the analysis of glycerophospholipids. Examination of the product ion mass spectrum of the deprotonated molecular ion provided sufficient information to identify both the class of glycerophospholipid and the molecular weights of the two fatty acid moieties. This technique was applied to the profiling of glycerophospholipids present in the chloroform/methanol extracts of four different bacterial species. The principal bacterial phospholipids detected by this technique were phosphatidylglycerols and diphosphatidylglycerols, accompanied by small amounts of phosphatidylethanolamines for two of the bacterial species examined. The fatty acid composition of the phosphatidylglycerols for each bacteria was determined by tandem mass spectrometry and presented graphically. Differences in the fatty acid composition for each bacterial species were readily apparent from a visual examination of the data sets.     

Using matrix-assisted laser desorption ionization mass spectrometry to map the quinol binding site of cytochrome bo3 from Escherichia coli

The cytochrome bo3 ubiquinol oxidase contains at least one and possibly two binding sites for ubiquinol/ubiquinone. Previous studies used the photoreactive affinity label 3-[3H]azido-2-methyl-5-methoxy-6-geranyl-1,4-benzoquinone (azido-Q), a substrate analogue, to demonstrate that subunit II contributes to at least one of the quinol binding sites. In the current work, mass spectroscopy is used to identify a peptide within subunit II that is photolabeled by the azido-Q. Purified cytochrome bo3 was photolabeled as previously described using azido-Q that was not tritiated (i.e., not radiolabeled). Subunit II was then isolated from an SDS-PAGE gel and proteolyzed in situ with trypsin. The resulting peptides were eluted from the gel and then identified using matrix-assisted laser desorption ionization mass spectrometry. The resulting mass spectrum was compared to that obtained by analysis of subunit II that had not been exposed to the photolabel. Using the amino acid sequence, each peak in the mass spectrum of the unlabeled subunit II could be assigned to an expected trypsin fragment. Two additional peaks were observed in the mass spectrum of the photolabeled subunit with m/z 1931.9 and 2287.7. Subtraction of the mass of azido-Q from the peak at m/z 1931.9 results in a mass equivalent to that of a peptide consisting of amino acids 165-178. The assignment of the peak at m/z 2287.7 cannot be made unequivocally and may correspond either to the covalent attachment of azido-Q to peptide 254-270 or to a peptide resulting from incomplete proteolysis. The labeled peptide, 165-178, is within the water-soluble domain of subunit II, whose X-ray structure is known. This peptide is located near the site where CuA is located in the homologous cytochrome c oxidases and can be placed near the interface between subunits I and II.     

Characterization of Spectral Analysis of Surface Waves Shear Wave Velocity Measurement Uncertainty

The spectral analysis of surface waves (SASW) method is a nondestructive test for characterization of the variation with depth of the shear modulus of soils. While the testing procedure is well developed, only one preliminary study has investigated measurement uncertainty associated with SASW, and the methods utilized to quantify measurement uncertainty were prohibitive to routine assessment. Knowledge of this uncertainty, and ability to include its assessment in routine testing, would allow for inclusion of SASW results in reliability-based design and in assessment of the spatial variability of shear modulus. In this study, a large sample of test data was collected from two test sites. Characteristic statistics, statistical distribution, and measurement uncertainty were determined for each phase of SASW. Using the empirical statistical properties and measurement uncertainty results as validation criteria, an analytically based uncertainty assessment system was developed. Phase angle, inverse phase angle, and phase velocity data typically display a coefficient of variation (COV) of 2%, and the COV for combined phase velocity data is typically 1.5%. The COV for shear wave velocity is typically between 5 and 10%, and thus the inversion appears to magnify measurement uncertainty. Phase angle, inverse phase angle, phase velocity, and combined phase velocity data are normally distributed. Shear wave velocity samples at a given depth are generally normally distributed. Using a small sample of experimental data and the analytically based process developed in this study, the measurement uncertainty of SASW test results can be assessed as part of routine testing.     

Length and base composition of PCR-amplified nucleic acids using mass measurements from electrospray ionization mass spectrometry

A generally applicable algorithm has been developed to allow base composition of polymerase chain reaction (PCR) products to be determined from mass spectrometrically measured molecular weights and the complementary nature of DNA. Mass measurements of arbitrary precision for single-stranded DNA species are compatible with an increasingly large number of possible base compositions as molecular weight increases. For example, the number of base compositions that are consistent with a molecular weight of 35,000 is approximately 6000, based on a mass measurement precision of 0.01%. However, given the low misincorporation rate of standard DNA polymerases, mass measurement of both of the complementary single strands produced in the PCR reduces the number of possibilities to less than 100 at 0.01% mass precision, and base composition is uniquely defined at 0.001% mass precision. Taking into account the low misincorporation rate of standard DNA polymerases and the fact that the final PCR product also contains primers of known sequence (generally 15-20-mer in size, which flank the targeted region), this reduces the number of possible base combinations to only approximately 3 at MW = 35,000. In addition, the number of base pairs (i.e., length of the DNA molecule) is uniquely defined. We show that the use of modified bases in PCR or post-PCR modification chemistry allows unique solutions for the base composition of the PCR product with only modest mass measurement precision.     

A spectrometric method for determining the capability of intermolecular interaction: mono- and dideoxynucleotides

A method for detecting the dimer of mono- and oligodeoxynucleotides is presented by using fast atom bombardment mass spectrometry (FAB-MS). The mass spectrum of a mononucleotide dpC showed an intense peak of the dimeric ion dpC:::dpC, compared with those of dpA, dpG and dpT. The mass spectrum of an equimolar mixture of dpC and dpG showed the highest peak of the dimeric ion dpC:::dpG, compared with all other combinations. The dimeric ion peaks in the mass spectra of dinucleotides d(ApT) and d(CpG) were relatively high and it may reflect the base-pairing energy due to hydrogen bonding. The degradation patterns of each dimers for d(ApT) and d(CpG) obtained by using the collision-induced dissociation (CID) technique which reflected the strength of each base-pairing.     

Colonoscopy: diagnostic and treatment methods

The late troponin T (TnT) peak concentration, which is known to be independent of reperfusion of the infarcted zone in acute myocardial infarction (MI), has been suggested to be correlated with clinical estimates of cardiac function and myocardial infarct size. To refine the clinical application of the late TnT peak in infarct sizing, and to examine differences in this estimation in different infarct sites, we measured the serum concentrations of TnT and myosin light chain 1 (MLC1), and compared these values with left ventricular ejection fraction (LVEF) obtained from left ventriculography, and extent score (ES) and severity score (SS) obtained from 201Tl scintigraphy in patients with anterior and inferior myocardial infarction. The late TnT peak concentration was strongly correlated with the MLC1 peak value in patients with anterior MI (r = 0.67, p < 0.05) and in those with inferior MI (r = 0.92, p < 0.0005). Furthermore, there were strong linear correlations between the late TnT peak values and all of the clinical data (LVEF; r = -0.79, p < 0.01, ES; r = 0.75, p < 0.05, SS; r = 0.75, p < 0.05, respectively) in patients with anterior MI. However, these correlations were weak in patients with inferior MI. Similar correlations were observed between MLC1 and the clinical data. Thus, TnT and MLC1 have similar kinetics in the serum at the late phase and can be used to estimate the size of anterior infarct.     

Analysis of estrone, estradiol and estriol in serum and urine by mass fragmentography using GC-MS (author's transl)

The first successful analysis of estrogens in serum and urine was performed by mass fragmentography using a GC-MS combined system. The equipment used was Shimadzu LKB 9000 GC-MS (MID-PM). The TMSi derivative of the compounds were analyzed using the GC-MS system equipped with a 3 ft x 3mm column packed with 1.5% OV-1 and the temperature was programed from 200 degrees to 260 degrees C at 10 degrees C/min increments. The mass spectrum showed molecular ions at m/e 342, 416 and 504 which correspond to the TMSi derivatives of Estrone (E-1), Estradiol (E-2) and Estriol (E-3) respectively. Molecular ion peak of each compound was applied to establish the precise quantitative evaluation of E-1, E-2 and E-3. 1) The minimum detectable limits of the compounds injected into the column were ca. 2 pg for E-1, E-2 and 5 pg for E-3 respectively. 2) The sensitivity was of the order of ng or pg which enables quantitation with 2 ml of human serum and urine samples obtained from normally ovulating women. 3) This method was very convenient for extracting the compounds from biological fluids, and the procedure can be carried out easily in a short time. 4) Mass fragmentography makes possible the simultaneous measurements of E-1, E-2 and E-3 in samples obtained from pregnant women.     

Framework for Estimating Uncertainty of ADCP Measurements from a Moving Boat by Standardized Uncertainty Analysis

In spite of the extensive use of acoustic-Doppler current profilers (ADCP) for measurement of velocity and discharge in open-channel and riverine environments, a rigorous methodology for estimating ADCP discharge measurement uncertainty that follows current engineering standards for uncertainty analysis is not yet available. In this paper, we apply the broadly accepted engineering standard for uncertainty analysis put forth by the American Institute of Aeronautics and Astronautics in 1995 (AIAA) to develop a framework for the estimation of uncertainty in ADCP measurements from a moving boat. First, we summarize the terminology and methodology of measurement uncertainty analysis and review the data reduction equations used by ADCPs to estimate the total discharge in measurements from a moving boat. Second, we discuss briefly the various elemental error sources that contribute to the uncertainties of the ADCP measured variables, which in turn contribute to the total uncertainty of ADCP discharge measurements. In discussing the elemental errors, we look into what determines their uncertainties and whether they can be evaluated using available information. We then apply the guidelines of the AIAA standard to develop an analytical framework for propagating the uncertainties from the elemental sources to obtain the total uncertainty of ADCP discharge measurements from a moving boat.     

Determinants of peak bone mass in Chinese women aged 21-40 years. III. Physical activity and bone mineral density

Previous studies on the relation between moderate physical activity and bone mass have observed conflicting results. Many of these studies have not dissociated the role of physical activity by age groups and in relation to the period of peak bone mass formation. Our cross-sectional analysis of the baseline data of a longitudinal study of 273 women aged 21-40 attempted to evaluate the role of moderate physical activity on bone mass around the period of peak bone mass attainment. The analyses were carried out separately for the two age groups--21-30 and 31-40--and had also taken into account the effects of age, dietary calcium intake, and lean body mass on bone mineral density (BMD). The total metabolic equivalent values (MET) of leisure time physical activity was based on the MET values for each activity and the reported time spent on each activity in the past year. The results indicated that among the younger group of women, high level of leisure time physical activity was associated with higher bone mass at both the spine and the hip. Additive effects of physical activity and dietary calcium intake on the spine and the hip BMD were observed. Together with age and lean body mass, physical activity and dietary calcium intake accounted for 19% of the variances of bone mineral at the spine and 9-11% at the hip. Among women aged 31-40, presumably after the peak bone mass formation, lean body mass as well as fat mass have independent strong association with BMD. Physical activity was not associated with bone mass in this age group.     

Phase correction for collision model analysis and enhanced resolving power of fourier transform ion cyclotron resonance mass spectra

Phase correction of FT-ICR data yields an absorption spectrum that offers a gain by up to a factor of 2 in mass resolving power (at half-maximum peak height), compared to conventional magnitude-mode display. That improvement is equivalent to doubling the applied magnetic field strength, without loss in signal-to-noise (S/N) ratio, provided that the time-domain data are padded with an equal number of zeroes before FFT. Our simple, visual, user-interactive algorithm quickly corrects for zero-order and first-order variation of phase with frequency. We find that the theoretical mass resolving power enhancement for pressure-limited absorption-mode over magnitude-mode line shape depends on the collision mechanism: factor of 1.40 for hard sphere vs 3(1/2) for Langevin (ion: induced dipole). Thus, the experimental enhancement in mass resolving power (factor of 1.43 +/- 0.09) for isotopically resolved peaks in the FT-ICR mass spectra of electrosprayed bovine carbonic anhydrase (approximately 29 kDa) directly supports the hard-sphere collision model. Optimal implementation of phasing requires the following: (a) a delay between excitation and detection of less than half of one sampling interval to avoid baseline "roll" and Gibb's oscillations; (b) accurate analog-to-digital conversion; (c) a sufficiently long acquisition period to yield several data points per absorption-mode peak width at half-maximum peak height; and (d) avoidance of FT-ICR apodization functions (e.g., Hamming and Hanning) that suppress the initial time-domain data. Pulsed single-frequency excitation (duration much less than the reciprocal of the Nyquist bandwidth) can eliminate higher than first-order variation of phase with frequency. Phased FT-ICR spectra should prove especially desirable for analysis of complex mixtures, for resolving isotopic distributions in electrosprayed multiply charged macromolecules and for characterizing ion collisions (and thus ion size and shape).     

Determination of aluminium-26 in biological materials by accelerator mass spectrometry

Studies of the biological chemistry of aluminium can gain significantly from the use of the long-lived isotope 26Al as a tracer, although the cost of the isotope often precludes its determination by radiochemical counting techniques. Accelerator mass spectrometry (AMS) provides an ultra-sensitive method of determination, free from isobaric interference from atomic (26Mg) or molecular species. The source materials for AMS can be aluminium oxide or phosphate, both of which can be readily prepared at a sufficient level of purity from biological substrates. Natural aluminium (27Al, 100%) is added to the preparations as a chemical yield monitor and to provide the reference for the isotope ratio measurement. 26Al/27Al ratios can be determined over the range 10(-14)-10(-7), implying a limit of detection for 26Al of around 10(-18) g. The precision of measurement and long-term reproducibility are < 5% and < 7% (RSD), respectively. Chemical methodologies for routine measurements on blood and urine samples have been developed.     

Automated interpretation of high-energy collision-induced dissociation spectra of singly protonated peptides by 'SeqMS', a software aid for de novo sequencing by tandem mass spectrometry

SeqMS, a software program designed for the automated interpretation of high-energy collision-induced dissociation (CID) mass spectra of singly protonated peptides ionized by fast atom bombardment, has been developed. The software is capable of probing the sequence of an unknown peptide, and even of certain modified peptides. The program, compiled for WINDOWS95 or NT, also permits the retrieval of raw data and the reconstruction of the spectra on a user-friendly graphical interface with the aid of several tools for processing the spectra, which include setting multiple threshold levels and automatic peak detection. SeqMS is capable of generating candidate sequences, based on the detected peaks, and of displaying the resulting assignments for each candidate in a spectrum or in tabular form. The software has the following capabilities: 1) the ions derived from backbone and side-chain fragmentations, internal and immonium ions, and side-chain loss ions can be used for calculation; 2) 18O-labeling of a peptide at the C terminus, a methodology which was developed to differentiate N-terminal from C-terminal ions, is applicable as an optional setting; 3) modified amino acids and N- or C-terminal blocking groups are taken into account for calculation according to the user's setting in a library; 4) amino acid composition and partial or complete amino acid sequence of a peptide can be used as input for calculation; 5) the assignments of signal output in a spectrum can be graphically edited, and then re-calculated based on the edited peaks. The efficacy of the program is demonstrated by testing 74 high-energy CID spectra, obtained using a four-sector instrument, of synthetic, proteolytic, and biologically active peptides, some of which contain modified groups.