Gas phase hydrogen/deuterium exchange reactions of peptide ions in a quadrupole ion trap mass spectrometer

Hydrogen/deuterium exchange reactions of protonated and sodium cationized peptide molecules have been studied in the gas phase with a MALDI/quadrupole ion trap mass spectrometer. Unit-mass selected precursor ions were allowed to react with deuterated ammonia introduced into the trap cell by a pulsed valve. The reactant gas pressure, reaction time, and degree of the internal excitation of reactant ions were varied to explore the kinetics of the gas phase isotope exchange. Protonated peptide molecules exhibited a high degree of reactivity, some showing complete exchange of all labile hydrogen atoms. On the contrary, peptide molecules cationized with sodium exhibited only very limited reactivity, indicating a vast difference between the gas phase structures of the two ions.

Structure of the monophosphoryl lipid A moiety obtained from the lipopolysaccharide of Chlamydia trachomatis

Monophosphoryl lipid A was prepared from the lipopolysaccharide of Chlamydia trachomatis, converted to the methyl ester, and fractionated by reverse-phase high-performance liquid chromatography. The peak fractions were collected and analyzed by mass spectrometry. Matrix-assisted laser desorption/ionization and liquid secondary ion mass spectrometry of the first of two major high-performance liquid chromatographic fractions showed multiple quasi-molecular ions of MNa+ at m/z 1780, 1794, 1808, 1822, and 1836. The positive-ion liquid secondary ion mass spectrometry spectrum also showed a minor series of peaks at m/z 1916, 1930, 1944, 1958, and 1971, consistent with the formation of matrix adducts with 3-nitrobenzyl alcohol. Oxonium ions representing the distal subunit were observed at m/z 1057, 1071, 1085, 1099, and 1113. The second fraction was similarly analyzed and found to contain structural homologs of the first fraction. Based on this study, the major lipid A component of chlamydial lipopolysaccharide is a glucosamine disaccharide that contains five fatty acids and a phosphate in the distal segment. Three fatty acyl groups are in the distal segment, and two are in the reducing end segment. The acyloxyacyl group is located in the distal segment in amide linkage. Two structural series, differing by 14 atomic mass units in the reducing subunit, were observed. Chlamydial lipid A is complex and consists of at least 20 homologous structural components. The relatively low potency of Chlamydia trachomatis lipopolysaccharide in activating lipopolysaccharide-responsive cells might be related to the unusual fatty acid composition of the lipid A moiety.

Dominance of a single peptide bound to the class I(B) molecule, Qa-1b

One of the hallmarks of class I(A) molecules is their ability to bind and present a wide array of peptides to CD8 T cells. This diversity is consistent with their ability to restrict a variety of pathogenic peptide epitopes as well as elicit strong transplantation responses. In contrast, class I(B) molecules appear to be involved in presentation of pathogenic epitopes to a relatively lesser extent as well as play a minor role in transplantation responses. Here we have examined the peptides bound and presented by the class I(B) molecule Qa-1b in order to determine if their diversity was similar to that reported for class I(A) Ags. First, we show that bulk-cultured anti-Qa-1b CTL predominantly recognize a single peptide (Qdm) derived from the leader segment of class I(A) alloantigens. These CTL are peptide specific and reflect the activity of previously described CTL clones. Second, we find approximately 4.6 x 10(4) copies of the Qdm peptide/cell. Most of the peptide is Qa-1b associated since the recovery of this peptide from anti-Qa-1b immunoprecipitates is approximately 75% of that seen in whole cell extracts and no detectable activity is observed in Kb or Db extracts from H-2b lymphoblasts. Third, the expression of Qa-1b on lymphoblasts is approximately 1 to 1.25 x 10(4) molecules/cell indicating that the Qdm peptide must be derived from both cell membrane and intracellular compartments. Finally, examination of the diversity of peptides associated with Qa-1b as determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry indicates few detectable peptide species associated with this molecule. Taken together, Qa-1b appears to predominantly bind a single peptide species that is recognized by alloreactive CD8 T cells. This feature may account, in part, for the class I(B) properties of this molecule.

Dominance of a single peptide bound to the class I(B) molecule, Qa-1b

One of the hallmarks of class I(A) molecules is their ability to bind and present a wide array of peptides to CD8 T cells. This diversity is consistent with their ability to restrict a variety of pathogenic peptide epitopes as well as elicit strong transplantation responses. In contrast, class I(B) molecules appear to be involved in presentation of pathogenic epitopes to a relatively lesser extent as well as play a minor role in transplantation responses. Here we have examined the peptides bound and presented by the class I(B) molecule Qa-1b in order to determine if their diversity was similar to that reported for class I(A) Ags. First, we show that bulk-cultured anti-Qa-1b CTL predominantly recognize a single peptide (Qdm) derived from the leader segment of class I(A) alloantigens. These CTL are peptide specific and reflect the activity of previously described CTL clones. Second, we find approximately 4.6 x 10(4) copies of the Qdm peptide/cell. Most of the peptide is Qa-1b associated since the recovery of this peptide from anti-Qa-1b immunoprecipitates is approximately 75% of that seen in whole cell extracts and no detectable activity is observed in Kb or Db extracts from H-2b lymphoblasts. Third, the expression of Qa-1b on lymphoblasts is approximately 1 to 1.25 x 10(4) molecules/cell indicating that the Qdm peptide must be derived from both cell membrane and intracellular compartments. Finally, examination of the diversity of peptides associated with Qa-1b as determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry indicates few detectable peptide species associated with this molecule. Taken together, Qa-1b appears to predominantly bind a single peptide species that is recognized by alloreactive CD8 T cells. This feature may account, in part, for the class I(B) properties of this molecule.

Hydrogen peroxide-mediated alteration of the heme prosthetic group of metmyoglobin to an iron chlorin product: evidence for a novel oxidative pathway

Treatment of metmyoglobin with H2O2 is known to lead to the crosslinking of an active site tyrosine residue to the heme [Catalano, C. E., Y. S. Choe, and P. R. Ortiz de Montellano (1989) J. Biol. Chem. 264, 10534-10541]. We have found in this study that this reaction also leads to an altered heme product not covalently bound to the protein. This product was characterized by visible absorption, infrared absorption, and mass and NMR spectrometry as an iron chlorin product formed from the saturation of the double bond between carbon atoms at positions 17 and 18 of pyrrole ring D with concomitant addition of a hydroxyl group on the carbon atom at position 18 and lactonization of the propionic acid to the carbon atom at position 17. Studies with the use of (18)O-labeled H2O2, O2, and H2O clearly indicate that the source of the added oxygen on the heme is water. Evidently, water adds regiospecifically to a cationic site formed on a carbon atom at position 18 after oxidation of the ferric heme prosthetic group with peroxide. Prolonged incubation of the reaction mixture containing the iron hydroxychlorin product led to the formation of an iron dihydroxychlorin product, presumably from a slow addition of water to the initial iron hydroxychlorin. The iron chlorin products characterized in this study are distinct from the meso-oxyheme species, which is thought to be formed during peroxide-mediated degradation of metmyoglobin, cytochrome P450, ferric heme, and model ferric hemes, and give further insight into the mechanism of H2O2-induced heme alterations.

A strategy for rapid and efficient DNA sequencing by mass spectrometry

Two methods of solid-phase Sanger DNA sequencing followed by detection with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry are demonstrated. In one method, sequencing ladders generated on an immobilized synthetic template were resolved up to the 63-mer including the primer. Detection sensitivity and resolution were sufficient for sequence analysis in the given range. This approach is particularly suitable for comparative (diagnostic) DNA sequencing. A second method that has the potential for high throughput de novo DNA sequencing is also presented; it uses immobilized duplex probes with five-base single-stranded overhangs to capture an unknown DNA template serving as primers for Sanger DNA sequencing. The power of mass spectrometry is demonstrated not only by its very high speed, but also by its ability to identify sequences that are not readable using gel electrophoresis.

Morphology and toxicity of Abeta-(1-42) dimer derived from neuritic and vascular amyloid deposits of Alzheimer's disease

In the course of analyzing the chemical composition of Alzheimer's disease neuritic and vascular amyloid, we have purified stable dimeric and trimeric components of Abeta peptides. These peptides (molecular mass 9.0 and 13.5 kDa) were separated by size exclusion chromatography in the presence of 80% formic acid or 5 guanidine thiocyanate, pH 7.4. The average ratio of monomers, dimers, and trimers was 55:30:15, respectively. Similar structures were produced over time upon incubation of synthetic Abeta-(1-42) at pH 7.4. The stability of these oligomeric forms was also demonstrated by Western blot and mass spectrometry. Atomic force microscopy and electron microscopy rotary shadowing revealed that the monomers polymerized into 8-10-nm filaments, whereas the dimers generated prolate ellipsoids measuring 3-4 nm in diameter. The pathogenic effects of the dimeric Abeta-(1-40/42) were tested in cultures of rat hippocampal neuron glia cells. Only in the presence of microglia did the dimer elicit neuronal killing. It is possible that these potentially pathogenic Abeta-(1-40/42) dimers and trimers from Alzheimer's disease amyloid represent the soluble oligomers of Abeta recently described in Alzheimer's disease brains (Kuo, Y.-M., Emmerling, M. R., Vigo-Pelfrey, C., Kasunic, T. C., Kirkpatrick, J. B., Murdoch, G. H., Ball, M. J., and Roher, A. E. (1996) J. Biol. Chem., 271, 4077-4081).

Hedgehog patterning activity: role of a lipophilic modification mediated by the carboxy-terminal autoprocessing domain

Autocatalytic processing mediated by the carboxyterminal domain of the hedgehog (hh) protein precursor (Hh) generates an amino-terminal product that accounts for all known signaling activity. The role of autoprocessing biogenesis of the hh signal has been unclear, since a truncated unprocessed protein lacking all carboxy-terminal domain sequences retains signaling activity. Here, we present evidence that the autoprocessing reaction proceeds via an internal thioester intermediate and results in a covalent modification that increases the hydrophobic character of the signaling domain and influences its spatial and subcellular distribution. We demonstrate that truncated unprocessed amino-terminal protein causes embryonic mispatterning, even when expression is localized to cells that normally express Hh, thus suggesting a role for autoprocessing in spatial regulation of hh signaling. This type of processing also appears to operate in the biogenesis of other novel secreted proteins.

Matrix-assisted laser desorption/ionization tandem reflectron time-of-flight mass spectrometry of fullerenes

Atandem reflectron time-of-flight mass spectrometer developed in our laboratory provides a unique opportunity to investigate the collision-induced dissociation of fullerene ions formed by matrix-assisted laser desorption/ionization (MALDI). Specifically, this opportunity arises from the ability to utilize high energy collisional activation (normally available only on tandem sector instruments by using continuous ionization techniques) for ions formed by pulsed laser desorption, whereas most MALDI time-of-flight instruments record product ion mass spectra of ions formed by metastable or postsource decay. In this study we investigate the products of mass-selected and collisionally activated C 60 (+) and C 70 (+) ions by using different target gases over a range of target gas pressures. In general, heavier target gases produce more extensive fragmentation and improve the mass resolution of lower mass ionic products because a greater portion of these ions are formed by single collisions. Additionally, the tandem time-of-flight instrument utilizes a nonlinear (curved-field) reflectron in the second mass analyzer that enables high energy collision-induced dissociation spectra to be recorded without scanning or stepping the reflectron voltage.

Dynamic O-GlcNAcylation of the small heat shock protein alpha B-crystallin

alphaB-Crystallin, originally described as a structural lens protein, is now known to be a member of the small heat shock protein family and is expressed in a number of nonlens tissues. This highly conserved 20 kDa protein aggregates with homologous proteins, including alphaA-crystallin and the small heat shock protein HSP28, to form large heteromeric complexes. Recently, Roquemore et al. (1992) have established that both phosphorylated and unphosphorylated forms of lens alphaB-crystallin are modified with O-linked N-acetylglucosamine, a dynamic posttranslational modification abundant on nuclear and cytoplasmic proteins. In this paper, we have identified the major site of O-GlcNAcylation on lens alphaB as Thr 170. We have further shown that this modification is not restricted to lens alphaB-crystallin but occurs on alphaB isolated from rat heart tissue and human astroglioma cells. Two-dimensional electrophoresis of rat heart alphaB-crystallin revealed two O-GlcNAcylated forms with mobilities corresponding to the unphosphorylated form (alphaB2) and an unidentified, slightly more acidic form. Phosphorylated alphaB-crystallin (alphaB1) was not detected in the rat heart preparation. The major O-GlcNAcylation site on alphaB-crystallins from rat heart also appears to be at Thr 170. Metabolic pulse-chase labeling studies of U373-MG astroglioma cells indicated that turnover of the carbohydrate on alphaB-crystallin is not static but proceeds many-fold more rapidly than turnover of the protein backbone itself, consistent with a regulatory role for O-GlcNAc on this small heat shock protein.

Pulsed gas introduction for increasing peptide CID efficiency n a MALDI/quadrupole ion trap mass spectrometer

A pulsed valve was used for studying the effects of introducing heavy gases at different stages of operation of a quadrupole ion trap and for increasing the efficiency of collision-induced dissociation (CID) of peptide ions at low values of the Mathieu parametere qz. When amounts of heavy gases comparable to that of the helium buffer gas were introduced during the ion trapping, ion isolation, and mass spectral recording stages, the effects on performance were generally small or negative. However, injection of heavy gases during CID provided considerable improvement in fragmentation efficiency that depended upon the particular gas used, its mass and pressure, and the amplitude of the excitation voltage. Efficient peptide fragmentation could be demonstrated for values of qz as low as 0.05, which permitted trapping of low-mass product ions and (in many cases) full recovery of the amino acid sequence. In this report, examples are provided of monoisotopic tandem mass spectra of peptide ions with masses up to 1570 Da.

Class I-restricted presentation of an HIV-1 gp41 epitope containing an N-linked glycosylation site. Implications for the mechanism of processing of viral envelope proteins

Uncertainty exists over the site of processing of viral envelope (env) proteins for recognition by CTL. The extracellular domains of env proteins are not present in the cytosol, the site where the class I Ag processing pathway begins. Rather, the ecto-domains of env proteins are cotranslationally translocated into the endoplasmic reticulum during biosynthesis. To clarify the site of processing of viral env proteins, we examined the processing of an HLA B*3501-restricted epitope in the extracellular domain of the HIV-1 env protein. Although this epitope contains an N-linked glycosylation signal sequence, CTL specific for this epitope recognize a nonameric peptide that has not been previously modified by attachment of oligosaccharide. This was demonstrated in two ways. First, an env-specific B*3501-restricted CTL clone recognized a nonglycosylated, synthetic nonamer representing the minimal B*3501-restricted epitope, but not the glycosylated or deglycosylated forms. Second, the naturally processed, B*3501-restricted, env peptide is identical with a nonglycosylated, synthetic nonamer. Thus, the naturally processed form of an env epitope containing an N-linked glycosylation site is derived from env protein that is not glycosylated at the relevant asparagine during biosynthesis. Since the addition of N-linked oligosaccharides occurs only after the glycosylation signal sequence (N-X-S/T) is translocated into the endoplasmic reticulum, the initial processing reaction for this epitope may take place in the cytosol. Low-frequency failure of signal sequence containing polypeptides to engage the translocation apparatus, resulting in synthesis and degradation in the cytosol, may represent an important mechanism for the generation of class I-restricted CTL responses.

Class I-restricted presentation of an HIV-1 gp41 epitope containing an N-linked glycosylation site. Implications for the mechanism of processing of viral envelope proteins

Uncertainty exists over the site of processing of viral envelope (env) proteins for recognition by CTL. The extracellular domains of env proteins are not present in the cytosol, the site where the class I Ag processing pathway begins. Rather, the ecto-domains of env proteins are cotranslationally translocated into the endoplasmic reticulum during biosynthesis. To clarify the site of processing of viral env proteins, we examined the processing of an HLA B*3501-restricted epitope in the extracellular domain of the HIV-1 env protein. Although this epitope contains an N-linked glycosylation signal sequence, CTL specific for this epitope recognize a nonameric peptide that has not been previously modified by attachment of oligosaccharide. This was demonstrated in two ways. First, an env-specific B*3501-restricted CTL clone recognized a nonglycosylated, synthetic nonamer representing the minimal B*3501-restricted epitope, but not the glycosylated or deglycosylated forms. Second, the naturally processed, B*3501-restricted, env peptide is identical with a nonglycosylated, synthetic nonamer. Thus, the naturally processed form of an env epitope containing an N-linked glycosylation site is derived from env protein that is not glycosylated at the relevant asparagine during biosynthesis. Since the addition of N-linked oligosaccharides occurs only after the glycosylation signal sequence (N-X-S/T) is translocated into the endoplasmic reticulum, the initial processing reaction for this epitope may take place in the cytosol. Low-frequency failure of signal sequence containing polypeptides to engage the translocation apparatus, resulting in synthesis and degradation in the cytosol, may represent an important mechanism for the generation of class I-restricted CTL responses.

Advanced stored waveform inverse Fourier transform technique for a matrix-assisted laser desorption/ionization quadrupole ion trap mass spectrometer

The stored waveform inverse Fourier transform (SWIFT) technique is used for broadband excitation of ions in an ion-trap mass spectrometer to perform mass-selective accumulation, isolation, and fragmentation of peptide ions formed by matrix-assisted laser desorption/ionization. Unit mass resolution is achieved for isolation of ions in the range of m/z up to 1300 using a two-step isolation technique with stretched-in-time narrow band SWIFT pulses at the second stage. The effect of 'stretched-in-time' waveforms is similar to that observed previously for mass-scan-rate reduction. The asymmetry phenomenon resulting from the stretched ion-trap electrode geometry is observed during application of normal and time-reversed waveforms and is similar to the asymmetry effects observed for forward and reverse mass scans in the resonance ejection mode. Mass-selective accumulation of ions from multiple laser shots was accomplished using a method described earlier that involves increasing the trapping voltage during ion introduction for more efficient trapping of ions.

Effect of phase locking AC and RF voltages for high mass analysis in a quadrupole ion trap mass spectrometer

Experiments on the influence of locking the AC and RF frequency phases on the mass resolution and line position in the mass spectra from a quadrupole ion trap mass spectrometer were carried out at low ejection values of beta z to investigate the possibility of using this effect for high mass analysis. At a typical mass scan rate of 1000 u/s the improvement for the mass resolution in these experiments did not exceed 10-20% at beta z = 0.25 compared with 200-250% at beta z = 0.5. However, without phase locking, the mass resolution at beta z = 0.25 was about two times higher than that at beta z = 0.5. Thus, the absolute values for the mass resolution observed without phase-locked AC and RF frequencies at beta z = 0.25 were about the same as at beta z = 0.5 with phase locking. This observation was explained by a significant negative contribution to the mass resolution of the ion microoscillations along the trajectory at the fundamental RF frequency which is different for the cases of beta z = 0.25 and beta z = 0.5.

Matrix-assisted laser desorption/ionization mass spectrometry of immobilized duplex DNA probes

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry was used to analyze short DNA duplex probes with one strand immobilized on solid supports (straptavidin-coated magnetic beads or controlled pore glass beads). Only the non-immobilized strand could be detected. Partial denaturation was found when the duplex probes were mixed with 3-hydroxypicolinic acid, ammonium citrate matrix. The strategy has several applications, such as fast DNA sequence analysis and DNA diagnostics.

High-performance collision-induced dissociation of peptide ions formed by matrix-assisted laser desorption/ionization in a quadrupole ion trap mass spectrometer

A modified ion trap detector has been utilized to obtain high-performance collision-induced dissociation (CID) mass spectra of peptide ions formed by matrix-assisted laser desorption/ionization (MALDI). MALDI ions are trapped while increasing the fundamental radio frequency field, obviating the need for elevated helium gas pressures. Molecular ion isotopic clusters are then isolated by a reverse-forward-reverse scan sequence. A single species within the isotopic cluster (generally the monoisotopic mass) is then selected for activation. Finally, modulation of the amplitude of the resonant excitation voltage on the end-cap electrodes, used previously to improve mass calibration in normal mass spectra, is now utilized to provide high mass accuracy for the product ions. The CID mass spectra of several protonated and sodium-cationized peptides are presented and are often characterized by a series of rearrangement ions that can be utilized in the determination of amino acid sequences.

Molecular pharmacology of hepsulfam, NSC 3296801: identification of alkylated nucleosides, alkylation site, and site of DNA cross-linking

We have determined that hepsulfam, in common with its structural homologue busulfan, alkylates both free guanosine and GMP in DNA at the 7 nitrogen. Mass spectral analysis of the products of the reaction of hepsulfam with guanosine has identified the mono- and bis-alkylated guanosine adducts. UV spectrophotometry and mass spectrometry were used to confirm that alkylation occurred at the 7 nitrogen by following the formation of the formamidopyrimidyl form of the hepsulfam-guanosine adduct at high pH. We have also isolated and identified 1-guanyl,7-hydroxyheptane, 1-guanyl,7-sulfamylheptane, and 1,7-bis(guanyl)heptane from in vitro reaction mixtures of hepsulfam and calf thymus DNA. We have isolated bis-(7-formamidopyrimidyldeoxyguanosinyl)-heptane from an enzymatic digest of DNA treated with hepsulfam. Finally, we have found that hepsulfam forms interstrand cross-links at 5'-GXC-3' sites in model oligonucleotides.

Simplified high-sensitivity sequencing of a major histocompatibility complex class I-associated immunoreactive peptide using matrix-assisted laser desorption/ionization mass spectrometry

Cytotoxic T cells (CTL) are known to recognize small peptide fragments of cytoplasmic proteins bound to major histocompatibility complex (MHC) class I molecules on cell surfaces. Recent work indicates that tumor antigens are processed and presented in a manner similar to viral antigens. Identification of the peptides recognized by tumor-specific CTL would provide valuable information about their parent proteins, as well as allowing for the development of recombinant antigen-specific tumor vaccines. While highly represented MHC-bound peptides have been routinely purified by reversed-phase HPLC for Edman degradation sequencing, identification and sequencing of infrequent peptides that represent the biologically relevant targets of tumor-specific CTL have proved elusive. We have combined matrix-assisted laser desorption/ionization mass spectrometry with on-slide exopeptidase digestion to successfully identify and directly sequence a model tumor-specific peptide antigen derived from an integrated viral gene. The enhanced sensitivity of this technique (femtomolar range) allows for the sequencing of specific MHC-bound peptides derived from as few as 1 x 10(9) cells.

Sequencing electroblotted proteins by tandem mass spectrometry

Electroblotting proteins separated by gel electrophoresis provides a suitable support for further manipulations and analysis of small amounts of relatively pure samples. On-membrane digestion, peptide mapping by mass spectrometry, and database searching offer sensitive and fast tools to identify the analyte. By providing sequence information, tandem mass spectrometry can go a step further, confirming the database identification, solving problems connected with post-translational modifications and sequence variations, or supplying the stretches of internal sequence necessary to synthesize an oligonucleotide probe for gene isolation. The viability of this approach was successfully evaluated using different tandem mass spectrometric techniques: metastable decomposition in a matrix-assisted laser desorption/ionization (MALDI) time-of-flight instrument with a curved-field reflectron; low energy collision-induced dissociation in a MALDI quadrupole ion trap mass spectrometer; and high energy collision-induced dissociation in a high-performance four-sector mass spectrometer with massive cluster-impact ionization.

Sequencing peptides without scanning the reflectron: post-source decay with a curved-field reflectron time-of-flight mass spectrometer

A time-of-flight mass spectrometer has been developed using a reflectron in which the voltages placed on the lens elements correspond to a function describing the arc of a circle. This curved-field reflectron enables acquisition of focused product-ion mass spectra at a single reflectron voltage. In this paper, we present results from this instrument for the amino acid sequencing of several peptides and describe the method of mass calibration.

Proteolysis of A beta peptide from Alzheimer disease brain by gelatinase A

It has been recently reported that the 72 kDa proteolytic enzyme gelatinase A/type IV collagenase/matrix metalloproteinase 2 (MMP2) hydrolyzed the Lys 16-Leu 17 peptide bond of a synthetic decapeptide (YEVHHQKLVFF) representing the soluble A beta sequence of amino acid residues 10-20. Our aim was to test if this enzyme could also degrade the insoluble 40-42 residues long A beta peptides purified from Alzheimer Disease brain. Our results indicate that MMP2 hydrolyzes A beta 1-40 and A beta 1-42 peptides at Lys 16-Leu 17, at Leu 34-Met 35, and Met 35-Val 36 peptide bonds. These results suggest that MMP2 has the ability of degrading A beta of AD in vitro. If this hydrolysis also occurs in the brain's extracellular matrix, the enzymatic action of gelatinase a could prevent the generation of amyloidogenic A beta 1-40(42).

Identification of a Tap-dependent leader peptide recognized by alloreactive T cells specific for a class Ib antigen

Recognition of the class Ib antigen Qa-1 by a portion of alloreactive cytotoxic T lymphocyte (CTL) clones requires that the target cell express a second gene, termed Qa-1 determinant modifier (Qdm). We show that Qdm is identical to most D allele genes, excepting Dk, and that a nonamer peptide derived from D alloantigens restores CTL recognition on cells that lack the Qdm-encoded determinant. The equivalent Dk peptide has an Ala-->Val interchange at P3 and requires approximately 4 logs more peptide than the AlaP3 peptide for target cell lysis. Two of five CTL clones, not dependent on Qdm for target cell recognition, also recognize the Qdm peptide as well as the ValP3 variant. Although the Qdm peptide spans residues 3-11 from the leader, it requires the Tap transporters for its expression. Thus, the response against this class Ib molecule provides a tool for dissecting alloreactivity as well as pathways for antigen presentation.

Inactivation of horseradish peroxidase by 3,5-dicarbethoxy-2,6-dimethyl-4-ethyl-1,4-dihydropyridine

In the presence of H2O2, horseradish peroxidase (HRP) catalyzes the one-electron oxidation of a porphyrinogenic agent, 3,5-dicarbethoxy-2,6-dimethyl-4-ethyl-1,4-dihydropyridine (DDEP), leading to formation of an ethyl radical, inactivation of the enzyme, and formation of an altered heme product. The loss of heme during the inactivation of HRP was dependent on the duration of exposure to DDEP as well as the concentration of H2O2 and DDEP. The pseudo first order rate constant for the oxidation of DDEP by compound I of HRP at pH 7.4 was 0.07 min-1, and the maximal extent of heme loss was 35%. The altered heme product, which was isolated by reverse phase HPLC, was characterized by the use of mass and 1H NMR spectrometry as a substitution product of a C2H4OH moiety for a meso proton of the prosthetic heme [meso-(hydroxyethyl)heme]. The source of the oxygen in the C2H4OH moiety appeared not to be H2O2 or H2O as 18O was not incorporated in the heme adduct when H2(18)O2 or H2(18)O was used. The DDEP-mediated reaction did not form the expected delta-meso-ethylheme adduct analogous to the ethyl radical-mediated inactivation of HRP by ethylhydrazine (EH) [Ator et al. (1987) J. Biol. Chem. 262, 14954-14960]. However, we have found that meso-(hydroxyethyl)heme was formed in the EH-mediated reaction, albeit in apparently lower amounts than delta-meso-ethylheme. Perhaps the proximity of the heme to the ethyl radical may play a role in determining the nature of the heme products formed.

A curved field reflectron time-of-flight mass spectrometer for the simultaneous focusing of metastable product ions

The ability to simultaneously focus a wide mass range of metastable fragment ions formed after the initial ionization event in a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer has been made possible by the development of a new type of ion reflector. This coaxially designed time-of-flight instrument employs a modified single stage reflector whose axial voltage gradient rises differentially in order to produce an alignment of energy focal points for product ions. In contrast, product-ion focusing in conventional constant field reflectors occurs over a broad range of distances from the reflectron exit. Approximately 90% of the product-ion mass spectrum can be collected without adjustment, thereby eliminating the need to scan the reflector voltage. Design considerations of the curved field reflectron, its calibration properties and representative metastable spectra of several peptides are discussed.

Structure of the novel heme adduct formed during the reaction of human hemoglobin with BrCCl3 in red cell lysates

It was previously shown that the reductive debromination of BrCCl3 to trichloromethyl radical by human hemoglobin leads to formation of dissociable altered heme products, two of which are identical to those formed from myoglobin and one which is novel. In this study, we have elucidated the structure of this novel adduct with the use of mass spectrometry, as well as 1H and 13C NMR as a substitution product of a -C(Cl) = CCl2 moiety for a beta-hydrogen atom on the prosthetic heme's ring I vinyl group. From studies with the use of 13C-enriched BrCCl3, it was determined that the added carbon atoms were derived from 2 eq of BrCCl3. A mechanism that involves multiple reductive events and a radical cation heme intermediate is proposed. Consistent with this mechanism, cellular reductants were found to selectively enhance the amount of this novel dissociable heme adduct. These studies reveal fine differences between myoglobin and hemoglobin in the accessibility of reactive intermediates to the ring I vinyl group, as well as the potential importance of cellular reductants on the course of heme alteration.

Molecular structures that influence the immunomodulatory properties of the lipid A and inner core region oligosaccharides of bacterial lipopolysaccharides

The relationship between chain length as well as the position of fatty acyl groups to the ability of lipid A to abolish the expression of suppressor T-cell (Ts) activity was examined. Fatty acyl chain lengths of C12 to C14, as in the lipid A of Escherichia coli and Salmonella minnesota, appear to be optimal for this bioactivity, since lipid A preparations with fatty acyl groups of relatively short chain length (C10 to C12 for Pseudomonas aeruginosa and Chromobacterium violaceum) or predominantly long chain length (C18 for Helicobacter pylori) are without effect. The presence of an acyloxyacyl group of appropriate chain length at the 3' position of the glucosamine disaccharide backbone of lipid A also plays a decisive role. By contrast, the lipid A proximal inner core region oligosaccharides of some bacterial lipopolysaccharides increase the expression of Ts activity; this is due mainly to the capacity of such oligosaccharides, which are relatively conserved in structure among gram-negative bacteria, to enlarge or expand upon the population of CD8+ Ts generated during the course of a normal antibody response to unrelated microbial antigens. The minimal structure required for the expression of the added immunosuppression observed appears to be a hexasaccharide containing one 2-keto-3-deoxyoctonate residue, two glucose residues, and three heptose residues to which are attached two pyrophosphorylethanolamine groups. The relevance of these findings to virulence and to the pathogenesis of gram-negative infections is discussed.

Chemical characterization of A beta 17-42 peptide, a component of diffuse amyloid deposits of Alzheimer disease

A peptide corresponding to the amino acid sequence of A beta 17-42 (LVFFAEDVGSNKGAIIGLMVGGVVIA) was isolated from Alzheimer Disease patient brains containing large deposits of diffuse-type amyloid. Brain homogenates were lysed in SDS and submitted to high speed centrifugations. A beta peptides were purified by size exclusion chromatography on Superose 12 and TSK 3000 SW columns. An A beta peptide with M(r) of 3,000 was recovered that on automatic gas-phase Edman degradation yielded the amino acid sequence of A beta starting at residue 17 (Leu). The 3-kDa peptide was subsequently hydrolyzed with trypsin and reacted with CNBr, and the resulting peptides were separated by reverse phase high pressure liquid chromatography and characterized by amino acid analyses, peptide microsequencing, and mass spectrometry. Hydrolysis of beta-amyloid precursor protein 695 at Lys612-Leu613 or at Lys16-Leu17 of its A beta 1-42 derivative prevents the generation of neurotoxic A beta filaments, thus leading to the formation of A beta 17-42 localized in the diffuse amyloid deposits. An outstanding feature in the pathology of Alzheimer Disease is that the predominant A beta peptides have their C termini at position 42, whether in the cores of the neuritic plaques, in the vascular walls, or in the diffuse deposits. Based on these observations, we postulate that the accumulation of insoluble A beta N-42 in Alzheimer Disease is due to the anomalous processing of the C-terminal region.

beta-Amyloid-(1-42) is a major component of cerebrovascular amyloid deposits: implications for the pathology of Alzheimer disease

Reinvestigation of the chemical structure of beta-amyloid peptide (A beta) deposits in the vascular tissue of Alzheimer disease brains revealed that the 42-residue form A beta-(1-42), rather than the more soluble A beta-(1-40) form, is the predominant peptide. Following removal of the surrounding tissue with SDS and collagenase, A beta was solubilized in formic acid and purified by Superose 12 chromatography. Peptides generated by enzymatic and chemical digestion of the A beta were purified by HPLC and characterized by amino acid analysis, sequence analysis, and mass spectrometry. In the leptomeningeal vessels, the average ratio of A beta-(1-42)/A beta-(1-40) was 58:42, whereas in the parenchymal vessels this ratio was 75:25. Interestingly, vascular A beta contains considerably less isomerized and racemized aspartyl residues than does neuritic plaque A beta, suggesting that the vascular amyloid is "younger." The discrete nature of the bands and spherical deposits of A beta associated with arterioles and capillaries, respectively, suggests that this amyloid arises from the vascular tissue itself. Increasing A beta deposition appears to lead to the distortion and occlusion of capillaries, which may contribute significantly to the pathology of Alzheimer disease.

A curved-field reflectron for improved energy focusing of product ions in time-of-flight mass spectrometry

A new type of curved-field reflectron has been developed for the energy focusing of ions formed after initial acceleration in time-of-flight (TOF) mass spectrometers. These include ions generated in the dissociation region of a tandem TOF, as well as metastable decay products formed in the field-free drift region prior to their reflection. Unlike conventional linear-field reflectrons, which focus product ions to different focal lengths that are proportional to the mass (energy) of the fragment, the new curved-field reflectron energy focuses all ions to within a small region near the exit of the reflectron. Thus, the collection of resolved fragment peaks is possible without scanning or stepping the potential gradient of the reflectron, enabling faster acquisition of the production spectrum and, more importantly, true multiplex recording of the spectra from each ionization event. Theoretical considerations of the design are discussed along with an evaluation of collision-induced dissociation data, demonstrating the performance of the new reflectron in a tandem TOF instrument.

Glycosylation of mammalian neurofilaments. Localization of multiple O-linked N-acetylglucosamine moieties on neurofilament polypeptides L and M

Neurofilaments are neuronal intermediate filaments that play an important role in the growth and maintenance of large myelinated axons. Mammalian neurofilaments are composed of three polypeptide subunits, designed as NF-L, NF-M, and NF-H, all of which are phosphorylated. Here, we demonstrate by several criteria that neurofilament polypeptides are also modified by an abundant type of intracellular protein glycosylation in which single N-acetylglucosamine monosaccharides are O-glycosidically (O-GlcNAc) linked to serine or threonine residues. In purified neurofilament proteins, the O-GlcNAc modifications occur at a stoichiometry of approximately 0.1 and 0.15 mol of GlcNAc/mol of NF-L and NF-M, respectively. The predominant sites of O-GlcNAc attachment on NF-L and NF-M are identified using proteolysis, purification of the glycopeptides, and subsequent analysis by automated gas-phase sequencing, manual Edman degradation, and laser desorption mass spectrometry. For NF-L, both major sites of glycosylation (Thr21 and Ser27) are located at the NH2-terminal head domain. For NF-M, one major site (Thr48) lies within the NH2-terminal head domain, whereas the other (Thr431) is located at the tail domain. Deletions encompassing these sites have been shown previously to have a dominant detrimental effect upon neurofilament assembly, raising questions about the specific function(s) of the saccharide moieties at these sites. Specific identification of these O-GlcNAc attachment sites has set the stage for more detailed mutagenic analysis of O-GlcNAc functions on neurofilaments.

Tandem time-of-flight mass spectrometer

A compact, laser desorption tandem time-of-flight mass spectrometer is described. The instrument incorporates two dual-stage reflectron analyzers and a collision region for producing product ions by collision-induced dissociation. Selection of ions of a particular mass is accomplished by deflection of ions from stable trajectory angles entering the second reflectron, while the use of a pulsed valve for introduction of the collision gas obviates the need for differential pumping of the collision region. Initial results are presented, as well as a discussion for optimizing the performance of tandem time-of-flight instruments.

Structural alterations in the peptide backbone of beta-amyloid core protein may account for its deposition and stability in Alzheimer's disease

The structure of beta-amyloid (beta A) from Alzheimer disease brains was examined to determine if post-translational modifications might be linked to the abnormal deposition of this peptide in the diseased tissue. The beta A peptides were isolated from the compact amyloid cores of neuritic plaques and separated from minor glycoprotein components by size-exclusion high-pressure liquid chromatography (HPLC). This parenchymal beta A has a maximal length of 42 residues, but shorter forms with "ragged" NH2 termini are also present. Tryptic peptide analysis revealed heterogeneity in the beta A1-5 and beta A6-16 peptides, each of which eluted as four peaks on reverse phase HPLC. Amino acid composition and sequence analyses, mass spectrometry, enzymatic methylation, and stereoisomer determinations revealed that these multiple peptide forms resulted from structural rearrangements of the aspartyl residues at beta A positions 1 and 7. The L-isoaspartyl form predominates at each of these positions, whereas the D-isoaspartyl, L-aspartyl, and D-aspartyl forms are present in lesser amounts. beta A purified from the leptomeningeal microvasculature contains the same structural alterations as parenchymal beta A, but is 2 residues shorter at its COOH terminus. Using two different purification protocols, and using a synthetic beta A1-42 peptide as a control, we show that these modifications arose endogenously and were not caused by the experimental manipulations. The abundance of structurally altered aspartyl residues may profoundly affect the conformation of the beta A protein within plaque cores and thus significantly impact normal catabolic processes designed to limit its deposition. These alterations may therefore contribute to the production and stability of beta-amyloid deposits in Alzheimer brain tissue.

Mass spectrometric analysis of proteins

The past year has seen greatly increased acceptance and application of the analytical capabilities of mass spectrometry by the biochemical community. The technique has been used to provide accurate mass determinations of non-covalently bound protein complexes, rapid mapping of molecular weights of altered peptides in protease digests, sequencing by collisional activation in tandem mass spectrometry, characterization of glycosylation and other modifications, and quantitation of peptides used in clinical diagnostics.

Preparation and characterization of biologically active 6'-O-(6-aminocaproyl)-4'-O-monophosphoryl lipid A and its conjugated derivative

N-tert-butyloxycarbonyl (t-Boc) protected 6-aminocaproic (Cap) anhydride was reacted with unprotected hexaacyl-4'-O-monophosphoryl lipid A (MLA) obtained from the lipopolysaccharide of Escherichia coli J5 to yield t-Boc-Cap-MLA. After a column purification step, the t-Boc group was removed by incubating the sample at low temperature in the presence of acid to yield Cap-MLA. This product was analyzed by californium plasma desorption mass spectrometry (PDMS). Purified t-Boc-Cap-MLA was further fractionated by reverse-phase high-performance liquid chromatography as its methyl ester and characterized by laser desorption mass spectrometry, PDMS, and proton nuclear magnetic resonance spectroscopy. These analyses revealed that the Cap group was selectively introduced into the 6'-position of MLA. To demonstrate that Cap-MLA can be conjugated to other compounds, it was reacted with biotin-Cap N-hydroxysuccinimide ester to yield biotin-(Cap)2-MLA. Analysis of this product by PDMS confirmed its expected molecular weight of 2171 and showed the presence of fragments containing the biotin and Cap groups. Monoclonal antibodies and streptavidin were used to show the presence of both lipid A and biotin in this conjugated product. These two novel lipid A derivatives were then tested for their bioactivities. Although both Cap-MLA and biotin-(Cap)2-MLA showed mitogenic activity using murine splenocytes, they were about 4-8 times less active than MLA at 20 micrograms/mL or less and only one-half as active at 100 micrograms/mL.(ABSTRACT TRUNCATED AT 250 WORDS)

Covalent alteration of the prosthetic heme of human hemoglobin by BrCCl3. Cross-linking of heme to cysteine residue 93

Recent studies have shown that a protein-bound heme adduct formed from the reaction of BrCCl3 with myoglobin was due to bonding of the proximal histidine residue through the ring I vinyl of a heme-CCl2 moiety. The present study reveals that BrCCl3 also reacts with the heme of reduced human hemoglobin to form two protein-bound heme adducts. Edman degradation and mass spectrometry provided evidence that these protein-bound heme adducts were addition products in which heme-CCL2 or heme-CCl3 were bound to cysteine residue 93 of the beta-chain of hemoglobin. It appeared that the cysteine residue was bonded regiospecifically to the ring I vinyl group of the altered heme moiety, because the nonprotein-bound products of the reaction included the beta-carboxyvinyl and alpha-hydroxy-beta-trichloromethylethyl derivatives of the ring I vinyl moiety of heme. The absorption spectra of the protein-bound adducts in both the oxidized and reduced states were highly similar to those described for hemichromes, which are thought to be involved in the formation of Heinz bodies and subsequent red cell lysis.

Resolution of a protein sequence ambiguity by X-ray crystallographic and mass spectrometric methods

Ambiguities in amino acid sequences are a potential problem in X-ray crystallographic studies of proteins. Amino acid side chains often cannot be reliably identified from the electron density. Many protein crystal structures that are now being solved are simple variants of a known wild-type structure. Thus, cloning artifacts or other untoward events can readily lead to cases in which the proposed sequence is not correct. An example is presented showing that mass spectrometry provides an excellent tool for analyzing suspected errors. The X-ray crystal structure of an insertion mutant of Staphylococcal nuclease has been solved to 1.67 Å resolution and refined to a crystallographic R value of 0.170 [Keefe & Lattman (1992). In preparation]. A single residue has been inserted in the C-terminal α helix. The inserted amino acid was believed to be an alanine residue, but the final electron density maps strongly indicated that a glycine had been inserted instead. To confirm the observations from the X-ray data, matrix-assisted laser desorption mass spectrometry was employed to verify the glycine insertion. This mass spectrometric technique has sufficient mass accuracy to detect the methyl group that distinguishes glycine from alanine and can be extended to the more common situation in which crystallographic measurements suggest a problem with the sequence, but cannot pinpoint its location or nature.

A herpesvirus maturational proteinase, assemblin: identification of its gene, putative active site domain, and cleavage site

A herpesvirus proteinase activity has been identified and partially characterized by using the cloned enzyme and substrate genes in transient transfection assays. Evidence is presented that the proteinase gene of cytomegalovirus strain Colburn encodes a 590-amino acid protein whose N-terminal 249 residues contain the proteolytic activity and two domains that are highly conserved in the homologous protein of other herpesviruses. Insertion of a short amino acid sequence between these domains abolished proteinase activity, suggesting that this region constitutes part or all of the enzyme active site. Plasma desorption mass spectrometry was used to identify the C terminus of the mature assembly protein as alanine, enabling the recognition of a consensus proteinase cleavage sequence of V/L-X-A decreases S/V, near the C-terminal end of all herpesvirus assembly protein homologs. Interestingly, the proteinase and its substrate, the assembly protein precursor, are encoded by opposite halves of the same open reading frame.

Secretion of the beta/A4 amyloid precursor protein. Identification of a cleavage site in cultured mammalian cells

Alzheimer's disease, a progressive neurodegenerative disorder, affects greater than 10% of the population of individuals greater than 65 years of age. A principal neuropathological feature of this disease is the senile plaque, a fibrillar extracellular deposit primarily composed of a approximately 4-kDa peptide, beta/A4, derived from the amyloid precursor protein (APP). Studies in cultured cells have documented that APP matures through a constitutive secretory pathway and is cleaved at or near the cell surface to release a large ectodomain into the extracellular space. To define the APP cleavage site, we constructed a Chinese hamster ovary cell line, which constitutively overexpresses human APP-770, and analyzed the COOH termini of secreted APP-770-related molecules. Using plasma desorption mass spectrometry and chemical microsequencing, we document that an APP cleavage site in Chinese hamster ovary cells leading to secretion occurs immediately COOH-terminal to lysine residue 687, which lies adjacent to the hydrophobic membrane-spanning domain.

Endothermic ion molecule reactions

Endothermic ion-molecule reactions in a tandem mass spectrometer have been used for a number of years for determining thermodynamic quantities, such as heats of formation and proton affinities, for gaseous ions. Recently, the reactive, endothermic collision has been exploited as an analytical technique for the structural analysis of peptides and other biomolecules. The technique is based upon the endothermic transfer of protons associated with amide bonds to ammonia. This reaction proceeds via a long-lived collision complex. When additional beam energy is supplied, other dissociation channels are opened up, leading to the production of sequence ions for the mass-selected, protonated analyte that are normally observed in high energy collision-induced dissociation spectra. The advantage, however, is that such spectra can be produced at very low beam energies. In this article, the rationale for developing this scheme, and its roots in previous ion-molecule studies, are explored.

Chemical reduction of 3-oxo and unsaturated groups in fatty acids of diphosphoryl lipid A from the lipopolysaccharide of Rhodopseudomonas sphaeroides. Comparison of biological properties before and after reduction

Unlike the diphosphoryl lipid A (DPLA) derived from toxic lipopolysaccharide of Escherichia coli and Salmonella strains, the DPLA from nontoxic lipopolysaccharide of Rhodopseudomonas sphaeroides ATCC 17023 is biologically inactive. This could be due to the presence of 3-oxotetradecanoic and delta 7-tetradecenoic acids. These two fatty acids in R. sphaeroides DPLA were catalytically reduced in platinum oxide/H2 to the 3-hydroxy and saturated fatty acids, respectively. The biologically active E. coli DPLA was also treated with platinum oxide/H2, but as expected, the reduction step did not change the structure. These two preparations were then compared with the untreated samples for biological activity in three select in vitro assays. Over a range of 0.01-100 ng/ml, both normal and reduced DPLA from R. sphaeroides were inactive in priming phorbol myristate acetate-stimulated superoxide anion release in human alveolar macrophages. Over a range of 10-10(3) ng/ml, both samples failed to induce tumor necrosis factor in the RAW 264.7 murine macrophage cell line. The reduced DPLA marginally activated 70Z/3 pre-B cells at concentrations of 0.1-30 micrograms/ml. In every case, both normal and platinum oxide/H2-treated E. coli DPLA were biologically active. These results indicate that the lack of biological activity of R. sphaeroides DPLA is not due to the presence of 3-oxo and unsaturated fatty acids, but rather to one or more of the following: (i) presence of only five fatty acyl groups (compared to six in active lipid A); (ii) presence of 3-hydroxydecanoic acids (rather than 3-hydroxytetradecanoic, in active lipid A); (iii) greater variation in size of the fatty acids.

High-performance liquid chromatography-time-of-flight mass spectrometry and its application to peptide analyses

High-performance liquid chromatography (HPLC) has been successfully interfaced on-line with liquid secondary-ion time-of-flight mass spectrometry, utilizing a continuous-flow interface. Time-of-flight mass spectrometry (TOF-MS) is a low-resolution, high-mass-range technique, compatible with extremely rapid data acquisition rates. Thus a TOF-MS system is extremely well suited for coupling with HPLC. This paper describes the interface used to couple the HPLC and TOF-MS as well as the basic operating principles of such a system. Using both standard and packed-capillary reversed-phase HPLC columns, the HPLC-TOF-MS system has been successfully used to separate and detect peptides, providing molecular weight information for the peptide analytes. Experimental data, including chromatograms (UV, reconstructed ion and selected ion) and mass spectra, are presented to demonstrate the ability of the HPLC-liquid secondary-ion TOF-MS system to resolve chromatographically analytes as well as to resolve mass spectrometrically analytes which are unresolved on the chromatographic column.

Effects of peptide hydrophobicity and charge state on molecular ion yields in plasma desorption mass spectrometry

Plasma desorption mass spectra were obtained for a series of peptides, grouped in four mass ranges having approximately 9, 20, 30, and 40 amino acid residues. Within each group, the individual peptides differed in hydrophobicity, charge state, and retention time, as measured on a reversed-phase HPLC column. Comparison of the molecular ion intensities in the positive ion mass spectra of peptides from each group showed a strong dependence upon hydrophobicity and no correlation with charge state. Plasma desorption mass spectra of mixtures of all the peptides within each mass range generally resulted in the desorption of a single residue and suppression of the ion signal from other components. In most cases, this could be correlated with hydrophobicity, as calculated from the Bull and Breese index; however, a better correlation existed when the results were compared with reversed-phase retention times. In general the spectra of mixtures were not influenced by charge state (except in the absence of hydrophobic peptides), as the same component in each peptide mixture produced the most abundant ions in both positive and negative ion spectra.

Liquid chromatography/time-of-flight mass spectrometry with high-speed integrated transient recording

High-performance liquid chromatography (HPLC) has been interfaced to a time-of-flight mass spectrometer. The interface is a continuous flow probe and ions are desorbed from the liquid matrix by energetic ion bombardment. Pulsed and delayed ion extraction from the source permits the use of broad ionization times, results in the production of analog signals in each time-of-flight cycle, and provides both energy and spatial focusing. A high-speed integrated transient recording system has been developed and is also reported. This instrument is the prototype for development of a high-speed, high-mass range LC detector with high duty cycle. Its performance is demonstrated for the separation of several mixtures of small peptides.

Oligopeptide fragmentation viewed as constant neutral loss

Spectra were recorded of all fragment ions formed by elimination of 28-u neutral fragments in fast atom bombardment spectra of peptides in the mass range 1000-1800 u, This approach can provide less complex spectra than either conventionally scanned spectra or product ion scans from collisionaIly activated four-sector experiments, and spectra that contain information that is both overlapping and complementary to those from the other techniques. Constant neutral loss spectra may provide a reading frame for distinguishing sequence ion series in tandem or single analyzer spectra.