Assignment of disulfide bonds in proteins by fast atom bombardment mass spectrometry

Identification and characterization of disulfide bonds in proteins and peptides from tandem MS data by use of the MassMatrix MS/MS search engine

A new database search algorithm has been developed to identify disulfide-linked peptides in tandem MS data sets. The algorithm is included in the newly developed tandem MS database search program, MassMatrix. The algorithm exploits the probabilistic scoring model in MassMatrix to achieve identification of disulfide bonds in proteins and peptides. Proteins and peptides with disulfide bonds can be identified with high confidence without chemical reduction or other derivatization. The approach was tested on peptide and protein standards with known disulfide bonds. All disulfide bonds in the standard set were identified by MassMatrix. The algorithm was further tested on bovine pancreatic ribonuclease A (RNaseA). The 4 native disulfide bonds in RNaseA were detected by MassMatrix with multiple validated peptide matches for each disulfide bond with high statistical scores. Fifteen nonnative disulfide bonds were also observed in the protein digest under basic conditions (pH = 8.0) due to disulfide bond interchange. After minimizing the disulfide bond interchange (pH = 6.0) during digestion, only one nonnative disulfide bond was observed. The MassMatrix algorithm offers an additional approach for the discovery of disulfide bond from tandem mass spectrometry data.

Determination of the disulfide bond arrangement of dengue virus NS1 protein

The 12 half-cystines of NS1 proteins are absolutely conserved among flaviviruses, suggesting their importance to the structure and function of these proteins. In the present study, peptides from recombinant Dengue-2 virus NS1 were produced by tryptic digestion in 100% H(2)(16)O, peptic digestion in 50% H(2)(18)O, thermolytic digestion in 50% H(2)(18)O, or combinations of these digestion conditions. Peptides were separated by size exclusion and/or reverse phase high performance liquid chromatography and examined by matrix-assisted laser desorption ionization-time of flight mass spectrometry, matrix-assisted laser desorption ionization post-source decay, and matrix-assisted laser desorption ionization tandem mass spectrometry. Where digests were performed in 50% H(2)(18)O, isotope profiles of peptide ions aided in the identification and characterization of disulfide-linked peptides. It was possible to produce two-chain peptides containing C1/C2, C3/C4, C5/C6, and C7/C12 linkages as revealed by comparison of the peptide masses before and after reduction and by post-source decay analysis. However, the remaining four half-cystines (C8, C9, C10, and C11) were located in a three-chain peptide of which one chain contained adjacent half-cystines (C9 and C10). The linkages of C8/C10 and C9/C11 were determined by tandem mass spectrometry of an in-source decay fragment ion containing C9, C10, and C11. This disulfide bond arrangement provides the basis for further refinement of flavivirus NS1 protein structural models.

Protein disulfide bond determination by mass spectrometry

The determination of disulfide bonds is an important aspect of gaining a comprehensive understanding of the chemical structure of a protein. The basic strategy for obtaining this information involves the identification of disulfide-linked peptides in digests of proteins and the characterization of their half-cystinyl peptide constituents. Tools for disulfide bond analysis have improved dramatically in the past two decades, especially in terms of speed and sensitivity. This improvement is largely due to the development of matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI), and complementary analyzers with high resolution and accuracy. The process of pairing half-cystinyl peptides is now generally achieved by comparing masses of non-reduced and reduced aliquots of a digest of a protein that was proteolyzed with intact disulfide bonds. Pepsin has favorable properties for generating disulfide-linked peptides, including its acidic pH optimum, at which disulfide bond rearrangement is precluded and protein conformations are likely to be unfolded and accessible to cleavage, and broad substrate specificity. These properties potentiate cleavage between all half-cystine residues of the substrate protein. However, pepsin produces complex digests that contain overlapping peptides due to ragged cleavage. This complexity can produce very complex spectra and/or hamper the ionization of some constituent peptides. It may also be more difficult to compute which half-cystinyl sequences of the protein of interest are disulfide-linked in non-reduced peptic digests. This ambiguity is offset to some extent by sequence tags that may arise from ragged cleavages and aid sequence assignments. Problems associated with pepsin cleavage can be minimized by digestion in solvents that contain 50% H(2) (18)O. Resultant disulfide-linked peptides have distinct isotope profiles (combinations of isotope ratios and average mass increases) compared to the same peptides with only (16)O in their terminal carboxylates. Thus, it is possible to identify disulfide-linked peptides in digests and chromatographic fractions, using these mass-specific markers, and to rationalize mass changes upon reduction in terms of half-cystinyl sequences of the protein of interest. Some peptides may require additional cleavages due to their multiple disulfide bond contents and/or tandem mass spectrometry (MS/MS) to determine linkages. Interpretation of the MS/MS spectra of peptides with multiple disulfides in supplementary digests is also facilitated by the presence of (18)O in their terminal carboxylates.

Identification of disulfide-linked peptides by isotope profiles produced by peptic digestion of proteins in 50% (18)O water

Determination of the disulfide-bond arrangement of a protein by characterization of disulfide-linked peptides in proteolytic digests may be complicated by resistance of the protein to specific proteases, disulfide interchange, and/or production of extremely complex mixtures by less specific proteolysis. In this study, mass spectrometry has been used to show that incorporation of (18)O into peptides during peptic digestion of disulfide-linked proteins in 50% (18)O water resulted in isotope patterns and increases in average masses that facilitated identification and characterization of disulfide-linked peptides even in complex mixtures, without the need for reference digests in 100% (16)O water. This is exemplified by analysis of peptic digests of model proteins lysozyme and ribonuclease A (RNaseA) by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry (MS). Distinct isotope profiles were evident when two peptide chains were linked by disulfide bonds, provided one of the chains did not contain the C terminus of the protein. This latter class of peptide, and single-chain peptides containing an intrachain disulfide bond, could be identified and characterized by mass shifts produced by reduction. Reduction also served to confirm other assignments. Isotope profiling of peptic digests showed that disulfide-linked peptides were often enriched in the high molecular weight fractions produced by size exclusion chromatography (SEC) of the digests. Applicability of these procedures to analysis of a more complex disulfide-bond arrangement was shown with the hemagglutinin/neuraminidase of Newcastle disease virus.

Complete analysis of the glycosylation and disulfide bond pattern of human beta-hexosaminidase B by MALDI-MS

beta-hexosaminidase B is an enzyme that is involved in the degradation of glycolipids and glycans in the lysosome. Mutation in the HEXB gene lead to Sandhoff disease, a glycolipid storage disorder characterized by severe neurodegeneration. So far, little structural information on the protein is available. Here, the complete analysis of the disulfide bond pattern of the protein is described for the first time. Additionally, the structures of the N-glycans are analyzed for the native human protein and for recombinant protein expressed in SF21 cells. For the analysis of the disulfide bond structure, the protein was proteolytically digested and the resulting peptides were analyzed by MALDI-MS. The analysis revealed three disulfide bonds (C91-C137; C309-C360; C534-C551) and a free cysteine (C487). The analysis of the N-glycosylation was performed by tryptic digestion of the protein, isolation of glycopeptides by lectin chromatography and mass measurement before and after enzymatic deglycosylation. Carbohydrate structures were calculated from the mass difference between glycosylated and deglycosylated peptide. For beta-hexosaminidase B from human placenta, four N-glycans were identified and analyzed, whereas the recombinant protein expressed in SF21 cells carried only three glycans. In both cases the glycosylation belongs to the mannose-core- or high-mannose-type, and some carbohydrate structures are fucosylated.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric observation of a peptide triplet induced by thermal cleavage of cystine

Heat-induced (90 degrees C, 30 min) beta-elimination of a cystine residue leads to cleavage of a disulfide bond and produces a set of three peptides with a cysteine residue, a thiocysteine residue (+32Da), and a dehydroalanine residue (-34Da). This characteristic feature was observed from somatostatin and insulin by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Mass spectrometric observation of this triplet is useful in identifying the presence of a cystine residue in a peptide, and could assist mass spectrometric identification of the peptide from a database.

Determination of the disulfide bond arrangement of Newcastle disease virus hemagglutinin neuraminidase. Correlation with a beta-sheet propeller structural fold predicted for paramyxoviridae attachment proteins

Disulfide bonds stabilize the structure and functions of the hemagglutinin neuraminidase attachment glycoprotein (HN) of Newcastle disease virus. Until this study, the disulfide linkages of this HN and structurally similar attachment proteins of other members of the paramyxoviridae family were undefined. To define these linkages, disulfide-linked peptides were produced by peptic digestion of purified HN ectodomains of the Queensland strain of Newcastle disease virus, isolated by reverse phase high performance liquid chromatography, and analyzed by mass spectrometry. Analysis of peptides containing a single disulfide bond revealed Cys(531)-Cys(542) and Cys(172)-Cys(196) linkages and that HN ectodomains dimerize via Cys(123). Another peptide, with a chain containing Cys(186) linked to a chain containing Cys(238), Cys(247), and Cys(251), was cleaved at Met(249) with cyanogen bromide. Subsequent tandem mass spectrometry established Cys(186)-Cys(247) and Cys(238)-Cys(251) linkages. A glycopeptide with a chain containing Cys(344) linked to a chain containing Cys(455), Cys(461), and Cys(465) was treated sequentially with peptide-N-glycosidase F and trypsin. Further treatment of this peptide by one round of manual Edman degradation or tandem mass spectrometry established Cys(344)-Cys(461) and Cys(455)-Cys(465) linkages. These data, establishing the disulfide linkages of all thirteen cysteines of this protein, are consistent with published predictions that the paramyxoviridae HN forms a beta-propeller structural fold.

Strategies for locating disulfide bonds in a monoclonal antibody via mass spectrometry

The location of the disulfide bonds in a recombinant monoclonal antibody was confirmed by matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry (MS). A non-reduced Endoproteinase Lys-C (Endo Lys-C) digest of the antibody was analyzed directly by MALDI-TOFMS. The sample was then reduced on-plate by depositing dithiothreitol (DTT) on the sample spot and re-analyzed by MALDI-TOFMS. The disulfide bonds were assigned based on the disappearance of certain mass ions in the non-reduced digest and the appearance of product ions in the reduced digest. A rapid LC/ESI-MS protocol was also developed to determine the location of the disulfide bonds. The peptides generated from the Endo Lys-C digest of the antibody were partially separated on a high performance liquid chromatography (HPLC) column by utilizing a steep gradient and analyzed by ESI-MS. The masses of the partially resolved peptides were determined by deconvoluting the mass spectra.

Determination of disulfide bonds in highly bridged disulfide-linked peptides by matrix-assisted laser desorption/ionization mass spectrometry with postsource decay

Matrix-assisted laser desorption/ionization mass spectrometry with postsource decay was used to generate fragment ions from peptide fragments containing heteropeptides linked together by two disulfide bonds. Postsource decay analysis of these peptide samples generates a series of singly charged fragment ions that, in addition to the peptide sequence ions, provide useful information for assigning disulfide arrangement in highly bridged disulfide-linked peptides. The assignment was made possible by fragmentation at peptide bonds between two Cys residues in a peptide that constitutes the highly bridged fragment, while retaining the disulfide linkage to the other peptide. Fragmentation using other types of instruments, such as quadrupole ion-trap mass spectrometry with collision-induced dissociation, usually did not generate such fragment ions. The data obtained from postsource decay also provide fragment ions derived from both symmetric and nonsymmetric cleavages of disulfide bonds. The present method is a highly sensitive technique which requires no further sample handling and should be complementary to other classical chemical methods. The method proved useful in facilitating the assignment of disulfide structure in tumor necrosis factor binding protein (TNFbp), which contains 162 amino acids and 13 disulfide bonds (Jones, M.; et al. Biochemistry, in press). Postsource decay analysis of large disulfide-containing peptides usually produces no fragmentation but generates a series of high-intensity ions derived from both symmetric and nonsymmetric cleavages of disulfide bonds.

Biochemical characterization and mass spectrometric disulfide bond mapping of periplasmic alpha-amylase MalS of Escherichia coli

Periplasmic alpha-amylase of Escherichia coli, the malS gene product, hydrolyzes linear maltodextrins. The purified enzyme exhibited a Km of 49 microM and a Vmax of 0.36 micromol of p-nitrophenylhexaoside hydrolyzed per min per mg of protein. Amylase activity was optimal at pH 8 and was dependent on divalent cations such as Ca2+. MalS exhibited altered migration on SDS-polyacrylamide gel electrophoresis under nonreducing conditions. Analytical ultracentrifugation and electrospray mass spectrometry indicated that MalS is monomeric. The four cysteine residues are involved in intramolecular disulfide bonds. To map disulfide bonds, MalS was proteolytically digested. The resulting peptides were separated by reverse phase-high performance liquid chromatography, and matrix-assisted laser desorption/ionization mass spectrometry analysis indicated the presence of two disulfide bonds, i.e. Cys40-58 and Cys104-520. The disulfide bond at Cys40-58 is located in an N-terminal extension of about 160 amino acids which has no homology to other amylases but to the proposed peptide binding domain of GroEL, the Hsp60 of E. coli. The N-terminal extension is linked to the C-terminal amylase domain via disulfide bond Cys104-520. Reduction of disulfide bonds by dithiothreitol treatment led to aggregation suggesting that the N terminus of MalS may represent an internal chaperone domain.

Determination of the disulfide bond arrangement of human respiratory syncytial virus attachment (G) protein by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The attachment protein or G protein of the A2 strain of human respiratory syncytial virus (RSV) was digested with trypsin and the resultant peptides separated by reverse-phase high-performance liquid chromatography (HPLC). One tryptic peptide produced a mass by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) corresponding to residues 152-187 with the four Cys residues of the ectodomain (residues 173, 176, 182, and 186) in disulfide linkage and absence of glycosylation. Sub-digestion of this tryptic peptide with pepsin and thermolysin produced peptides consistent with disulfide bonds between Cys173 and Cys186 and between Cys176 and Cys182. Analysis of ions produced by post-source decay of a peptic peptide during MALDI-TOF-MS revealed fragmentation of peptide bonds with minimal fission of an inter-chain disulfide bond. Ions produced by this unprecedented MALDI-induced post-source fragmentation corroborated the existence of the disulfide arrangement deduced from mass analysis of proteolysis products. These findings indicate that the ectodomain of the G protein has a non-glycosylated subdomain containing a "cystine noose."

Detection, number, and sequence location of sulfur-containing amino acids and disulfide bridges in peptides by ultrahigh-resolution MALDI FTICR mass spectrometry

Here, we present several strategies for determining the number of sulfur atoms and disulfide bridges in selected biologically active peptides, based on MALDI FTICR mass spectrometry at femtomole sample consumption level. First, based on the 2-Da mass increase per disulfide bridge reduction, we show that repeated laser shots on the same sample spot can reduce (and therefore reveal the presence of) the disulfide bridge in oxytocin. Second, we show that the primary sequence positions of the disulfide-bridged cystines can be inferred from the presence/absence of MALDI-induced reduction in cystine-containing fragment ions. Third, we show that the presence and number of sulfur atoms as well as the degree of reduction in a peptide can all be determined directly from isotopic relative abundances of mass-resolved 34S, 13C2, and reduced all-12C species in a single ultrahigh-resolution MALDI FTICR mass spectrum. Methods for achieving such ultrahigh mass resolution of peptide ions of closely spaced m/z (m/delta m50% approximately 950,000 at m/z approximately 650) at modest magnetic field (3 T) are discussed.

Assignment of protein disulphides by a computer method using mass spectrometric data

We designed a computer program for the assignment of protein disulphides using mass spectrometric data. All the theoretical linear peptides containing from one to three cysteines are generated on the basis of the protein sequence. Their combination ways are determined in order to create all the possible disulphide-bridged fragments containing from two to six cysteines and to calculate their molecular weight. One, two and three S-S bridges per linked fragment were considered, taking into account the possibility that the fragments contain unabridged residues. The mass data obtained from the spectral analysis of peptide mixtures of the digested protein are then associated to the fitting structures of disulphide-bridged peptides, giving rise to the primary output. This output can then be screened by using information on the specificity of the proteolytic agent(s) used and/or any further mass data provided by Edman degradation and/or carboxypeptidase treatment of the peptide mixtures. The need for such a computer aid is discussed and examples of application are given.

Characterization of disulfide linkages and disulfide bond scrambling in recombinant human macrophage colony stimulating factor by fast-atom bombardment mass spectrometry of enzymatic digests

Fast-atom bombardment mass spectrometry was used to study disulfide bonding patterns in heat-denatured human recombinant macrophage colony stimulating factor (rhM-CSF). The heat-denaturated protein was studied by analysis of the pattern of peptides in the proteolytic digests. Native rhM-CSF is a homodimer with intramolecular disulfide linkages between Cys7-Cys90, Cys48-Cys139, and Cys102-Cys146 and intermolecular linkages between Cys31-Cys31, and the pairs Cys157 and Cys159. Brief heating for 1 min leads to partial disulfide bond scrambling. In addition to the native disulfide bonds between Cys7-Cys90, Cys48-Cys139, and Cys31-Cys31, nonnative disulfide bonds were detected between Cys48-Cys90 and Cys48-Cys102. When heated for 5 min the disulfide bonds of rhM-CSF are completely scrambled and lead to nonnative intramolecular disulfide bonds between Cys48-Cys102 and Cys90-Cys102 and one intermolecular disulfide bond between Cys102-Cys102.

Assignment of all four disulfide bridges in echistatin

Echistatin is a 49-amino-acid protein from Echis carinatus venom. It contains four disulfide bonds. Since the disulfide bonding is critical for biological activity; it is very important to assign the disulfide linkage in this protein. Echistatin was incubated in 250 mM oxalic acid at 100 degrees C for 4 hr under nitrogen. Under these conditions, many overlapping disulfide-containing peptides were identified by ionspray mass spectrometry. Ionspray MS/MS data indicate that the four disulfide bonds are Cys 2-Cys 11, Cys 7-Cys 32, Cys 8-Cys 37, and Cys 20-Cys 39. To our knowledge, this is the first time all four disulfide bonds in echistatin have been assigned in one experiment without disulfide bond exchange. This approach, which combines oxalic acid hydrolysis and ionspray MS/MS, may be very useful for assigning disulfide bridges in other proteins from the disintegrin family.

Assignment of the inter- and intramolecular disulfide linkages in recombinant human macrophage colony stimulating factor using fast atom bombardment mass spectrometry

The disulfide bridges in recombinant human macrophage colony stimulating factor (rhM-CSF), a 49-kDa homodimeric protein, were assigned. The 18 cysteines in the dimer form three intermolecular and two sets of three intramolecular disulfide bonds. The intermolecular disulfide bridges hold the dimer together and form symmetric bonds in which Cys31 and Cys157/Cys159 from one monomer unit are linked to the corresponding cysteines of the second monomer. The intramolecular disulfide bonds are located between Cys7-Cys90, Cys48-Cys139, and Cys102-Cys146, respectively. The resistance of native M-CSF to proteolytic cleavage was overcome by an initial chemical cleavage reaction using BrCN. The close proximity of four cysteines (Cys139, Cys146, Cys157, and Cys159) results in a tight core complex that makes the protein undigestable for most proteases. Digestion using endoprotease Asp-N resulted in cleavage at Asp156 near the C-terminal end of this region, thereby opening the complex structure.

Mass spectrometric analysis of the structure of gamma II bovine lens crystallin

The amino acid sequence of bovine gamma II-crystallin has been verified by a combination of electrospray and fast atom bombardment mass spectrometry. The molecular weight of gamma II, isolated by gel filtration and ion exchange chromatography, was determined to be 20,967 +/- 3 by electrospray mass spectrometry. Another aliquot of gamma II was completely digested by trypsin in a medium of 20% CH3CN and 0.1 M Tris, pH 8.2. The tryptic peptides were separated by reversed phase HPLC and identified by their molecular weights, as determined by fast atom bombardment mass spectrometry (FABMS). The identification of each peptide was confirmed by digesting the peptide further to give new peptides whose molecular weights were also determined by FABMS and related to the proposed amino acid sequences. The data from both types of mass spectrometric analyses were consistent with the sequence previously proposed by Hay et al. (J. Biol. Chem. 1987, 146, 332-338), including threonine at position 119. The FAB mass spectrum of one HPLC fraction suggested that disulfide bonding between Cys 18 and Cys 22 was present in at least half the protein preparation. Whether the Cys 18/Cys 22 disulfide bond was present in native gamma II or was produced during isolation or enzymic digestion could not be determined from these studies. Samples that had been stored for several weeks showed that several of the cysteines had become disulfide bonded. These studies illustrate the power of mass spectrometric techniques to accurately confirm the primary structure of proteins and to identify post-translational modifications.

Factors affecting the fast atom bombardment mass spectrometric analysis of proteolytic digests of proteins

The fast atom bombardment (FAB) mass spectrometric analysis of proteolytic digests of proteins is currently used in protein structural characterization. The major current limitation of this procedure is that not all the peptides generated by enzyme digestion can be observed in the spectra. Previous studies showed that in a mixture the more hydrophilic peptides are suppressed. Several enzymatic digests of 18 different proteins ranging from 10 kDa to 67 kDa in molecular weight were examined using FAB mass spectrometry. It was observed that, even though the hydrophobicity of peptides is a factor in determining their presence or absence in the spectra, the predictions of whether or not a peptide would be detected based on this criterion varies in a wide range of values. Moreover, present results seem to indicate that the presence of particular amino acid side chains within a peptide sequence capable of forming hydrogen bonds with the matrix heavily affects the behaviour of that peptide in the mixture, despite the overall hydrophobicity of the peptide itself.

Assignment of disulphide bonds in synthetic endothelin-1 isomers by fast atom bombardment mass spectrometry

Endothelin-1 (ET-1), a 21-residue vasoconstrictor peptide possessing four cysteinyl residues at positions 1, 3, 11 and 15, was synthesized by random oxidation of a tetrahydro-ET-1. On reverse-phase high-performance liquid chromatography, crude product was shown to be a mixture of two disulphide isomers. A method was developed to determine the disulphide structure of the isomers. The method consisted of (a) limited digestion with chymotrypsin, (b) cleavage with cyanogen bromide and (c) manual Edman degradation. Through this procedure, each isomer afforded specific fragments containing a single disulphide bond, which were identified by fast atom bombardment mass spectrometry. Isomer 1, the minor component, afforded a fragment containing Cys 3 and Cys 15, and isomer 2, the major component, afforded fragments containing Cys 3 and Cys 11. Since little disulphide exchange was observed, it could be concluded clearly that the disulphide bond pairs in isomer 1 were Cys 1-Cys 11 and Cys 3-Cys 15, while those in isomer 2 were Cys 1-Cys 15 and Cys 3-Cys 11 (the same as natural ET-1). The procedure was successfully applied to two synthetic analogues, [Gly18]-ET-1 and [Pro16]-ET-1.

Simultaneous detection of thiol- and disulfide-containing peptides by electrochemical high-performance liquid chromatography with identification by mass spectrometry

A new HPLC electrochemical detector that can be used to detect selectively and simultaneously both thiol- and disulfide-containing peptides is described. One electrode responds only to thiol-containing peptides, while a second electrode located downstream from a third electrode responds to thiol- as well as disulfide-containing peptides. All three electrodes are located in a single block and sample the HPLC effluent simultaneously. Since the electrochemical detector responds only to peptides that contain thiol or disulfide functionalities, it is ideal for detecting these types of peptides when they are present in complex mixtures. Peptides can be identified by their retention times if reference peptides are available, or by their molecular weights if the appropriate chromatographic fractions are collected and analyzed by mass spectrometry. The utility of the three-electrode electrochemical detector for detecting thiol- and disulfide-containing peptides in a single chromatographic analysis is illustrated with proteolytic digests of bovine alpha A-crystallin and partially reduced bovine insulin.

Assignment of the five disulfide bridges in an alpha-amylase inhibitor from wheat kernel by fast-atom-bombardment mass spectrometry and Edman degradation

The assignment of the five disulfide bridges in an alpha-amylase monomeric inhibitor from wheat kernel (coded 0.28) was achieved by combining fast-atom-bombardment mass spectrometry (FAB-MS) and automatic sequencing based on Edman degradation. Direct FAB-MS analysis of the native and reduced enzymatic digests of the protein allowed the assignment of three disulfide bridges out of five, including those involving two adjacent cysteine residues. The remaining two disulfide bridges were assigned by sequencing automatically the peptide clusters purified from the tryptic digest of the native protein.

Incorporation of tandem mass spectrometric detection to the analysis of peptide mixtures by continuous flow fast atom bombardment mass spectrometry

The ability to acquire structurally informative daughter ion spectra for individual peptides undergoing separation and analysis by continuous flow fast atom bombardment (CF FAB) is demonstrated. To illustrate the potential of this methodology, tryptic and chymotryptic digests of the 29-residue peptide glucagon were analyzed by CF FAB using mass spectrometric and tandem mass spectrometric detection in consecutive analyses. Daughter ion spectra were recorded using B/E linked scans for the major hydrolysis products observed by liquid chromatography/mass spectrometry. The peptide mixtures were separated by gradient capillary high-performance liquid chromatography with the FAB matrix being added post-column using a coaxial flow interface between the column and flow probe. The entire effluent (3 microl min(-1)) was sampled by the mass spectrometer. Results obtained using less than 300 pmol of digested glucagon indicated several advantages to tandem mass spectrometric detection including the ability to confirm identities for products of enzymatic digestion and the potential use of this method for tandem sequence analysis of peptide mixtures.

Determination of disulfide bridges in natural and recombinant insect defensin A

The primary-structure comparison of natural insect defensin A from Phormia terranovae and recombinant insect defensin A from Saccharomyces cerevisiae has been accomplished using a combination of Edman degradation and liquid secondary ion mass spectrometry. The natural and recombinant proteins have the same primary structure with identical disulfide-bond designations (formula; see text) as determined from the peptides obtained after thermolysin digestion. The combined use of Edman degradation and mass spectometry allowed the disulfide-bridge structure to be determined with a total of only 40 micrograms (9.9 nmol) natural peptide. Mass spectrometry provides a rapid means of disulfide-bridge verification, requiring not more than 20 micrograms recombinant insect defensin A, which is compatible with use in batch analysis.

Location of disulfide bonds in antithrombin III

Proteolytic digests of human antithrombin III (ATIII) have been analyzed by a combination of reversed-phase high-performance liquid chromatography and fast atom bombardment (FAB) mass spectrometry for disulfide-containing peptides which are diagnostic for disulfide linkages in ATIII. These results indicate that disulfide bonds join Cys 8 and Cys 128, Cys 21 and Cys 95, and Cys 247 and Cys 430. In addition, these results demonstrate that systematic searches of the amino acid sequence of a large protein for segments with molecular weights matching FAB mass spectral information is a viable method for identifying peptides independent of the specificity of the enzyme used to fragment the protein.

Strategies for determination of disulphide bridges in proteins using plasma desorption mass spectrometry

Disulphide bridges have been assigned in three different proteins by locating possible disulphide-linked peptides in enzymic digests of the proteins based on their molecular weight determined by plasma desorption mass spectrometry. Different strategies have been employed including in situ reduction of the nitrocellulose-bound peptides and confirmation of peptide identity by methyl esterification reactions or Edman degradation. The latter was needed for identification of glycosylated disulphide-linked peptides. For insulins cleavage between cysteine residues in close proximity was not possible; but a combination of molecular mass information, enzymic cleavage with two different enzymes and sequence analysis including identification of di-phenylthiohydantoin-cystine could ensure an unambiguous assignment of the disulphide bridges.

Structural characterization by mass spectrometry of native and recombinant human relaxin

Mass spectrometry has played a key role in characterizing the primary structure of native and recombinant relaxin, a peptide hormone that induces ripening of the cervix prior to childbirth. The peptide is composed of two chains, A and B, and is formed from a single-chain prohormone, as is insulin. Aside from conserved cysteines, though, it has little sequence homology with insulin. Due to the small amounts of native peptide initially available (less than 10 pmol), traditional techniques could not provide information on the blocked A-chain sequence, on the carboxyterminal sequences, nor on other possible post-translational modifications. Mass measurements by fast atom bombardment (FAB) were made on reduced human relaxin isolated from corpora lutea. The detection limit by FAB for reduced relaxin was 500 fmol. The B-chain was four amino acids shorter than expected from comparison of the previously known cDNA sequence with homologous rat and porcine sequences. The A-chain, as predicted, was 24 amino acids in length and had a pyroglutamic acid residue on the amino-terminus. The purified samples were homogeneous with no other post-translational modifications. The recombinant relaxin molecule was also extensively characterized by mass spectrometry. In addition to the intact molecule, all tryptic peptides were characterized by FAB. A capillary high-performance liquid chromatography continuous-flow FAB system, developed for high-sensitivity peptide mapping, aided in these analyses. Finally, the three disulfide bonds were shown by tandem mass spectrometry to match those of insulin.

Assignment of disulfide bonds in proteins by partial acid hydrolysis and mass spectrometry

A new method is described for locating disulfide bonds in proteins which cannot be cleaved between half-cystinyl residues by enzymic methods, as is often the case for tightly coiled proteins, or for proteins in which half-cystinyl residues are not separated by residues required for enzymic cleavage. Partial acid hydrolysis of a model protein, hen egg-white lysozyme, produces a mixture of disulfide-containing peptides from which the disulfide connections may be deduced. The usefulness of a combination of HPLC, fast atom bombardment mass spectrometry, and computer-assisted analysis to identify disulfide-containing peptides present in the partial acid hydrolysate of the model protein is demonstrated. Chromatographic fractions of the hydrolysate were analyzed by mass spectrometry before and after chemical reduction of the disulfide bonds to determine the molecular weights of disulfide-containing peptides. Computer-assisted analysis was then used to relate the molecular weights of these peptides to specific segments of the protein from which the disulfide connectivities could be determined. Partial acid hydrolysis of proteins, which is attractive because it proceeds relatively independent of the amino acid sequence and structure, and because disulfide interchange is unlikely to occur in dilute acid, has become practical because disulfide-containing peptides present in complex mixtures can be identified rapidly and definitively by this method.

Identification of disulfide-containing peptides in endocrine tissue extracts by HPLC-electrochemical detection and mass spectrometry

A new procedure to selectively identify disulfide-containing peptides in extracts of biological tissues is described. Disulfide-containing peptides are detected by their UV absorbance and electrochemical (EC) activity after chromatographic separation, and subsequently identified by fast atom bombardment mass spectrometry (FABMS). This combination of fractionation by HPLC and selective detection is attractive because it is rapid, highly specific for disulfide-containing peptides, and applicable to all disulfide-containing peptides that may be present in complex biological mixtures. Useful procedures for applying the method are demonstrated with tissue extracts from bovine pituitary and catfish pancreas. In addition to finding the expected disulfide-containing peptides, evidence for two forms of catfish insulin are presented. The merits of this and other methods used to detect peptides in similar tissue extracts are discussed.

Application of fast atom bombardment mass spectrometry to posttranslational modifications of neuropeptides

FABMS is a powerful and sensitive analytical technique capable of providing structural information unattainable by standard methods of peptide analysis. Many posttranslational modifications are undetectable by other routine analytical methods. In addition, FABMS is capable of providing information regarding posttranslational modifications at levels of peptide comparable to those required for other methods of analysis (10-1000 pmol). FABMS has had the effect on protein structure analysis that structure determination of any neuropeptide might now be considered incomplete without some form of mass spectrometric analysis. Much of the recent explosive increase in the use of mass spectrometry for solving problems in peptide structure analysis can be traced to improvements in methods capable of producing molecular ions from nonvolatile species. With the development of these methods, it can be expected that refinements of existing methods and new ionization methods will continue to increase the mass range and sensitivity available for peptide structure determination. For a brief review of other mass spectrometric methods applicable to peptides, see Delgass and Cooks.

Identification of disulfide-containing peptides by performic acid oxidation and mass spectrometry

In addition to reducing the analysis time, the direct examination of proteolytic digests by fast atom bombardment mass spectrometry (FABMS) greatly extends the information that is available from peptide mapping experiments. Mass spectral data are particularly useful for identifying post-translationally modified peptides. For example, the molecular weight of a disulfide-containing peptide may be used to locate the disulfide bond in the protein from which the peptide was derived. This paper describes a new procedure, which is useful for identifying disulfide-bonded peptides. Peptides are treated with performic acid to modify certain residues and thereby cause a characteristic change in the peptide molecular weight. This change in molecular weight is determined by FABMS and used to help identify peptides. Results for a series of small peptides demonstrate that Cys, Met, and Trp are the only residues that undergo a change in molecular weight under the conditions used here. Furthermore, these changes in molecular weight are diagnostic for each of the residues. Cysteinyl-containing peptides are of particular interest, because their identification is essential for locating disulfide bonds. The molecular weight of a peptide increases by 48 mu for each cysteinyl residue present. This approach is used to identify peptides that contain both cysteinyl and cystinyl residues in the peptic digest of bovine insulin. The method is extended to the analysis of a tryptic digest of cyanogen bromide-treated ribonuclease A. A computer-assisted analysis procedure is used to demonstrate the specificity with which peptide molecular weight is related to specific segments of the protein.(ABSTRACT TRUNCATED AT 250 WORDS)

A determination of the positions of disulphide bonds in Paim I, alpha-amylase inhibitor from Streptomyces corchorushii, using fast atom bombardment mass spectrometry

Paim I, a protein alpha-amylase inhibitor, is a single-chain polypeptide which consists of 73 amino acids, including 4 half-cystine residues. The positions of disulphide bonds in Paim I have been determined with the combination of enzymatic digestion and fast atom bombardment (FAB) mass spectrometry. Denatured Paim I was digested to peptides with Staphylococcus aureus V8 protease. These peptides were subjected to FAB mass spectrometry, with or without isolation by high-performance liquid chromatography. The positions of disulphide bonds in Paim I were determined from the relative molecular masses of the peptides containing a disulphide bond and by the enzyme specificity of S. aureus V8 protease. It is deduced that Paim I has two disulphide bridges at Cys(8)--Cys(24) and Cys(42)--Cys(70).

Characterization by tandem mass spectrometry of structural modifications in proteins

Tandem mass spectrometry can be used to solve a number of protein structural problems that are not amenable to conventional methods for amino acid sequencing. Typical problems that use this approach involve characterization of peptides with blocked amino termini or peptides that have been otherwise posttranslationally processed, such as, by phosphorylation or sulfation. The structure and homogeneity of synthetic peptides can also be evaluated. Since peptides can be selectively characterized in the presence of other peptides or contaminants, the need for extensive purification is reduced or eliminated.