Sequence database searches via de novo peptide sequencing by tandem mass spectrometry

A method is described for searching protein sequence databases using tandem mass spectra of tryptic peptides. The approach uses a de novo sequencing algorithm to derive a short list of possible sequence candidates which serve as query sequences in a subsequent homology-based database search routine. The sequencing algorithm employs a graph theory approach similar to previously described sequencing programs. In addition, amino acid composition, peptide sequence tags and incomplete or ambiguous Edman sequence data can be used to aid in the sequence determinations. Although sequencing of peptides from tandem mass spectra is possible, one of the frequently encountered difficulties is that several alternative sequences can be deduced from one spectrum. Most of the alternative sequences, however, are sufficiently similar for a homology-based sequence database search to be possible. Unfortunately, the available protein sequence database search algorithms (e.g. Blast or FASTA) require a single unambiguous sequence as input. Here we describe how the publicly available FASTA computer program was modified in order to search protein databases more effectively in spite of the ambiguities intrinsic in de novo peptide sequencing algorithms.     

Determination of calcium binding sites in gas-phase small peptides by tandem mass spectrometry

Low-energy (LE) and high-energy (HE) collisionally activated decompositions (CAD) of calcium/peptide complexes of the form [M - H + Ca]+ and [M + Ca]2+ reflect the site of calcium binding in various gas-phase peptides that are models of the calcium binding site III of rabbit skeletal troponin C. The Ca2+ binding sites involve an aspartic acid, glutamic acid, and asparagine, which are in the metal-binding loops of calcium-binding proteins. Both fast atom bombardment (FAB) and electrospray ionization (ESI) were used to generate the metal/peptide complexes. When submitted to LE CAD, ESI-produced Ca2+/peptide complexes undergo fragmentations that are controlled by Ca2+ binding and provide information on the Ca2+ binding site. The LE CAD spectra are simple, indicating that Ca2+ binding involves specific oxygen ligands including acidic side chains and that only a few low-energy fragmentation channels exist. The HE CAD spectra of FAB-produced Ca2+/peptide complexes are more complex, owing to the introduction of high internal energy into the precursor ion. Interactions of the other alkaline-earth metal ions Mg2+ and Ba2+ with these peptides reveal that the ligand preferences of these metal ions are slightly different than those of Ca2+.     

Analysis of testosterone esters by tandem mass spectrometry

OBJECTIVE: To assess the efficacy of external cephalic version, including safety, cost-benefit analysis, and impact on the cesarean delivery rate. DATA SOURCES: A MEDLINE search was conducted to identify all articles published in English between 1980-1991 on external cephalic version. References were also cross-checked for all reports. METHODS OF STUDY SELECTION: We reviewed only those articles providing sufficiently detailed data to determine actual numbers of subjects. In cases of duplicate results, only the latest publication was used. Rates of successful version, cesarean delivery, and fetal and maternal complications were presented. DATA EXTRACTION AND SYNTHESIS: Among the United States trials, the success rate was approximately 65% (range 48-77%), and once version succeeded, almost all the fetuses stayed in the vertex position until birth. Among those in whom external version was performed, the mean cesarean delivery rate was 37%, compared with 83% in controls (P < .001). External version would also save 12.3% of the costs of delivering breech patients overall. CONCLUSION: External cephalic version is safe and cost-effective. It substantially reduces the cesarean delivery rate among breech presentations, decreases the risk related to breech delivery, and avoids cesarean delivery in subsequent pregnancies. However, external version will not have a major impact on the high overall cesarean birth rate.     

Mapping of phosphorylation sites of gel-isolated proteins by nanoelectrospray tandem mass spectrometry: potentials and limitations

Precursor ion scans have proven to be extremely useful for the characterization of unseparated peptide mixtures. In conjunction with the nanoelectrospray source, precursor ion scans provide a sensitive tool for the detection of posttranslationally modified peptides and have been used to determine phosphorylation sites of proteins digested in solution. In this report, we extend our previous work to the determination of protein phosphorylation sites of gel-isolated proteins. The in-gel digestion procedure developed in our laboratory for protein microsequencing was found to be suitable for phosphorylation mapping as well. The risk of losing hydrophilic peptides in the desalting step was decreased by using column packing material designed for the purification of oligonucleotides and by adjusting the pH conditions to the needs of phosphopeptide analysis. With this method, the tryptic phosphopeptides of beta-casein were detected after in-gel digestion at a sensitivity of 250 fmol of protein applied to the gel. The phosphorylation sites of two other proteins, Src-delta U and Op18, have similarly been mapped. Subpicomole to low-picomole amounts of protein starting material are needed in general, although we and others have reported attomole sensitivity for the detection of model phosphopeptides using precursor ion scans. This indicates that the success in determining phosphorylation sites depends crucially on the digestion, extraction, and detection efficiency for individual phosphopeptides.     

Cloning of a human UDP-N-acetyl-alpha-D-Galactosamine:polypeptide N-acetylgalactosaminyltransferase that complements other GalNAc-transferases in complete O-glycosylation of the MUC1 tandem repeat

A fourth human UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase, designated GalNAc-T4, was cloned and expressed. The genomic organization of GalNAc-T4 is distinct from GalNAc-T1, -T2, and -T3, which contain multiple coding exons, in that the coding region is contained in a single exon. GalNAc-T4 was placed at human chromosome 12q21.3-q22 by in situ hybridization and linkage analysis. GalNAc-T4 expressed in Sf9 cells or in a stably transfected Chinese hamster ovary cell line exhibited a unique acceptor substrate specificity. GalNAc-T4 transferred GalNAc to two sites in the MUC1 tandem repeat sequence (Ser in GVTSA and Thr in PDTR) using a 24-mer glycopeptide with GalNAc residues attached at sites utilized by GalNAc-T1, -T2, and -T3 (TAPPAHGVTSAPDTRPAPGSTAPPA, GalNAc attachment sites underlined). Furthermore, GalNAc-T4 showed the best kinetic properties with an O-glycosylation site in the P-selectin glycoprotein ligand-1 molecule. Northern analysis of human organs revealed a wide expression pattern. Immunohistology with a monoclonal antibody showed the expected Golgi-like localization in salivary glands. A single base polymorphism, G1516A (Val to Ile), was identified (allele frequency 34%). The function of GalNAc-T4 complements other GalNAc-transferases in O-glycosylation of MUC1 showing that glycosylation of MUC1 is a highly ordered process and changes in the repertoire or topology of GalNAc-transferases will result in altered pattern of O-glycan attachments.     

Direct analysis of protein mixtures by tandem mass spectrometry

Methods to identify proteins contained in mixtures are described. The approach uses microcolumn liquid chromatography and automated tandem mass spectrometry in conjunction with protein and nucleotide database searching algorithms. This approach is applied to the identification of proteins obtained by immunoprecipitation reactions, interaction with a GST protein fusion products and interaction with a macromolecular complex.     

Multiple-stage tandem mass spectrometry for structural characterization of saponins

Nanoelectrospray ion trap multiple-stage tandem mass spectrometry was applied to characterize saponins present in HPLC fractions from Quil A, a commercially available bark extract. An analytical strategy was developed based on recognition of carbohydrate sequence ions as well as glycosidic ring-cross ions formed by gamma-hydrogen rearrangements and successive retro-Diels-Alder fragmentations. These ions could be used for the determination of several glycosidic linkages, ring sizes, and positions of acyl groups. The presence of an acyl group on a monosaccharide residue facilitated the determination of the substitution pattern, due to the induction of ring-cross fragmentation. Deuteriomethylation resulted in a more extended set of ring-cross ions, thus allowing determination of additional glycosidic linkages. An analysis typically consumed 200 ng of sample and a total of 1-4 h for measurement and interpretation. The applied method is attractive as a pre-NMR analysis, especially because it resulted rapidly in an overall idea of the structure even when starting from scratch. The multiple-stage tandem approach enabled structural determination of saponins to a more detailed level than achievable with current single-stage tandem mass spectrometry.     

Complete structural elucidation of triacylglycerols by tandem sector mass spectrometry

We developed a method to elucidate the complete structure of triacylglycerols by means of high-energy collisional activation tandem mass spectrometry (MS/MS). Both ESI- and FAB-produced [M + NH4]+ and [M + met.]+ ions (where met. = Li, Na, and Cs) of triacylglycerols undergo charge-remote and charge-driven fragmentations. We emphasize the study of fragment ions from ESI-produced [M + NH4]+ and [M + Na]+ ions and FAB-produced [M + Na]+ ions. ESI-produced [M + NH4]+ ions fragment to produce four types of ions, [M + NH4 - RnCOONH4]+, [RnCO + 128]+, [RnCO + 74]+, and RnCO+ ions, from which the carbon number and the degree of unsaturation of each acyl group are obtained. In addition, three series of ions are produced by charge-remote fragmentations (CRFs), and analysis of their patterns gives the position and the number of double bonds on the acyl groups. Information about the position of each acyl group on the glycerol backbone, however, is not provided by collisionally activated dissociation of [M + NH4]+ ions. On the other hand, ESI- and FAB-produced [M + Na]+ ions fragment to form eight types of ions (named A-J ions) that, like those produced by CRF, are highly structurally informative. The absence of certain series members also carries useful structural information. Interpretation of these patterns enables one to obtain the number of carbons, degrees of unsaturation, and location of double bonds, as well as the positions of acyl groups on the glycerol backbone.     

Characterization of bacterial phospholipids by electrospray ionization tandem mass spectrometry

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

Differentiation between selected pairs of tripeptide diastereomers by tandem mass spectrometry on a hybrid tandem mass spectrometer

Two cases of transposition of the great arteries (TGA) with posterior aorta are reported. The first was submitted to the Senning procedure with good outcome; the other had the diagnosis of double outlet right ventricle with severe pulmonary stenosis, and a Blalock-Taussig shunt was accomplished for hypoxic crisis. The patient died 11 days after surgery and the necropsy demonstrated TGA with posterior aorta. In both cases there was a sub-pulmonary infundibulum. The presence of ventricular septal defects allowed aortic-mitral fibrous continuity, a finding previously described in anatomical reports. Clinical and angiographic aspects are discussed.     

Specific metal-oligonucleotide binding studied by high resolution tandem mass spectrometry

BACKGROUND: Benign reactive lymphoid hyperplasia is an uncommon uveal tumor. Misdiagnosis may lead to unnecessary enucleations. Clinical evaluation alone is usually not sufficient to diagnose this tumor. OBJECTIVE: To evaluate the utility of standardized echography in the recognition of this disease. METHODS: Retrospective review of the medical and echographic records of 6 patients with choroidal involvement of benign reactive lymphoid hyperplasia. RESULTS: Extraocular episcleral lymphoid nodules were present in 5 of the 6 patients and were usually seen as a late manifestation of the disease. Two patients had repeated echography after treatment of the tumor and showed marked regression of the episcleral nodules. CONCLUSIONS: A combination of clinical and echographic findings can assist in the accurate diagnosis of this rare uveal tumor. The presence of episcleral nodules on standardized echography supports the diagnosis.     

Detection and identification of carcinogen-peptide adducts by nanoelectrospray tandem mass spectrometry

Leukoencephalopathy syndromes encompass a variety of neurologic abnormalities that affect cerebral white matter. Known etiologies include malignant hypertension, eclampsia, renal failure, CNS infection, and drug therapy with cyclosporine, tacrolimus (FK506) and interferon-alpha. Symptoms vary according to sites of involvement; they include altered mentation, visual disturbances, focal neurologic signs, and seizures. Characteristic radiologic findings are hypodense areas without contrast enhancement on CT and an increased T2 signal on MRI. The hypodense areas are often symmetric. The clinical symptoms and neuroimaging abnormalities are often reversible with treatment of the underlying condition or removal of the offending drug. We describe a patient with non-Hodgkin's lymphoma treated with conventional cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) chemotherapy and high-dose steroids who developed a rapidly progressive fatal leukoencephalopathy. Her neurologic symptoms and findings on CT are consistent with reported cases of leukoencephalopathy; however, in this instance, the syndrome was not reversible and was ultimately fatal. None of the previously described etiologies could be demonstrated in association with the patient's illness. There are no prior reports of fatal leukoencephalopathy in adult patients treated with standard-dose CHOP. We believe the concurrent immunosuppression from chemotherapy and high-dose steroids resulted in this patient's fatal complication.     

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

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

Identification of synaptic metabolites of dynorphin A (1-8) by electrospray ionization and tandem mass spectrometry

Synaptic metabolism of the endogenous opioid octapeptide dynorphin (Dyn) A (1-8) (Tyr-Gly-Gly-Phe-Leu-Arg-Arg-Ile) was studied in vitro upon its incubation with synaptosomes and with synaptosomal plasma membranes isolated from rat brain tissue. Electrospray ionization (ESI) and tandem mass spectromety were performed using an ion trap instrument, and afforded the identification of Dyn A (2-8), Dyn A (1-6) and leucine enkephalin [Dyn A (1-5)] as major metabolites. Preliminary quantitative data on the kinetics of Dyn A (1-8) degradation and metabolite formation was obtained by size-exclusion chromatography/ESI tandem mass spectrometry, and revealed an apparent involvement of several enzymes in the metabolism upon incubation with synaptosomes. Predominant formation of Dyn A (1-6) was observed with the synaptosomal plasma membranes.     

Determination of nifedipine in human plasma by flow-injection tandem mass spectrometry

Using the murine teratocarcinoma cell line F9 we investigated the influence of serum stimulation and cisplatin treatment on the p53, CK2, MDM2 levels. Both treatments led to an increase of p53, though with different kinetics; the other proteins investigated were not affected. We present direct evidence by immunoprecipitation for an association of protein kinase CK2 holoenzyme (alpha2beta2), p53, and the ribosomal protein L5. The results suggest complexes between the CK2 holoenzyme and p53 but also p53/CKbeta complexes. Furthermore we provide evidence for the existence of high molecular mass complexes of CK2 in vivo. This is the first evidence that, under physiological conditions, protein kinase CK2 does not exist solely as a heterotetramer, but predominantly in association with other proteins.     

Application of tandem mass spectrometry for the analysis of long-chain carboxylic acids

The application of MS-MS for the analysis of long-chain carboxylic acids and their esters has proved enormously successful but expensive. It is discussed mainly on basis of results obtained with different instruments with lesser attention to principles of the method, which have been adequately reviewed elsewhere. The use of electrospray ionization (ESI) has greatly increased the sensitivity of the method and has permitted assay of total lipid extracts. The combination of HPLC with electrospray and single quadrupole mass spectrometry, LC-ESI-CID-MS, rivals the triple quadrupole MS-MS application in many instances at considerably lower cost. However, LC-ESI-MS-MS remains the most desirable system at the present time for lipid ester analyses.     

Direct sequencing of neuropeptides in biological tissue by MALDI-PSD mass spectrometry

Dissected tissue pieces of the pituitary pars intermedia from the amphibian Xenopus laevis was directly subjected to matrix-assisted laser desorption/ionization (MALDI) mass analysis. The obtained MALDI peptide profile revealed both previously known and unexpected processing products of the proopiomelanocortin gene. Mass spectrometric peptide sequencing of a few of these neuropeptides was performed by employing MALDI combined with postsource decay (PSD) fragment ion mass analysis. The potential of MALDI-PSD for sequence analysis of peptides directly from unfractionated tissue samples was examined for the first time for the known desacetyl-alpha-MSH-NH2 and the presumed vasotocin neuropeptide. In addition, the sequence of an unknown peptide which was present in the pars intermedia tissue sample at mass 1392.7 u was determined. The MALDI-PSD mass spectrum of precursor ion 1392.7 u contained sufficient structural information to uniquely identify the sequence by searching protein sequence databases. The determined amino acid sequence corresponds to the vasotocin peptide with a C-terminal extension of Gly-Lys-Arg ("vasotocinyl-GKR"), indicating incomplete processing of the vasotocin precursor protein in the pituitary pars intermediate of X. laevis. Both vasotocin and vasotocinyl-GKR are nonlinear peptides containing a disulfide (S-S) bridge between two cysteine residues. Interpretation of the spectra of these two peptides reveals three different forms of characteristic fragment ions of the cysteine side chain: peptide-CH2-SH (regular mass of Cys-containing fragment ions), peptide-CH2-S-SH (regular mass + 32 u) and peptide = CH2 (regular mass -34 u) due to cleavage on either side of the sulfur atoms.     

Selective detection and sequencing of phosphopeptides at the femtomole level by mass spectrometry

We describe a new procedure that enables selective detection and sequencing of Ser-, Thr-, and Tyr-phosphopeptides at the low femtomole level in protein digests. Radiolabeling with 32P is not required, nor is prior chromatographic separation of the peptide mixture. One to two microliters of the unfractionated protein digest is infused at basic pH into an electrospray mass spectrometer at a flow rate of 20-40 nl/min using an ultra-low flow sprayer. A precursor-ion scan of m/z 79 (PO-3) produces a mass spectrum containing only the molecular ions of the phosphopeptides that are present in the sample. In cases where the protein sequence is known, the peptide molecular weights obtained are often sufficient to identify the specific sequences that are phosphorylated. If the protein sequence is not known, tandem MS with collision-induced dissociation of phosphopeptide precursor-ions may be used to obtain the amino acid sequences including the site(s) of phosphorylation. We demonstrate that phosphopeptides may be selectively detected using as little as 3 fmol of a 10 fmol/microl solution and that sequence information for a phosphopeptide in the mixture may be obtained using as little as 3 femtomole of the same solution. In addition, we show that the stoichiometry of phosphorylation at specific sites may be estimated from the ratio of the ion signals for the respective forms of the peptides observed in the normal full-scan mass spectra of the digest. These procedures are illustrated here to identify and sequence phosphopeptides from alpha-casein, a milk-derived protein possessing up to nine phosphorylation-sites. Numerous MS and tandem MS experiments were carried out on a single, 250 fmol/microl loading of the phosphoprotein digest. Phosphopeptides derived from an unexpected variant of the protein were also observed.     

Characterization of polar urinary metabolites by ionspray tandem mass spectrometry following dansylation

The present report illustrates the application of dansyl chloride coupled with ion spray tandem mass spectrometry (IS-MS/MS) in identifying polar urinary metabolites. In the course of the metabolism studies of a drug that is currently in development, the urine from rats and dogs was collected following oral administration of radiolabelled compound. Urinary metabolic profiles of the rat and dog indicated the presence of four major peaks and one major peak, respectively, in the radiochromatogram. Since all attempts to identify the peaks by conventional MS/MS techniques failed, the metabolites were isolated by fraction collection and dansylated. Derivatization of the metabolites resulted in the formation of more hydrophobic, readily ionizable species which were more sensitive in IS-MS/MS analysis than the underivatized metabolites. Examination of the molecular ions and the product ion mass spectra of these derivatives revealed the structures of all the urinary metabolites. The metabolites in the rat and the dog were 4-hydroxyphenylpiperazine glucuronide (M1), 1,4-dihydroxyphenyl glucuronide (M2), 1,4-dihydroxyphenyl sulfate (M3) and phenylpiperazine (M4). Thus, derivatization with dansyl chloride in conjunction with tandem mass spectrometry is a useful tool in identifying polar urinary metabolites.