Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Peptide Mapping”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 451 records · Page 25Linked to original sources
PubMedDate not supplied

Peptide mapping of proteins in human body fluids using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

Human body fluids have been rediscovered in the post-genomic era as great sources of biological markers and perhaps particularly as sources of potential protein biomarkers of disease. Analytical tools that allow rapid screening, low sample consumption, and accurate protein identification are of great importance in studies of complex biological samples and clinical diagnosis. Mass spectrometry is today one of the most important analytical tools with applications in a wide variety of fields. One of the fastest growing applications is in proteomics, or the study of protein expression in an organism. Mass spectrometry has been used to find post-translational modifications and to identify key functions of proteins in the human body. In this study, we review the use of human body fluids as sources for clinical markers and present new data that show the ability of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) to identify and characterize proteins in four human body fluids: plasma, cerebrospinal fluid (CSF), saliva, and urine. The body fluids were tryptically digested without any prior separation, purification, or selection, and the digest was introduced into a 9.4 T FTICR mass spectrometer by direct-infusion electrospray ionization (ESI). Even though these samples represent complex biological mixtures, the described method provides information that is comparable with traditional 2D-PAGE data. The sample consumption is extremely low, a few microliters, and the analysis time is only a few minutes. It is, however, evident that the separation of proteins and/or peptides must be included in the methodology, in order to detect low-abundance proteins and other proteins of biological relevance.

Biomarkers↗
PubMed1996

Carboxymethylation of the human estrogen receptor ligand-binding domain-estradiol complex: HPLC/ESMS peptide mapping shows that cysteine 447 does not react with iodoacetic acid.

Experiments were carried out to determine the degree of solvent and reagent accessibility of the cysteines in the ligand-binding domain of the human estrogen receptor (hER LBD). The cysteine residues were alkylated when human ER LBD was present in its ligand (estradiol)-bound conformation. Direct electrospray ionization mass spectrometry (ESMS) as well as liquid chromatography coupled with ESMS, and matrix-assisted laser ionization desorption time-of-flight mass spectrometry were used to determine the location and the yield of the derivatized residues after proteolysis with trypsin. We observed that the cysteine 447 was protected against alkylation under these conditions, whereas cysteines 381, 417, and 530 were fully derivatized.

Alkylation↗
PubMed1992

Extracellular signal-regulated kinases 2 autophosphorylates on a subset of peptides phosphorylated in intact cells in response to insulin and nerve growth factor: analysis by peptide mapping.

The phosphorylation of extracellular signal-regulated kinases 1 and 2 (ERK1 and ERK2) in response to insulin in Rat 1 HIRc B cells and in response to nerve growth factor (NGF) in PC12 cells has been examined. ERK1 and ERK2 are phosphorylated on serine in the absence of the stimuli and additionally on tyrosine and threonine residues after exposure to NGF and insulin. NGF stimulates tyrosine phosphorylation of ERK1 more rapidly than threonine phosphorylation. Two-dimensional phosphopeptide maps of both ERK1 and ERK2 phosphorylated in intact cells treated with NGF or with insulin display the same three predominant phosphopeptides that comigrate when digests of ERK1 and ERK2 are mixed. As many as five additional phosphopeptides are detected under certain conditions. Autophosphorylated recombinant ERK2 also contains the three tryptic phosphopeptides found in ERKs labeled in intact cells. These experiments demonstrate that ERK1 and ERK2 are phosphorylated on related sites in response to two distinct extracellular signals. The data also support the possibility that autophosphorylation may be involved in the activation of the ERKs.

Amino Acid Sequence↗
PubMed1997

Characterization of the structural difference between active and inactive forms of the Ras protein by chemical modification followed by mass spectrometric peptide mapping.

Ras is one of the guanosine triphosphate (GTP) binding proteins that plays a significant role in signaling events of cell growth and differentiation. It can exist in two states: guanosine diphosphate (GDP)-bound from (Ras.GDP; inactive) and GTP-bound form (Ras.GTP; active). This paper discusses the difference in tertiary structure between the active and inactive forms using the combination of chemical modification and mass spectrometry. This difference can be clearly recognized in the presence of a target protein. Raf-1 RBD (Raf-1 Ras-binding domain), as differing glycinamidation of carboxyl groups. It was possible to observe the difference between these two states using several hundred picomoles of sample. While it is true that it is difficult to obtain the whole picture of a protein by the combination of chemical modification and mass spectrometry, it is a promising approach for the characterization of surface structure using very small amounts of sample.

Gas Chromatography-Mass Spectrometry↗
PubMed1999

Peptide mapping of proteins in cerebrospinal fluid utilizing a rapid preparative two-dimensional electrophoretic procedure and matrix-assisted laser desorption/ionization mass spectrometry.

A quick two-step procedure involving liquid phase isoelectric focusing in the Rotofor cell in combination with electroelution in the Mini whole cell gel eluter has been used for purification of proteins from human cerebrospinal fluid (CSF). Fractions, each highly enriched in a single protein band and virtually free of other proteins, were selected for characterization by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOFMS). Six CSF proteins, transferrin, alpha1-acid-glycoprotein, Zn-alpha2-glycoprotein, apolipoprotein A1, apolipoprotein E and beta-trace were identified by MALDI-TOFMS analysis of the tryptic digests. These results demonstrate that the combination of liquid phase IEF and electroelution is a rapid preparative two-dimensional separation which can provide single proteins of high purity, in yields sufficient for characterization by MALDI-TOFMS. Characterization of such brain-specific proteins in CSF will be useful in the investigation of the pathophysiology of different brain disorders.

Cerebrospinal Fluid Proteins↗
PubMed2004

Sequence and peptide map of guinea pig aquaporin 0.

PURPOSE: Hyperbaric oxygen-treated guinea pigs serve as a useful animal model of nuclear cataract. To understand the structure and function of major intrinsic proteins in this model, the primary sequence and major posttranslational modifications to guinea pig aquaporin 0 (AQP0) were determined. METHODS: The cDNA encoding guinea pig AQP0 was amplified by PCR, cloned and sequenced. After protein enrichment from guinea pig lens tissue, the protein sequence and the posttranslational modifications to AQP0 were determined by using combined chemical cleavage, trypsin and pepsin digestion with matrix assisted laser desorption/ionization mass spectrometry or capillary liquid chromatography tandem mass spectrometry. RESULTS: The primary structure of AQP0 was determined from the DNA sequence and the translated sequence confirmed by mass spectrometry. Serine 235 was identified to be the major phosphorylation site. CONCLUSIONS: Significant sequence homology was observed between species including putative regulatory sites of phosphorylation and pH regulation. These data form a foundation of information from which to begin assessing posttranslational modifications in cataract models.

Amino Acid Sequence↗
PubMedDate not supplied

Titania and alumina sol-gel-derived microfluidics enzymatic-reactors for peptide mapping: design, characterization, and performance.

The design and characterization of titania-based and alumina-based Poly(dimethylsiloxane) (PDMS) microfluidics enzymatic-reactors along with their analytical features in coupling with MALDI-TOF and ESI-MS were reported. Microfluidics with microchannel and stainless steel tubing (SST) were fabricated using PDMS casting and O(2)-plasma techniques, and were used for the preparation of an enzymatic-reactor. Plasma oxidation for the PDMS microfluidic system enabled the channel wall of the microfluidics to present a layer of silanol (SiOH) groups. These SiOH groups act as anchors onto the microchannel wall linked covalently with the hydroxyl groups of trypsin-encapsulated sol matrix. As a result, the trypsin-encapsulated gel matrix was anchored onto the wall of the microchannel, and the leakage of gel matrix from the microchannel was effectively prevented. A feature of the microfluidic enzymatic-reactors is the feasibility of performing on-line protein analysis by attached SST electrode and replaceable tip. The success of trypsin encapsulation was investigated by AFM imaging, assay of enzymatic activity, CE detection, and MALDI-TOF and ESI-MS analysis. The lab-made devices provide an excellent extent of digestion even at a fast flow rate of 7.0 microL/min, which affords the very short residence time of ca. 2 s. With the present device, the digestion time was significantly shortened compared to conventional tryptic reaction schemes. In addition, the encapsulated trypsin exhibits increased stability even after continuous use. These features are required for high-throughput protein identification.

Aluminum Oxide↗
PubMed1993

Validation of a peptide map for recombinant porcine growth hormone and application to stability assessment.

A reverse-phase HPLC method for the analysis of tryptic digests of recombinant porcine growth hormone (pGH) has been developed and validated. Digestion was performed at 4 degrees C for a 20-hr period with TPCK-treated trypsin at a 1:20 (w/w) trypsin:pGH ratio. Gradient elution HPLC, using an Aquapore RP300 C8 column, was incorporated for separation of the digestion products and peak identification was carried out by mass spectrometry (MS). The digestion procedure and subsequent chromatography were linear in the initial concentration range of 4.55-45.46 microM (100 to 1000 micrograms/mL) pGH. The variability in the fragment retention times was low and the normalized peak area variability was less than 5% for all but three of the fragments. The utility of the trypsin digestion and chromatography procedures has been demonstrated by assessing chemical changes in pGH induced by incubation at elevated pH. Upon incubation of pGH in 0.2 M Tris buffer at pH 9 (ionic strength adjusted to 0.5 with NaCl) and 37 degrees C over a period of 400 hr, significant degradation in the regions corresponding to the digestion fragments T23-T25 (residues 181-182 linked by a disulfide bond to residues 184-191), T9 (residues 96-108), and T5-T18 (residues 43-64 linked by a disulfide bond to residues 158-166) was observed. The disappearance of the peaks corresponding to fragments T23-T25 and T9 both displayed apparent first-order degradation kinetics over the time period investigated with half-lives of 131 and 154 hr, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1990

Photoaffinity labeling of the two forms of serotonin binding protein: peptide mapping of the binding sites.

Serotonin binding protein (SBP) is a vesicular protein found in neurectoderm-derived cells that store 5-hydroxytryptamine (5-HT, serotonin), such as central and peripheral serotonergic neurons and paraneurons (parafollicular cells of the thyroid). 5-HT is stored as a complex with SBP in vivo. Two forms of the protein are found. These differ in molecular mass: one is 45 kDa and the other 56 kDa. It has been suggested that the 56-kDa form of SBP may be the precursor of the 45-kDa form. To study the relationship between these two proteins, we have used a covalently bound radiolabeled probe to analyze their binding domains. A photoaffinity reagent, N-(4-azido-2-nitrophenyl)-5-hydroxytryptamine (NAP-5-HT), was synthesized and characterized by nuclear magnetic resonance spectroscopy, mass spectra, and UV-visible absorption spectra. A 1 M excess of NAP-5-HT inhibited the binding of [3H]5-HT to SBP by 50%. NAP[3H]5-HT was also synthesized and attached to both high- and low-affinity binding sites on both forms of SBP. The high-affinity constants for 45-kDa and 56-kDa proteins were 0.8 nM and 0.02 nM, respectively, whereas the low-affinity constants were 0.3 microM and 0.15 microM. When the high-affinity site of partially purified SBP was photoaffinity-labeled with the reagent, two covalently labeled proteins (45 kDa and 56 kDa) were found by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Inhibition of the labeling of both proteins by 50% was observed in the presence of a 15-fold molar excess of 5-HT.(ABSTRACT TRUNCATED AT 250 WORDS)

Affinity Labels↗
PubMed2004

Microfluidic enzymatic-reactors for peptide mapping: strategy, characterization, and performance.

The design and characterization of two kinds of poly(dimethylsiloxane)(PDMS) microfluidic enzymatic-reactors along with their analytical utility coupled to MALDI TOF and ESI MS were reported. Microfluidic devices integrated with microchannel and stainless steel tubing (SST) was fabricated using a PDMS casting technique, and was used for the preparation of the enzymatic-reactor. The chemical modification was performed by introducing carboxyl groups to PDMS surface based on ultraviolet graft polymerization of acrylic acid. The covalent and physical immobilization of trypsin was carried out with the use of the activation reagents 1-ethyl-3-(3-dimethyl aminopropyl)carbodiimide(EDC)/N-hydroxysuccinimide (NHS) and a coupling reagent poly(diallyldimethylammonium chloride)(PDDA), respectively. The properties and success of processes of trypsin immobilization were investigated by measuring contact angle, infrared absorption by attenuated total reflection spectra, AFM imaging and electropherograms. An innovative feature of the microfluidic enzymatic-reactors is the feasibility of performing on-line protein analysis by embedded SST electrode and replaceable tip. The lab-made devices provide an excellent extent of digestion of several model proteins even at the fast flow rate of 3.5 microL min(-1) for the EDC/NHS-made device and 0.8 microL min(-1) for the PDDA-made device, which afford very short residence times of 5 s and 20 s, respectively. In addition, the lab-made devices are less susceptive to memory effect and can be used for at least 50 runs in one week without noticeable loss of activity. Moreover, the degraded PDDA-made device can be regenerated by simple treatment of a HCl solution. These features are the most required for microfluidic devices used for protein analysis.

Dimethylpolysiloxanes↗
PubMed1986

Location of antigenic determinants on primary sequences of subunits of nicotinic acetylcholine receptor by peptide mapping.

The binding domains of 28 monoclonal antibodies (mAbs) against the alpha, beta, and delta subunits of the Torpedo acetylcholine receptor were mapped on the primary sequences of these subunits. Small peptide fragments (2000-20,000 daltons) of the purified subunits were obtained by digestion with staphylococcal V8 protease and papain, separated on a discontinuous polyacrylamide gel electrophoretic system, and electroblotted onto diaminophenyl thioether paper. The blots were probed with the various monoclonal antibodies and also with antibodies against carboxy-terminal decapeptides of the alpha, beta, and delta subunits to identify the carboxy-terminal fragments. From inspection of the binding patterns of the various antibodies to the subunits fragments and the molecular weights of these fragments, and by using the carboxy termini of the subunits as reference points, it was possible to deduce the regions on the primary sequence of each subunit in which the antibodies bound and in some cases to order the binding sites within these sequences. mAb 148, which inhibits receptor function by cross-linking receptor molecules on the cytoplasmic side, was mapped to the sequence beta 368-406. The main immunogenic region of the native receptor, which is of pathological importance in the autoimmune disease myasthenia gravis, was mapped by using mAb 210 to within 80 amino acid residues (alpha 46-127). The overall antigenic structure of alpha subunits was examined. Synthetic peptides have been used to locate determinants responsible for 83% of the antibodies in antisera to denatured alpha subunits and 46% of the antibodies to denatured alpha subunits in antisera to intact receptor. Theoretical models of the transmembrane orientation of the subunit polypeptide chains were tested by determining whether mapped monoclonal antibodies bound to the extracellular or intracellular surface of receptor-rich membranes. Our results confirm previous reports that the carboxy termini of the subunits are exposed on the intracellular surface, as is part of the region between a putative channel-forming domain (M5) and a putative membrane-spanning region (M3). However, contrary to current theoretical models, the region between M5 and the putative membrane-spanning sequence M4 also appears to be on the intracellular surface, implying that M4 and M5 are not membrane-spanning domains.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMedDate not supplied

Cyclization of N-terminal S-carbamoylmethylcysteine causing loss of 17 Da from peptides and extra peaks in peptide maps.

Enzymatic digests of proteins S-alkylated with iodoacetamide may contain peptides with N-terminal S-carbamoylmethylcysteine. These can be partly converted to a form with 17 Da lower mass and increased HPLC retention. Proof by synthesis supported by MS/MS and NMR spectroscopy was used to show that N-terminal S-carbamoylmethyl-L-cysteine can cyclize, losing NH3 to form an N-terminal residue of (R)-5-oxoperhydro-1,4-thiazine-3-carboxylic acid. The abbreviation Otc is proposed for the (R)-5-oxoperhydro-1,4-thiazine-3-carbonyl residue. The rate of cyclization is significant in 0.1 M NH4HCO3 at 37 degrees C, with the half-life of the acyclic form being 10-12 h for several peptides tested. This is similar to the rate at which N-terminal pyroglutamate forms from N-terminal glutamine.

Chromatography, High Pressure Liquid↗
PubMed1993

Identification of carbohydrate structures in glycoprotein peptide maps by the use of LC/MS with selected ion extraction with special reference to tissue plasminogen activator and a glycosylation variant produced by site directed mutagenesis.

Electrospray ionization mass spectrometry utilizing a single quadrupole on line with reversed-phase HPLC (LC/MS) enables the characterization of glycoproteins in a relatively short period of time. In this approach the protein is digested with a suitable protease and the peptides are separated by reversed-phase HPLC and detected by electrospray ionization mass spectrometry. The glycopeptides are initially observed as a cluster of negatively sloping ions in a contour plot of data from the LC/MS run (m/z vs retention time) or as a characteristics series of masses at different elution times. The search for a particular glycopeptide is based on previously known carbohydrate structures and on consensus glycosylation sites. Further structural information is obtainable with glycosidase digestion and LC/MS analysis. The mass shifts following glycosidase digestion allow further confirmation of the structure. This approach identifies the site of attachment of two hybrid glycoforms to the T11 tryptic peptide in a reversed-phase tryptic map of recombinant tissue plasminogen activator (rt-PA). Use of selected ion extraction of the LC/MS data files allows one to graphically describe the elution order of closely related glycopeptides. The potential of LC/MS for the characterization of small amounts of unknown glycoproteins is shown by the study of an rt-PA mutant. A new potential site for glycosylation is created by site directed mutagenesis of wild type rt-PA with replacement of a threonine residue with asparagine at residue 103. An examination of a tryptic map shows that the mutant contains two new complex carbohydrate chains. The introduction of the new asparagine proximal to asparagine 117 changes this native high-mannose site in rt-PA to a complex-type glycosylation. This method allows rapid identification of carbohydrate containing peptides and yields useful structural information on microgram amounts of material.

Amino Acid Sequence↗
PubMed2001

B-cell epitopes of the allergen Chi t 1.01: peptide mapping of epitopes recognized by rabbit, murine, and human antibodies.

BACKGROUND: Chi t 1.01, a hemoglobin of the midge Chironomus thummi thummi, is a widespread environmental and occupational allergen. The aim of the present investigation was to identify and compare peptides involved in B-cell epitopes of Chi t 1.01 recognized by 15 human IgE sera, six murine monoclonal antibodies (mAbs), and a polyclonal rabbit antiserum. METHODS: Synthetic peptides 19-21 amino acids long covering the whole Chi t 1.01-sequence were covalently coupled to activated paper disks as well as adsorbed to wells of immunoplates and used for enzyme-linked immunosorbent assay. For fine epitope mapping, we used overlapping synthetic octapeptides with one amino-acid offset. RESULTS: Peptides containing the amino acids 13-17, 23-29, and 40-50 were recognized by three of the mAbs, while three other mAbs reacting with none of the peptides obviously recognized conformational epitopes. Binding sites for rabbit antibodies and for human IgE antibodies were scattered over the whole molecule. The peptide 80-100 seemed to comprise at least one important IgE epitope. Depending on the method of antigen binding to the solid phase, differing results were obtained. CONCLUSIONS: Several linear epitopes in Chi t 1.01 are recognized by human IgE antibodies, by mAbs, and by polyclonal rabbit antibodies. In addition, the results indicate the presence of conformational epitopes.

Amino Acid Sequence↗
PubMedDate not supplied

[Amino acid composition and peptide maps of udder and serum albumins in lactating and nonlactating cows].

Amino acids and peptides of albumin hydrolyzates from the mammary gland and blood serum were studied for lactating and nonlactating (dry, pregnant 1-4.5 and 4.5-9 months) black-and-white cows. Most pronounced difference between the content of certain amino acids of the mammary gland and blood serum albumins are established for lactating cows and least pronounced for nonlactating dry cows. Dactylography detected 55-57 fragments of products resulted from trypsin hydrolysis of the mammary gland and blood serum albumins of the animals under study. Differences are found in the content and mobility of certain peptides.

Albumins↗
PubMed1977

Internal proteins of influenza virus: 35S-methionine peptide maps as genetic markers.

Methods are described for the preparation in vivo of 35S-methionine-labelled influenza viruses, the purifiction of the nucleoprotein (NP) and matrix (M) proteins and the separation of peptides obtained by protease digestion by two-dimensional thin-layer chromatography. The maps of the M proteins of A/Okuda/57(H2N2) and A/Finland/4/74(H3N2) were very similar overall but differed in three peptides. Hence they could be clearly distinguished. Maps of the NP proteins of the same strains showed a greater number of differences. A recombinant strain having the haemagglutinin and neuraminidase of the A/Finland/4/74 parent and the virulence of the A/Okuda/57 parent was shown to have the M and P proteins of A/okuda/57.

Chromosome Mapping↗