MS-Pep: a computer program for the interpretation of mass spectra of peptide libraries

Electrospray mass spectrometry (ESI-MS) is an established method for the qualitative analysis of synthetic peptide libraries and combinatorial mixtures or collections of small organic compounds. However, the calculation of the mass distribution of even small peptide mixtures is a time-consuming and error-proned task. Therefore, the computer program MS-Pep has been developed, which calculates the masses of expected peptides, byproducts and the mass distributions of peptide libraries.     

Characterisation of combinatorial libraries of mucin-2 antigen peptides by high-resolution mass spectrometry

An epitope motif, TX(1)TX(2)T, of mucin-2 glycoprotein was identified by means of a mucin-2-specific monoclonal antibody, mAb 994, raised against a synthetic mucin-derived 15-mer peptide conjugate. For determination of the epitope sequence recognised with highest affinity by mAb 994, a combinatorial approach was applied using the portioning-mixing technique excluding Cys. Antibody binding of libraries was most profound when Gln was at the X(1) position. Analytical characterisation of the TQTX(2)T library was conducted by amino acid analysis and matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) and electrospray ionisation Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometric methods. Control libraries were prepared by mixing 19 individual peptides corresponding to the TQTX(2)T sequence. Thus, mixtures of 6, 10 and 19 pentapeptides were analysed and compared with the combinatorial mixture. MALDI-TOFMS was able to detect only partially the components in the 6- and 10-member mixtures, but failed to characterise a more complex 19-member mixture. In contrast, ESI-FTICRMS resolved all mixtures of higher complexity and provided direct identification at monoisotopic resolution, such as for a peptide library containing 'isobaric' lysine and glutamine (Delta m = 0.0364 Da). The results of this study suggest that ESI-FTICRMS is a powerful tool for characterisation of combinatorial peptide libraries of higher complexity.     

PNA encoding (PNA=peptide nucleic acid): from solution-based libraries to organized microarrays

Microarray-based technologies have attracted attention in chemical biology by virtue of their miniaturized format, which is well suited to probe ligand-protein interactions or investigate enzymatic activity in complex biological mixtures. A number of research groups have reported the preparation of surfaces on microarrays with specific functional groups to chemoselectively attach small molecules from libraries. We have developed an alternative method whereby libraries are encoded with peptide nucleic acid (PNA), such that libraries which exist as mixtures in solution self-assemble into an organized microarray through hybridization to produce readily available DNA arrays. This allows libraries synthesized by split and mix methods to be decoded in a single step. An asset of this method compared to direct spotting is that libraries can be used in solution for bioassays prior to self-assembly into the microarray format.     

Rapidly measuring reactivities of carboxylic acids to generate equireactive building block mixtures: a spectrometric assay

The relative reactivity of building blocks is critical for a successful preparation of combinatorial libraries. Here, we present a method for measuring the reactivity of carboxylic acid building blocks in amide-forming reactions. The method involves competitive reactions between a reference and test acid and a tetraphenylporphyrin reaction partner with four reactive sites. Relative reactivities are calculated on the basis of the distribution of substituted porphyrins found in MALDI-TOF mass spectra. Reactivities thus determined were used to prepare reactivity-adjusted building block mixtures. These were reacted with amino-terminal oligonucleotide and peptide scaffolds on solid support, generating small libraries suitable for spectrometrically monitored selection experiments (SMOSE). The rate of building block "drop outs" that fail to couple as expected was not substantially lowered by acquiring spectra from two reactions, performed with different ratios of building blocks, where the effect of a given substituent on the desorption/ionization yield of the porphyrin can be eliminated. Instead, coupling building blocks of similar size together or employing N-hydroxysuccinimide esters rather than activating with a "uronium salt" were found to improve the quality of libraries generated via competitive reactions.     

Interaction of the Hepatitis A peptide VP3(110–121) with lipid mono and bilayer models of cellular membranes

 The surface activity of HAV-VP3(110–121) peptide was studied at different concentrations in an aqueous solution. Saturation was reached at 0.62 μM concentration. The ability of the peptide to insert into monolayers of CL, SA, DPPC, DPPC/5% CL and DPPC/5% SA was also performed. Mixed mono-layers composed of this peptide and the lipid mixtures were also studied as far as the miscibility of the two components is concerned. The mixed monolayers showing small negative deviations from ideality. The values of excess free energy of mixing (ΔG ^E _M) suggest that the energy associated to the miscibility process is almost non-significant except for a 0.2 molar fraction of DPPC/SA and 0.6 molar fraction of DPPC/CL. The peptide has an expanding effect upon the monolayers but due to its amphoteric character this interaction is not dependent on the electrical charge of the lipids. In fluorescence studies, the peptide showed some degree of interaction with the lipid polar heads, but no interactions were detected with its alkylchains. This results show that after incubation with DPPC/5% CL and DPPC/5% SA liposomes the peptide remains in the outer part of the bilayers. Received: 20 January 1997 Accepted: 28 May 1997     

Probing peptide libraries from Conus achatinus using mass spectrometry and cDNA sequencing: identification of delta and omega-conotoxins

The peptide library present in the venom of the piscivorous marine snail Conus achatinus has been probed using a combination of mass spectrometry and cDNA sequencing methods. Matrix assisted laser desorption ionization mass spectrometry (MALDI-MS) analysis, before and following global reduction/alkylation of peptide mixtures, permits the rapid classification of individual components on the basis of the number of disulfide bonds. Mass fingerprinting and the reverse phase HPLC retention times permit a further deconvolution of the library in terms of peptide size and hydrophobicity. Sequencing of cDNA derived using O-superfamily specific primers yielded five complete conotoxin precursor sequences, ranging in polypeptide length from 75-87 residues containing six Cys residues at the C-terminus. Sequence analysis permits classification of the five putative mature peptides (Ac 6.1 to Ac 6.5) as delta, omega, and omega-like conotoxins. The presence of these predicted peptides in crude venom was established by direct matrix assisted laser desorption ionization tandem mass spectrometry (MALDI-MS/MS) sequencing following trypsin digestion of the peptide mixture after global reduction/alkylation. The determination of partial peptide sequences and comparison with the predicted sequences resulted in the identification of four of the five predicted conotoxins. The characterization of posttranslationally modified analogs, which are hydroxylated at proline or amidated at the C-terminus is also demonstrated. Crude venom analysis should prove powerful in studying both inter- and intra-species variation in peptide libraries.     

Use of four-factorial design in ion-selective potentiometry for analysis of multi-ionic solutions

Even with small selectivity of electrodes the application of multi-factorial design produces good results for complex ion mixtures. Carrying out serial analyses with this method, the time for the preparation of specimens is shortened and the accuracy of the determination is increased. The electrode selectivity is characterized using regression equations and an interference level diagram. A graphical representation of data is suggested taking into account the dependence of response on the number of interfering cations. Received: 17 June 1997 / Revised: 3 November 1997 / Accepted: 8 November 1997     

Global transformation of OBOC combinatorial peptide libraries into OBOC polyamine and small molecule libraries

In "one-bead-one-compound" (OBOC) combinatorial chemistry, a compound-bead library with hundreds of thousands to millions of diversities can be rapidly generated such that each bead displays only one chemical entity. The highly efficient "libraries-from-libraries" approach involves the global transformation of a peptide library into many small molecule solution-phase mixture libraries, but this approach has never been successfully applied to OBOC libraries. Here we report a novel approach that allows us to combine these two enabling technologies to efficiently generate OBOC encoded small molecule bead libraries. By using a topologically segregated bilayer bead and a "ladder-synthesis" method, we can prepare peptide libraries with the peptide on the bead surface and a series of peptide ladders in the bead interior. Various global transformation reactions can then be employed to transform the starting peptide library into a variety of peptidomimetic libraries. During the transformation reactions, the peptide ladders in the bead interior are also transformed in a predictable manner. As a result, individual compound bead can be decoded by analyzing the hydrogen fluoride-released encoding tags with matrix-assisted laser desorption ionization Fourier transform mass spectrometry. Using this novel approach, a random encoded dipeptide library was prepared and subsequently transformed into polyamine and poly- N-acetylamine sublibraries. Random beads isolated from these sublibraries were reliably decoded.     

Identification of affinity ligands from peptide libraries and their applications

Summary Combinatorial peptide libraries may be screened to identify novel ligands for use in the affinity purification of proteins. Strategies for the screening of libraries are summarized and characterization of the interaction of a particular target protein (fibrinogen) with a ligand (FLLVPL) is described. Factors important for implementing an affinity resin in a production environment are highlighted. Presented at: Affinity Chromatography Conference, Cambridge, UK, July 1–3, 1997.     

Platinum speciation with hyphenated techniques: high performance liquid chromatography and capillary electrophoresis on-line coupled to an inductively coupled plasma-mass spectrometer – application to aqueous extracts from a platinum treated soil

1. An on-line hyphenation of reversed phase high-performance liquid chromatography (RP-HPLC) with inductively coupled plasma-mass spectrometry (ICP-MS) is applied, using an ultrasonic nebuliser combined with a membrane desolvator as the interface. Thus, organic solvents (e.g. methanol, hexane) or gradients (e.g. methanol/water) as well as aqueous NaHCO₃/NaCl mixtures can be directly used without influence on the plasma. The high resolution power of HPLC enables the separation of Pt-species, whereas ICP-MS is taken for element specific detection with low detection limits. 2. Additionally, a powerful on-line coupling of capillary electrophoresis (CE) and ICP-MS [1, 2] was used for platinum speciation in parallel. With these two methods, independent from each other, first characterisation is achieved about the nature of Pt species formed by interaction with a soil. Aqueous extracts of a clay-like humic soil, treated with a Pt contaminated tunnel dust and Pt model compounds [3] were examined to elucidate transformation processes of Pt-species in a soil. Received: 19 February 1997 / Revised: 15 April 1997 / Accepted: 18 April 1997     

Platinum speciation with hyphenated techniques: high performance liquid chromatography and capillary electrophoresis on-line coupled to an inductively coupled plasma-mass spectrometer – application to aqueous extracts from a platinum treated soil

1. An on-line hyphenation of reversed phase high-performance liquid chromatography (RP-HPLC) with inductively coupled plasma-mass spectrometry (ICP-MS) is applied, using an ultrasonic nebuliser combined with a membrane desolvator as the interface. Thus, organic solvents (e.g. methanol, hexane) or gradients (e.g. methanol/water) as well as aqueous NaHCO₃/NaCl mixtures can be directly used without influence on the plasma. The high resolution power of HPLC enables the separation of Pt-species, whereas ICP-MS is taken for element specific detection with low detection limits. 2. Additionally, a powerful on-line coupling of capillary electrophoresis (CE) and ICP-MS [1, 2] was used for platinum speciation in parallel. With these two methods, independent from each other, first characterisation is achieved about the nature of Pt species formed by interaction with a soil. Aqueous extracts of a clay-like humic soil, treated with a Pt contaminated tunnel dust and Pt model compounds [3] were examined to elucidate transformation processes of Pt-species in a soil. Received: 19 February 1997 / Revised: 15 April 1997 / Accepted: 18 April 1997     

Recent developments in protein–ligand affinity mass spectrometry

This review provides an overview of direct and indirect technologies to screen protein–ligand interactions with mass spectrometry. These technologies have as a key feature the selection or affinity purification of ligands in mixtures prior to detection. Specific fields of interest for these technologies are metabolic profiling of bioactive metabolites, natural extract screening, and the screening of libraries for bioactives, such as parallel synthesis libraries and small combichem libraries. The review addresses the principles of each of the methods discussed, with a focus on developments in recent years, and the applicability of the methods to lead generation and development in drug discovery.     

Quantitative analysis of complex peptide mixtures using FTMS and differential mass spectrometry

Label-free LC-MS profiling is a powerful quantitative proteomic method to study relative peptide abundances between two or more biological samples. Here we demonstrate the use of a previously described comparative LC-MS method, differential mass spectrometry (dMS), to analyze high-resolution Fourier transform mass spectrometry (FTMS) data for detection and quantification of known peptide differences between two sets of complex mixtures. Six standard peptides were spiked into a processed plasma background at fixed ratios from 1.25:1 to 4:1 to make two sets of samples. The resulting mixtures were analyzed by microcapillary LC-FTMS and dMS. dMS successfully identified five out of the six peptides as statistically significant differences (p 相似文献   

Multilayer adsorption with variable thickness at solid-liquid interfaces

 The multilayer adsorption on the solid/liquid interface in binary mixtures was studied by adsorption space filling with constant and variable layer thickness. Adsorption from benzene/n-heptane mixtures was examined on hydrophilic and hydro-phobic surfaces. The free enthalpy of adsorption, Δ₂₁ G=f (x ₁), was calculated from the adsorption excess isotherm by integration of the Gibbs equation. Supposing that the free enthalpy is mainly due to adsorption in the first layer, the composition of this layer can be calculated from the Δ₂₁ G=f (x ₁) function. It was established that the adsorption layer thickness in benzene/heptane mixtures increases significantly with increasing benzene content. This statement was supported by X-ray diffraction on hydrophobic clay minerals. Received: 2 April 1997 Accepted: 10 June 1997     

Field method for the micro-quantitative determination of tetracycline in human urine

A simple, fast and sensitive titrimetric method has been developed for the determination of tetracycline hydrochloride in human urine using m-dinitrobenzene as color agent and Dowex 1 × 8 as detection medium. Received: 26 February 1997 / Revised: 23 April 1997 / Accepted: 29. April 1997     

Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation.

We have demonstrated the use of per-methyl esterification of peptides for relative quantification of proteins between two mixtures of proteins and automated de novo sequence derivation on the same dataset. Protein mixtures for comparison were digested to peptides and resultant peptides methylated using either d0- or d3-methanol. Methyl esterification of peptides converted carboxylic acids, such as are present on the side chains of aspartic and glutamic acid as well as the carboxyl terminus, to their corresponding methyl esters. The separate d0- and d3-methylated peptide mixtures were combined and the mixture subjected to microcapillary high performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS). Parent proteins of methylated peptides were identified by correlative database searching of peptide tandem mass spectra. Ratios of proteins in the two original mixtures could be calculated by normalization of the area under the curve for identical charge states of d0- to d3-methylated peptides. An algorithm was developed that derived, without intervention, peptide sequence de novo by comparison of tandem mass spectra of d0- and d3-peptide methyl esters.     

Discerning matrix-cluster peaks in matrix-assisted laser desorption/ionization time-of-flight mass spectra of dilute peptide mixtures

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry is widely used for the analysis of peptide mixtures such as those resulting from protein digestion. Among several useful peptide matrices, alpha-cyano-4-hydroxycinnamic acid (4-HCCA) appears to be the most popular. This matrix does not generally give matrix-cluster peaks at the mass region covered by enzyme-digested peptides (i.e., m/z above approximately 500). However, when an analyte mixture is very dilute and/or the sample contains a large amount of salts, ion peaks from matrix clusters can be quite intense, compared to peptide peaks. This matrix-cluster interference becomes more pronounced as the amount of analyte decreases. In this paper, a simple scheme for matrix-cluster identification is reported. It is shown that matrix-cluster formation follows a systematic pattern, although the relative intensities of these cluster ions cannot be predicted. Discerning the matrix-cluster peaks from the peptide peaks is found to be critical in analyzing dilute peptide mixtures with both conventional and microspot MALDI-TOF techniques.     

Selective enrichment and ultrasensitive identification of trace peptides in proteome analysis using transient capillary isotachophoresis/zone electrophoresis coupled with nano-ESI-MS

Besides the complexity in protein samples of biological origin, probably the greatest challenge presently facing comprehensive proteome analysis is related to the large variation of protein relative abundances (>6 orders of magnitude), having potential biological significance in mammalian systems. As demonstrated in this work, transient capillary ITP/zone electrophoresis (CITP/CZE) provides selective analyte enrichment through electrokinetic stacking and extremely high resolving power toward protein and peptide mixtures. The result of the CITP process is that major components may be diluted, but trace compounds are concentrated. The on-column transition of CITP to CZE minimizes additional band broadening while providing superior analyte resolution. Online coupling of transient CITP/CZE with nano-ESI-MS allows ultrasensitive detection of trace peptides at levels of subnanomolar concentration or subfemtomole mass in complex peptide mixtures. More importantly, selective enrichment of trace peptides enables the identification and sequence analysis of low-abundance peptides co-migrated with highly abundant species at a concentration ratio of 1:500,000. The combined CITP/CZE-nano-ESI-MS system is demonstrated to be at least one to two orders of magnitude more sensitive than that attained in conventional electrophoretic and chromatographic-based proteome technologies over a wide dynamic concentration range, potentially allowing comprehensive analysis of protein profiles within a small cell population and limited tissue samples using conventional mass spectrometers. Furthermore, the speed of CITP/CZE separation and the lack of column equilibration in CITP/CZE not only improve the throughput of proteome analysis, but also facilitate its seamless integration with other separation technologies in a multidimensional protein identification platform.     

The use of proteotypic peptide libraries for protein identification

This paper describes an algorithm to apply proteotypic peptide sequence libraries to protein identifications performed using tandem mass spectrometry (MS/MS). Proteotypic peptides are those peptides in a protein sequence that are most likely to be confidently observed by current MS-based proteomics methods. Libraries of proteotypic peptide sequences were compiled from the Global Proteome Machine Database for Homo sapiens and Saccharomyces cerevisiae model species proteomes. These libraries were used to scan through collections of tandem mass spectra to discover which proteins were represented by the data sets, followed by detailed analysis of the spectra with the full protein sequences corresponding to the discovered proteotypic peptides. This algorithm (Proteotypic Peptide Profiling, or P3) resulted in sequence-to-spectrum matches comparable to those obtained by conventional protein identification algorithms using only full protein sequences, with a 20-fold reduction in the time required to perform the identification calculations. The proteotypic peptide libraries, the open source code for the implementation of the search algorithm and a website for using the software have been made freely available. Approximately 4% of the residues in the H. sapiens proteome were required in the proteotypic peptide library to successfully identify proteins.     

Principal component analysis of mass spectra of peptides generated from the tryptic digestion of protein mixtures

Principal component analysis (PCA) has been used to analyse mass spectral peptide profiles obtained from the enzymatic digestion of standard protein mixtures. Scores and loadings plots clearly revealed peptide fragments that differentiated one protein mixture from another. Peptide map search results identified with a high degree of certainty any additional proteins in these mixtures. As a proof-of-concept this methodology was applied to hepatic protein mixtures obtained from rats treated with two hepatotoxic compounds: methapyriline and SB-219994. Liver proteins were extracted, pre-separated by one-dimensional polyacrylamide gel electrophoresis, subjected to tryptic digestion and analysed by mass spectrometry. Two up-regulated proteins, glutathione S-transferase with methapyrilene and peroxisomal bifunctional enzyme with SB-219994, were identified in this manner.