Characterization of a phosphorylated peptide and peptoid and peptoid-peptide hybrids by mass spectrometry

Nano-electrospray tandem mass spectrometry (nano-ES-MS/MS) was used to record collision-induced dissociation (CID) spectra of a set of peptoid-peptide hybrids and the complete peptoid derived from the phosphopeptide Ac-pTyr-Glu-Thr-Leu-NH(2) (1). The presence of B and Y'-type fragment ions in the tandem mass spectra of the protonated molecular ions [M + H](+) allowed confirmation of sequence similar to mass spectrometric sequence analysis in peptides. In the isomeric peptoid compounds studied, one or several amino acid residues were replaced by peptoid residues (N-substituted glycine residues), which resulted in characteristic tandem mass spectra with differently increased relative abundances of Y'-and B-type fragment ions. The increment of a particular Y'-ion was directly correlated to the position of a peptoid residue present. In addition to these increased peak intensities, other characteristic peaks were also observed compared with the spectrum of reference peptide 1. When a peptoid phosphotyrosine was incorporated, the presence of this residue was apparent from the occurrence of a relatively intense peak at m/z 187 representing the positively charged side-chain of phosphotyrosine, which was almost absent in the spectrum of the reference peptide 1. Since the threonine side-chain had to be translated into the homo peptoid analog this substitution was apparent from the presence of [M + H](+) and fragment ions 14 mass units higher than observed in the spectrum of the reference phosphopeptide 1. The presence of an NLeu peptoid residue could be confirmed by the specific fragmentation of the immonium ion showing an intense peak in its tandem mass spectrum at m/z 57, which results from the loss of an neutral imine molecule leading to a positively charged [C(4)H(9)](+) ion. By means of these mass spectrometric characteristics, all isomeric peptoid compounds could be distinguished from each other and characterized. The methods used appear to be very useful in future studies of peptoids and peptoid-peptide hybrids.     

Generation of a basis set for the calculation of molecular magnetic properties

Completeness conditions have been applied in the theory of molecular magnetic properties to determine the best gauge for a given basis set. They can similarly be used to optimise the basis for a fixed gauge origin. Test results indicate that the gauge dependence of the calculated properties can be significantly reduced in this way.     

Pepto: An expert system for automatic peak assignment of two-dimensional nuclear magnetic resonance spectra of proteins

Two-dimensional Nuclear Magnetic Resonance (2DFTNMR) is presently the most powerful tool to determine protein structures in solution. Peak assignment (an interpretation of the two-dimensional spectra that leads to the individuation of pairs of Hydrogen atoms that are involved in an NOE peak) is a cornerstone of such use of 2DFTNMR. Manual peak assignment of a protein often requires months of work by a specialized equipe. An automation of this task could speed up the protein study process, or alternatively allow to study previously unmanageable proteins. This article describes PEPTO, an expert system for the interpretation of sets of 2DFTNMR spectra on proteins. The present version of the program deals with spectra obtained from NOESY and COSY experiments. Tests of PEPTO on simulated spectra of five proteins with known assignments are also described and dicussed.     

Development of a dedicated peptide tandem mass spectral library for conservation science

In recent years, the use of liquid chromatography tandem mass spectrometry (LC–MS/MS) on tryptic digests of cultural heritage objects has attracted much attention. It allows for unambiguous identification of peptides and proteins, and even in complex mixtures species-specific identification becomes feasible with minimal sample consumption. Determination of the peptides is commonly based on theoretical cleavage of known protein sequences and on comparison of the expected peptide fragments with those found in the MS/MS spectra. In this approach, complex computer programs, such as Mascot, perform well identifying known proteins, but fail when protein sequences are unknown or incomplete. Often, when trying to distinguish evolutionarily well preserved collagens of different species, Mascot lacks the required specificity. Complementary and often more accurate information on the proteins can be obtained using a reference library of MS/MS spectra of species-specific peptides. Therefore, a library dedicated to various sources of proteins in works of art was set up, with an initial focus on collagen rich materials. This paper discusses the construction and the advantages of this spectral library for conservation science, and its application on a number of samples from historical works of art.     

Tuning peptoid secondary structure with pentafluoroaromatic functionality: a new design paradigm for the construction of discretely folded peptoid structures

Peptoids, or oligomers of N-substituted glycine, are an important class of non-native polymers whose close structural similarity to natural alpha-peptides and ease of synthesis offer significant advantages for the study of biomolecular interactions and the development of biomimetics. Peptoids that are N-substituted with alpha-chiral aromatic side chains have been shown to adopt either helical or "threaded loop" conformations, depending upon solvent and oligomer length. Elucidation of the factors that impact peptoid conformation is essential for the development of general rules for the design of peptoids with discrete and novel structures. Here, we report the first study of the effects of pentafluoroaromatic functionality on the conformational profiles of peptoids. This work was enabled by the synthesis of a new, alpha-chiral amine building block, (S)-1-(pentafluorophenyl)ethylamine (S-2), which was found to be highly compatible with peptoid synthesis (delivering (S)-N-(1-(pentafluorophenyl)ethyl)glycine oligomers). The incorporation of this fluorinated monomer unit allowed us to probe both the potential for pi-stacking interactions along the faces of peptoid helices and the role of side chain electrostatics in peptoid folding. A series of homo- and heteropeptoids derived from S-2 and non-fluorinated, alpha-chiral aromatic amide side chains were synthesized and characterized by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. Enhancement of pi-stacking by quadrupolar interactions did not appear to play a significant role in stabilizing the conformations of heteropeptoids with alternating fluorinated and non-fluorinated side chains. However, incorporation of (S)-N-(1-(pentafluorophenyl)ethyl)glycine monomers enforced helicity in peptoids that typically exhibit threaded loop conformations. Moreover, we found that the incorporation of a single (S)-N-(1-(pentafluorophenyl)ethyl)glycine monomer could be used to selectively promote looped or helical structure in this important peptoid class by tuning the electronics of nearby heteroatoms. The strategic installation of this monomer unit represents a new approach for the manipulation of canonical peptoid structure and the construction of novel peptoid architectures.     

Quantitative mass spectrometry by internal standardisation using a single focusing mass spectrometer and the peak switching facilities of a peak matching device

A quantitative mass spectrometric method for the determination of small sample sizes is described. This method is applicable to both single and double focusing mass spectrometers, if a conventional peak matching device or any other suitable peak switching facility is attached to the instrument. In the conventional integrated ion current technique a constant pressure of the vapour of hepta-cosafluoro-tri-n-butylamine or a comparable standard is maintained in the analyser. By contrast to this in our method the calibrating substance is evaporated together with the sample from the same capillary of the probe. Substances with a similar chemical structure (in most cases higher or lower homologues) can be used as internal standards. Since thermal effects in the probe and sensitivity changes of the mass spectrometer during the flash evaporation of the substances affect the integrated ion current curves of both sample and standard equally, the ratio of the curves is largely independent of these parameters. With a single focusing mass spectrometer (CH-5 Varian, MAT) reproducibilities of the determinations were within ±10%, with substance amounts in the range between 10^?10 to 10^?11 mole.     

Automatic peak assignment and visualisation of copolymer mass spectrometry data using the ‘genetic algorithm’

Copolymer analysis is vitally important as the materials have a wide variety of applications due to their tunable properties. Processing mass spectrometry data for copolymer samples can be very complex due to the increase in the number of species when the polymer chains are formed by two or more monomeric units. In this paper, we describe the use of the genetic algorithm for automated peak assignment of copolymers synthesised by a variety of polymerisation methods. We find that in using this method we are able to easily assign copolymer spectra in a few minutes and visualise them into heat maps. These heat maps allow us to look qualitatively at the distribution of the chains, by showing how they alter with different polymerisation techniques, and by changing the initial copolymer composition. This methodology is simple to use and requires little user input, which makes it well suited for use by less expert users. The data outputted by the automatic assignment may also allow for more complex data processing in the future.     

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. Received: 2 December 1996 / Revised: 17 April 1997 / Accepted: 21 April 1997     

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.     

Vibrational assignment of the spectral data and thermodynamic properties of 2-chloro-4-fluorobenzophenone using DFT quantum chemical calculations

The FT-Raman (3500-100 cm⁻¹) and FT-IR (4000-450 cm⁻¹) spectra of 2-chloro-4-fluorobenzophenone were recorded in the solid phase. Density functional theory calculations with B3LYP/6-31G (d, p) basis set was used to determine the ground state molecular geometries (bond lengths and bond angles), harmonic vibrational frequencies, infrared intensities and Raman activities of this compound. Potential energy distributions (PEDs) and normal modes, for the spectral data computed at B3LYP/6-31G (d, p) level, have also been obtained from force-field calculations. The wavenumbers found after scaling of the force field showed very good agreement with the experimentally determined values. A comparison of the theoretical spectra and experimental FT-IR and FT-Raman spectra of the title molecule has been made and full vibrational assignments of the observed spectra have been proposed. On the basis of vibrational analyses, the thermodynamic properties of title compound at different temperatures have been calculated.     

Software utilities for the interpretation of mass spectrometric data of glycoconjugates: application to glycosphingolipids of human serum

Glycosphingolipids (GSLs) are major components of the outer leaflet of the cell membrane. These lipids are involved in many cell surface events and show disease‐related expression changes. GSLs could thus serve as useful targets for biomarker discovery. The GSL structure is characterized by two entities: a hydrophilic glycan and a hydrophobic ceramide moiety. Both components exhibit numerous structural variations, the combination of which results in a large diversity of GSL structures that can potentially exist. Mass spectrometry (MS) is a powerful tool for high‐throughput analysis of GSL expression analysis and structural elucidation. Yet, the assignment of GSL structures using MS data is tedious and demands highly specialized expertise. SysBioWare, a software platform developed for MS data evaluation in glycomics, was here applied for the MS analysis of human serum GSLs. The program was tuned to provide automated compositional assignment, supporting a variety of glycan and ceramide structures. Upon in silico fragmentation, the masses of predicted ions arising from cleavages in the glycan as well as the ceramide moiety were calculated, thus enabling structural characterization of both entities. Validation of proposed structures was achieved by matching in silico calculated fragment ions with those of experimental MS/MS data. These results indicate that SysBioWare can facilitate data interpretation and, furthermore, help the user to deal with large sets of data by supporting management of MS and non‐MS data. SysBioWare has the potential to be a powerful tool for high‐throughput glycosphingolipidomics in clinical applications. Copyright © 2010 John Wiley & Sons, Ltd.     

Facile assignment of sequence ions of a peptide labelled with 18O at the carboxyl terminus.

The combination of collision-induced dissociation (CID) and linked-scan analysis was used for analysing the sequence ions from the precursor ion of a peptide, which had been labelled with 18O at its carboxyl terminus (C-terminus) using 40 atom % H2 18O. The CID and linked-scan mass spectrum of the labelled peptide gave two series of sequence-ion signals: the one, originating from the C-terminus of the labelled peptide, showed a doublet signal due to the part-incorporation of 18O into the carboxyl group at the C-terminus, while the other, originating from the amino terminus (N-terminus), has the natural isotopic ion distribution. From the distribution of the isotopic ions in a single CID spectrum, the sequence ions containing the C-terminus could be readily differentiated from those containing the N-terminus, allowing the facile assignment of sequence ions to the amino-acid sequence of a peptide by CID and linked-scan analysis. This method was successfully applied to determination of the amino-acid sequence of the light-chain of mouse anti-porphyrin monoclonal antibody.     

Peak clustering in two-dimensional gas chromatography with mass spectrometric detection based on theoretical calculation of two-dimensional peak shapes: the 2DAid approach

A method is presented to facilitate the non-target analysis of data obtained in temperature-programmed comprehensive two-dimensional (2D) gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-ToF-MS). One main difficulty of GC×GC data analysis is that each peak is usually modulated several times and therefore appears as a series of peaks (or peaklets) in the one-dimensionally recorded data. The proposed method, 2DAid, uses basic chromatographic laws to calculate the theoretical shape of a 2D peak (a cluster of peaklets originating from the same analyte) in order to define the area in which the peaklets of each individual compound can be expected to show up. Based on analyte-identity information obtained by means of mass spectral library searching, the individual peaklets are then combined into a single 2D peak. The method is applied, amongst others, to a complex mixture containing 362 analytes. It is demonstrated that the 2D peak shapes can be accurately predicted and that clustering and further processing can reduce the final peak list to a manageable size.     

Improvement of an automatic HPLC system for nitropolycyclic aromatic hydrocarbons: removal of an interfering peak and increase in the number of analytes.

An automatic HPLC system for analyzing nitropolycyclic aromatic hydrocarbons (NPAHs, nitroarenes) in airborne particulates was previously described (Anal. Chim. Acta, 2001, 445, 20). Some problems with this system were that it generated a peak originating from an ascorbic acid solution that elutes at a retention time close to that of 1,6-dinitropyrene (DNP), and that it was able to analyze only 1,3-, 1,6-, 1,8-DNPs and 1-nitropyrene (I-NP). Here, we describe an improved system that effectively removes the interfering peak by introducing an ODS column just after the pump for the ascorbic acid solution, and which is capable of analyzing several additional compounds (2-, 4-NPs, 2-nitrofluorene. 6-nitrochrysene, 7-nitrobenz[a]anthracene, 3-nitroperylene and 6-nitrobenzo[a]pyrene etc.). The improved sensitivities were achieved by concentrating the compounds in a benzene-ethanol extract from airborne particulates, by increasing the loading time of the sample solution from 20 to 38 min, and by increasing the flow rate of an ascorbic acid solution from 1.3 to 1.8 mL/min.     

On the falsity of a claimed exact analytic formula for the calculation of Voigt spectral line profile

We provide a proof of the falsity of a recently claimed “exact analytic formula” for the calculation of the Voigt line profile [Jian He and Qingguo Zhang, An exact calculation of the Voigt spectral line profile in spectroscopy, J. Opt. A: Pure Appl. Opt. 9 (2007) 565–568]. The subsequent findings and claims based on this erroneous representation of the Voigt line profile should not be considered any further.