Ion-Mobility mass spectrometry as a potential tool to assign disulfide bonds arrangements in peptides with multiple disulfide bridges.

in Analytical Chemistry (2013)

Disulfide bridges play a major role in defining the structural properties of peptides and proteins. However, the determination of the cysteine pairing is still challenging. Peptide sequences are usually ... [more ▼]

Disulfide bridges play a major role in defining the structural properties of peptides and proteins. However, the determination of the cysteine pairing is still challenging. Peptide sequences are usually achieved using MS/MS spectra of the totally reduced unfolded species but the cysteine pairing information is lost. On the other hand, MS/MS experiments performed on native folded species show complex spectra composed of non-classical ions. MS/MS alone does not allow the cysteine pairing nor the full sequence of an unknown peptide to be determined. The major goal of this work is to set up a strategy for the full structural characterization of peptides including disulfide bridges annotation in the sequence. This strategy was developed by combining Ion Mobility Spectrometry (IMS)and Collision Induced Dissociation(CID). It is assumed that the opening of one S-S bridges in a peptide leads to a structural evolution which results in a modification of IMS drift time. In the presence of multiple S-S bridges, the shift in arrival time will depend on which disulfide(s) has (have) been reduced and on the shape adopted by the generated species. Due to specific fragmentations observed for each species, CID experiments performed after the mobility separation could provide not only information on peptide sequence, but also on the localization of the disulfide bridges. To achieve this goal, synthetic peptides containing two disulfides were studied. The openings of the bridges were carried out following different experimental conditions such as reduction, reduction/alkylation or oxidation. Due to disulfide scrambling highlighted with the reduction approaches, oxidation of S-S bonds into cysteic acids appeared to be the best strategy. Cysteines connectivity was then unambiguously determined for the two peptides, without any disulfide scrambling interference. [less ▲]

Characterization of Volatile Organic Compounds from Human Analogue Decomposition Using Thermal Desorption Coupled to Comprehensive Two-Dimensional Gas Chromatography-Time-of-Flight Mass Spectrometry

in Analytical Chemistry (2012), 85

Complex processes of decomposition produce a variety of chemicals as soft tissues, and their component parts are broken down. Among others, these decomposition byproducts include volatile organic ... [more ▼]

Complex processes of decomposition produce a variety of chemicals as soft tissues, and their component parts are broken down. Among others, these decomposition byproducts include volatile organic compounds (VOCs) responsible for the odor of decomposition. Human remains detection (HRD) canines utilize this odor signature to locate human remains during police investigations and recovery missions in the event of a mass disaster. Currently, it is unknown what compounds or combinations of compounds are recognized by the HRD canines. Furthermore, a comprehensive decomposition VOC profile remains elusive. This is likely due to difficulties associated with the nontarget analysis of complex samples. In this study, cadaveric VOCs were collected from the decomposition headspace of pig carcasses and were further analyzed using thermal desorption coupled to comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (TD-GC × GC−TOFMS). Along with an advanced data handling methodology, this approach allowed for enhanced characterization of these complex samples. The additional peak capacity of GC × GC, the spectral deconvolution algorithms applied to unskewed mass spectral data, and the use of a robust data mining strategy generated a characteristic profile of decomposition VOCs across the various stages of soft-tissue decomposition. The profile was comprised of numerous chemical families, particularly alcohols, carboxylic acids, aromatics, and sulfides. Characteristic compounds identified in this study, e.g., 1-butanol, 1-octen-3-ol, 2-and 3-methyl butanoic acid, hexanoic acid, octanal, indole, phenol, benzaldehyde, dimethyl disulfide, and trisulfide, are potential target compounds of decomposition odor. This approach will facilitate the comparison of complex odor profiles and produce a comprehensive VOC profile for decomposition. [less ▲]

Selection and characterization of PCB-binding DNA aptamers.

in Analytical Chemistry (2012), 84(3), 1669-76

Polychlorinated biphenyls (PCBs) are persistent organic pollutants (POPs) that resist natural degradation and bioaccumulate in nature. Combined with their toxicity, this leads them to cause cancer and ... [more ▼]

Polychlorinated biphenyls (PCBs) are persistent organic pollutants (POPs) that resist natural degradation and bioaccumulate in nature. Combined with their toxicity, this leads them to cause cancer and other health hazards. Thus, there is a vital need for rapid and sensitive methods to detect PCB residues in food and in the environment. In this study, PCB-binding DNA aptamers were developed using PCB72 and PCB106 as targets for aptamer selection. Aptamers are synthetic DNA recognition elements which form unique conformations that enable them to bind specifically to their targets. Using in vitro selection techniques and fluorometry, an aptamer that binds with nanomolar affinity to both the PCBs has been developed. It displayed high selectivity to the original target congeners and limited affinity toward other PCB congeners (105, 118, 153, and 169), suggesting general specificity for the basic PCB skeleton with varying affinities for different congeners. This aptamer provides a basis for constructing an affordable, sensitive, and high-throughput assay for the detection of PCBs in food and environmental samples and offers a promising alternative to existing methods of PCB quantitation. This study therefore advances aptamer technology by targeting one of the highly sought-after POPs, for the first time ever recorded. [less ▲]

An analytical pipeline for MALDI in-source decay mass spectrometry imaging

in Analytical Chemistry (2011), 83(15), 6090-6097

In-source decay (ISD) fragmentation as combined with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry allows protein sequencing directly from mass spectra. Acquisition of MALDI-ISD ... [more ▼]

In-source decay (ISD) fragmentation as combined with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry allows protein sequencing directly from mass spectra. Acquisition of MALDI-ISD mass spectra from tissue samples is achieved using an appropriate MALDI matrix, such as 1,5-diaminonaphthalene (DAN). Recent efforts have focused on combining MALDI-ISD with mass spectrometry imaging (MSI) to provide simultaneous sequencing and localization of proteins over a thin tissue surface. Successfully coupling these approaches requires the development of new data analysis tools, but first, investigating the properties of MALDI-ISD as applied to mixtures of protein standards reveals a high sensitivity to the relative protein ionization efficiency. This finding translates to the protein mixtures found in tissues and is used to inform the development of an analytical pipeline for data analysis in MALDI-ISD MS imaging, including software to identify the most pertinent spectra, to sequence protein mixtures, and to generate ion images for comparison with tissue morphology. The ability to simultaneously identify and localize proteins is demonstrated by using the analytical pipeline on three tissue sections from porcine eye lens, resulting in localizations for crystallins and cytochrome c. The variety of protein identifications provided by MALDI-ISD-MSI between tissue sections creates a discovery tool, and the analytical pipeline makes this process more efficient. [less ▲]

MALDI in-source decay of high mass protein isoforms: application to alpha- and beta-tubulin variants.

in Analytical Chemistry (2010), 82(14), 6176-6184

Tubulin is one of the major targets in cancer chemotherapy and the target of more than twenty percent of the cancer chemotherapic agents. The modulation of isoform content has been hypothesized as being a ... [more ▼]

Tubulin is one of the major targets in cancer chemotherapy and the target of more than twenty percent of the cancer chemotherapic agents. The modulation of isoform content has been hypothesized as being a cause of resistance to treatment. Isoform differences lie mostly in the C-terminus part of the protein. Extensive characterization of this polypeptide region is therefore of critical importance. MALDI-TOF fragmentation of tubulin C-terminal domains was tested using synthetic peptides. Then, isotypes from HeLa cells were successfully characterized for the first time by in-source decay (ISD) fragmentation of their C-terminus coupled to a pseudo MS3 technique named T3-sequencing. The fragmentation occurred in-source, preferentially generating yn-series ions. This approach required guanidination for the characterization of the βIII-tubulin C-terminus peptide. This study is, to our knowledge, the first example of reflectron in-source decay (reISD) of the C-terminus of a 50 kDa protein. This potentially occurs via a CID-like mechanism occurring in the MALDI plume. There are now new avenues for top-down characterization of important clinical biomarkers such as βIII-tubulin isotypes, a potential marker of drug resistance and tumor progression. This paper raises the challenge of protein isotypes characterization for early cancer detection and treatment monitoring. [less ▲]

Optimization of Matrix Conditions for the Control of MALDI In-Source Decay of Permethylated Glycans.

in Analytical Chemistry (2010), sous presee

Due to its fastness and its easiness to use, MALDI-MS is currently an analytical tool widely used in glycomic applications. However, the MALDI ionization process could result in the so-called "in-source ... [more ▼]

Due to its fastness and its easiness to use, MALDI-MS is currently an analytical tool widely used in glycomic applications. However, the MALDI ionization process could result in the so-called "in-source decay", or ISD, of analytes, leading to complex spectra. On the other hand, ISD opens the possibility to perform pseudo-MS(3) experiments. This phenomenon must therefore be controlled in order to be used on demand as a supplementary tool for the analysis of permethylated glycans by MALDI mass spectrometry. For this purpose, several matrices were tested and MALDI imaging was used to determine optimal conditions promoting or, inversely, avoiding ISD of permethylated glycans. 2,5-DHB was shown to be a versatile matrix allowing one to induce or prevent ISD according to the location of laser shots. Inversely, it was shown that 9-aminoacridine forms homogeneous spots and avoids completely ISD. This matrix would therefore be suitable for automatic analysis. [less ▲]

A Simple Method to Determine Electrospray Response Factors of Noncovalent Complexes

in Analytical Chemistry (2009), 81(16), 6708-6715

The quantitative study of noncovalent complexes by electrospray mass spectrometry requires the determination of the relative response of each species. The method proposed here to determine the ... [more ▼]

The quantitative study of noncovalent complexes by electrospray mass spectrometry requires the determination of the relative response of each species. The method proposed here to determine the electrospray response factors is based on the use of (1) an internal standard and (2) the mass balance equation applied to one binding partner M, for which different complexes MxLy are detected in the electrospray mass spectra. A set of experiments providing various ratios between the complexes (e.g. different ligand concentrations in a titration experiment or different time points in a kinetics experiment) is used to generate a set of independent linear equations that can be solved using simple matrix algebra to find the response factors of each MxLy complex relative to that of the internal standard. The response factors can then be used to determine equilibrium dissociation constants or for the quantitative monitoring of reaction kinetics. The first is illustrated with a study of DNA-ligand complexes, where we show that neither minor groove binding nor intercalation dramatically affects the DNA response factor. The second is illustrated with a study of the association kinetics of the telomeric G-quadruplex dGGG(TTAGGG)3 with its complementary strand, where the response factors allow correcting for the relative response of the quadruplex and the long duplex and obtaining reproducible association rate constants independently of the source tuning potentials. [less ▲]

Atomic force microscopy investigation of the morphology and the biological activity of protein-modified surfaces for bio- and immunosensors

in Analytical Chemistry (2007), 79(17), 6488-6495

With the purpose of developing biosensors, the reliable proof of the biological activity of two new sensor systems was obtained by atomic force microscopy (AFM) in both the imaging and the single-molecule ... [more ▼]

With the purpose of developing biosensors, the reliable proof of the biological activity of two new sensor systems was obtained by atomic force microscopy (AFM) in both the imaging and the single-molecule force spectroscopy modes. Antigens or antibodies of pharmacological interest were grafted onto self-assembled monolayers of thiols on gold, and AFM imaging demonstrated that the grafting process produced homogeneous submonolayers of isolated proteins. The analysis of the morphology of the surfaces at the different functionalization steps allowed evaluating the protein grafting density and showed that the recognition of complementary species present in the surrounding solution occurred. Single-molecule force spectroscopy experiments between the sensing surfaces and AFM probes, onto which the complementary species were grafted, enabled a direct and rapid test of the biological activity of the sensors by investigating the interaction occurring at the level of one single ligand-receptor bond. Ellipsometry and surface plasmon resonance allowed further characterization of the sensor surfaces and confirmed that the biological recognition took place. [less ▲]

Electron photodetachment dissociation of DNA polyanions in a quadrupole ion trap mass spectrometer

in Analytical Chemistry (2006), 78(18), 6564-6572

We hereby explore the effects of irradiating DNA polyanions stored in a quadrupole ion trap mass spectrometer with an optical parametric oscillator laser between 250 and 285 nm. We studied DNA 6-20-mer ... [more ▼]

We hereby explore the effects of irradiating DNA polyanions stored in a quadrupole ion trap mass spectrometer with an optical parametric oscillator laser between 250 and 285 nm. We studied DNA 6-20-mer single strands and 12-base pair double strands. In all cases, laser irradiation causes electron detachment from the multiply charged DNA anions. Electron photodetachment efficiency directly depends on the number of guanines in the strand, and maximum efficiency is observed between 260 and 275 nm. Subsequent collision-induced dissociation (CID) of the radical anions produced by electron photodetachment results in extensive fragmentation. In addition to neutral losses, a large number of fragments from the w, d, a*, and z* ion series are obtained, contrasting with the w and (a-base) ion series observed in regular CID. The major advantage of this technique, coined electron photodetachment dissociation (EPD) is the absence of internal fragments, combined with good sequence coverage. EPD is therefore a highly promising approach for de novo sequencing of oligonucleotides. EPD of nucleic acids is also expected to give specific radical-induced strand cleavages, with conservation of other fragile bonds, including noncovalent bonds. In effect, preliminary results on a DNA hairpin and on double strands suggest that EPD could also be used to probe intra- and intermolecular interactions in nucleic acids. [less ▲]

Measurement of selected polybrominated diphenyl ethers, polybrominated and polychlorinated biphenyls, and organochlorine pesticides in human serum and milk using comprehensive two-dimensional gas chromatography isotope dilution time-of-flight mass spectrometry

in Analytical Chemistry (2004), 76(21), 6313-6320

A new method using comprehensive two-dimensional gas chromatography and isotope dilution time-of-flight mass spectrometry (GC x GC-IDTOFMS) for the simultaneous measurement of selected polychlorinated ... [more ▼]

A new method using comprehensive two-dimensional gas chromatography and isotope dilution time-of-flight mass spectrometry (GC x GC-IDTOFMS) for the simultaneous measurement of selected polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), and brominated flame retardants is presented. In contrast to the reference methods based on classical GC/MS, a single injection of the extract containing all compounds of interest results in accurate identification and quantification. Using GC x GC ensures the chromatographic separation of most compounds, and TOFMS allows mass spectral deconvolution of coeluting compounds as well as the use of C-13-labeled internal standards for quantification. Isotope ratio measurements of the most intense ions for both native and labels ensure the required specificity. The use of this new method with an automated sample preparation procedure developed at the Centers for Disease Control and Prevention (CDC) for the analysis of human serum and milk compared favorably to conventional isotope-dilution one-dimensional gas chromatography-high-resolution mass spectrometty (GC-IDHRMS) for the different human serum and milk pools tested. The instrumental detection limits ranged between 0.5 pg/muL and 10 pg/muL and the method detection limits ranged between I and 15 pg/muL (N = 59 analytes). The reproducibility of the method was almost as good as with GC-IDHRMS, the relative standard deviations ranging between 1 and 11% for OCPs measured in human serum. OCP, PBDE, and PCB levels measured using the two methods were highly correlated, and the deviations between the two methods were below 20% for most analytes with concentrations above 1 ng/g milk lipids. [less ▲]