Processing MALDI Mass Spectra to Improve Mass Spectral Direct Tissue Analysis

Profiling and imaging biological specimens using MALDI mass spectrometry has significant potential to contribute to our understanding and diagnosis of disease. The technique is efficient and high-throughput providing a wealth of data about the biological state of the sample from a very simple and direct experiment. However, in order for these techniques to be put to use for clinical purposes, the approaches used to process and analyze the data must improve. This study examines some of the existing tools to baseline subtract, normalize, align, and remove spectral noise for MALDI data, comparing the advantages of each. A preferred workflow is presented that can be easily implemented for data in ASCII format. The advantages of using such an approach are discussed for both molecular profiling and imaging mass spectrometry.     

Protein partitioning in thermoseparating systems of a charged hydrophobically modified ethylene oxide polymer

The phase behavior of a thermoseparating cationic hydrophobically modified ethylene oxide polymer (HM-EO) containing tertiary amines has been investigated at different pH, salt and sodium dodecyl sulfate (SDS) concentrations, in order to find a water/HM-EO two-phase system suitable for protein partitioning. The used polymer forms micellar aggregates that can be charged. By changing pH and SDS concentrations the netcharge of the SDS/HM-EO aggregate can be shifted from positive to negative. Bovine serum albumin (BSA) and lysozyme were partitioned in the thermoseparated two-phase systems of the cationic polymer at different pH, salt and SDS concentrations. The dominant attractive interactions between the polymer aggregates and the studied proteins were shown to be of electrostatic (Coulomb) nature rather than hydrophobic interaction. At low ionic strength the positively charged polymeric aggregates attracted negatively charged BSA and repelled positively charged lysozyme. Upon addition of SDS the negatively charged aggregates attracted lysozyme and repelled BSA. Thus, it was possible to direct proteins with different charges to the polymeric phase and redirect them to a polymer-depleted phase by changing the netcharge of the polymeric aggregates. The effect of different salts on the partitioning of BSA in a system of slightly positively charged HM-EO was studied. NaCl and KBr have a significant effect on driving the BSA to the polymer-depleted phase, whereas KF and K2SO4 have a smaller effect on the partitioning. The cloud point temperature of the charged polymer decreased upon addition of SDS near the isoelectric molar ratio of SDS to polymer and also upon salt addition. In the latter case the decrease was smaller than expected from model calculations based on Flory-Huggins theory, which were performed for a charged thermoseparating polymer at different charges and salt concentrations.     

MS2Assign,automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides

In a previous report (Young et al., Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5802-5806), we provided a proof-of-principle for fold recognition of proteins using a homobifunctional amine-specific chemical crosslinking reagent in combination with mass spectrometry analysis and homology modeling. In this current work, we propose a systematic nomenclature to describe the types of peptides that are generated after proteolysis of crosslinked proteins, their fragmentation by tandem mass spectrometry, and an automated algorithm for MS/MS spectral assignment called "MS2Assign." Several examples are provided from crosslinked peptides and proteins including HIV-integrase, cytochrome c, ribonuclease A, myoglobin, cytidine 5-monophosphate N-acetylneuraminic acid synthetase, and the peptide thymopentin. Tandem mass spectra were obtained from various crosslinked peptides using post source decay MALDI-TOF and collision induced dissociation on a quadrupole-TOF instrument, along with their automated interpretation using MS2Assign. A variety of possible outcomes are described and categorized according to the number of modified lysines and/or peptide chains involved, as well as the presence of singly modified (dead-end) lysine residues. In addition, the proteolysis and chromatographic conditions necessary for optimized crosslinked peptide recovery are presented.     

On the semi-quantification of polycyclic aromatic hydrocarbons in contaminated soil by an enzyme-linked immunosorbent assay kit

Polycyclic aromatic hydrocarbons (PAHs) are of environmental concern, for instance when found in contaminated soils at sites where industrial activities have occurred. For efficient screening of such soils, the commercially available enzyme-linked immunosorbent assay (ELISA) kit, the PAH RIS^c® soil test, can be used. However, the site-specific performance may vary due to differences in soil properties and contamination profiles. Hence, in this study we have examined various contributing factors to the total ELISA measurements uncertainties. These factors include contributions from co-extracted (non-target) compounds, the extraction efficiency and differences in cross-reactivity among the target analytes. Reference values were obtained through pressurized liquid extraction (PLE) and gas chromatography coupled to mass spectrometry (GC-MS) analysis. The results showed that the ELISA does not seem to respond to non-target compounds in the soil extracts to any large extent. Furthermore, high molecular weight PAHs were found to be more efficiently extracted with PLE than with methanol agitation, which is used for ELISA. If this, and the cross-reactivity of the individual PAHs, were taken into consideration, the ELISA and GC-MS results were in good agreement.     

Photodissociation of diiodomethane in acetonitrile solution and fragment recombination into iso-diiodomethane studied with ab initio molecular dynamics simulations

Series of hydrates of the most stable glycine-H+/2H2+ in the gas phase are presented at the B3LYP level. The results show that only the amino hydrogens and hydroxyl hydrogens can be monohydrated for the glycine-H+, and the amino hydrogens are preferred. The H6(O4) of glycine-2H2+ is the best site for a water molecule to attach, i.e., the corresponding hydrate is the most stable one among its isomers. Calculations reveal that the binding energies of hydrated hydrogens decrease relative to their counterparts in the isolated glycine-H+/2H2+ complexes and they are positive values and without proton transfer except those of monohydrated glycine-2H2+ complexes with the combination modes of H3O+...(glycine-H+). The complex H3O+...(glycine-H+) is formed by the combination of a H2O molecule and one hydroxyl-site proton of glycine-2H2+, and with the proton transfer to H2O. Here the interaction between the proton of H3O+ and the glycine-H+ mainly depends on an electronic one instead of an initial covalent one of the isolated glycine-2H2+. The generation of the bond between the H3O+ and the glycine-H+ makes the energy of the complex higher than the energy sum of its two separated species (or two reactants of the complex), just like the case of M+...(glycine-H+) bond (M = Li,Na). The observation can explain satisfactorily why the combinations of both a proton and an alkali ion or two alkali ions to a glycine molecule can make the corresponding complex hold reservation energy bond(s), while the combination of two protons and a glycine in our previous work cannot [H. Ai et al., J. Chem. Phys. 117, 7593 (2002)]. For the glycine-2H2+, monohydration at the any site of its amino hydrogens can make the binding strength of any other neighboring proton (hydrogens) stronger relative to its counterpart in the isolated glycine-2H2+. Further hydration, especially at the site of either of hydroxyl hydrogens, would disfavor the reservation energy of the system.     

C-C versus C-H activation and versus agostic C-C interaction controlled by electron density at the metal center

Based on the PCN ligand 2, a remarkable degree of control over C-C versus C-H bond activation and versus formation of an agostic C-C complex was demonstrated by choice of cationic [Rh(CO)(n)(C(2)H(4))(2-n)] (n=0, 1, 2) precursors. Whereas reaction of 2 with [Rh(C(2)H(4))(2)(solv)(n)]BF(4) results in exclusive C-C bond activation to yield product 5, reaction with the dicarbonyl precursor [Rh(CO)(2)(solv)(n)]BF(4) leads to formation of the C-H activated complex 9. The latter process is promoted by intramolecular deprotonation of the C-H bond by the hemilabile amine arm of the PCN ligand. The mixed monocarbonyl monoethylene Rh species [Rh(CO)(C(2)H(4))]BF(4) reacts with the PCN ligand 2 to give an agostic complex 7. The C-C activated complex 5 is easily converted to the C-H activated one (9) by reaction with CO; the reaction proceeds by a unique sequence of 1,2-metal-to-carbon methyl shift, agostic interaction, and C-H activation processes. Similarly, the C-C agostic complex 7 is converted to the same C-H activated product 9 by treatment with CO.