Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry

A comparative analysis of protein identification for a total of 162 protein spots separated by two-dimensional gel electrophoresis from two fully sequenced archaea, Methanococcus jannaschii and Pyrococcus furiosus, using MALDI-TOF peptide mass mapping (PMM) and mu LC-MS/MS is presented. 100% of the gel spots analyzed were successfully matched to the predicted proteins in the two corresponding open reading frame databases by mu LC-MS/MS while 97% of them were identified by MALDI-TOF PMM. The high success rate from the PMM resulted from sample desalting/concentrating with ZipTip(C18) and optimization of several PMM search parameters including a 25 ppm average mass tolerance and the application of two different protein molecular weight search windows. By using this strategy, low-molecular weight (<23 kDa) proteins could be identified unambiguously with less than 5 peptide matches. Nine percent of spots were identified as containing multiple proteins. By using mu LC-MS/MS, 50% of the spots analyzed were identified as containing multiple proteins. mu LC-MS/MS demonstrated better protein sequence coverage than MALDI-TOF PMM over the entire mass range of proteins identified. MALDI-TOF and PMM produced unique peptide molecular weight matches that were not identified by mu LC-MS/MS. By incorporating amino acid sequence modifications into database searches, combined sequence coverage obtained from these two complimentary ionization methods exceeded 50% for approximately 70% of the 162 spots analyzed. This improved sequence coverage in combination with enzymatic digestions of different specificity is proposed as a method for analysis of post-translational modification from 2D-gel separated proteins.     

A determinantal approach to spin-orbit configuration interaction

A general configuration interaction (CI) algorithm incorporating one- and two-electron spin-orbit operators is presented. The algorithm is determinant based and enables the use of highly vectorized non-relativistic algorithms in the most operation-intensive part. Excitations between α and β spin orbitals are avoided in the time consuming parts by performing separate S ₊ and S ₋ operations. The relativistic CI expansions are often very large, so the algorithms require only the presence of segments of vectors in memory. Double-group symmetry is fully accounted for and time-reversal symmetry is exploited for both even and odd numbers of electrons. Received: 12 October 1996 / Accepted: 24 January 1997     

THE EPIDERMAL CELL KINETIC RESPONSE TO ULTRAVIOLET B IRRADIATION COMBINES REGENERATIVE PROLIFERATION AND CARCINOGEN ASSOCIATED CELL CYCLE DELAY

The cell cycle traverse of epidermal basal cells 24 h after in vivo exposure of ultraviolet B (UVB) irradiation was studied by immunochemical staining of incorporated bromodeoxyuridine (BrdU) and bivariate BrdU/DNA flow cytometric analysis. The results were compared with the cell kinetic patterns following topical application of the skin carcinogen methylnitrosourea (MNU) as well as the skin irritant cantharidin. Hairless mice were injected intraperitoneally with BrdU 24 h after treatment of their back skin with either a minimal erythema dose of UVB, or a single application of MNU or cantharidin dissolved in acetone. The cell cycle traverse of the BrdU-labelled cohorts of epidermal basal cells were then followed for the subsequent 12 h. At 6 h after BrdU-injection, when all labelled cells in the control group as well as in the cantharidin group had left the S phase, the bivariate distributions of the UVB-exposed and the MNU group showed that BrdU-positive cells were still present in S phase. Hence, UVB irradiation, similar to the carcinogen MNU, prolonged the S phase duration in some of the basal cells. At 12 h after pulse labelling, however, BrdU-positive cells from UVB-exposed mice were re-entering S phase from G1 phase, indicating that UVB irradiation induced a shortening of the cell cycle time as well, similar to the response observed after cantharidin. The present data can not tell whether these cells also were delayed in S phase. Thus, the cell cycle traverse in hairless mouse epidermis 24 h after in vivo exposure to UVB seemed to be a combination of the cell kinetic effects following chemical skin carcinogens and skin irritants. UVB irradiation induced both a delay in transit time through S phase, probably due to DNA damage and subsequent repair, as well as a reduction in the total cell cycle time consistent with rapid regenerative proliferation.     

A relativistic 4-component general-order multi-reference coupled cluster method: initial implementation and application to HBr

We present the initial implementation of a determinant-based general-order coupled cluster method which fully accounts for relativistic effects within the four-component framework. The method opens the way for the treatment of multi-reference problems through a state-selective expansion of the model space. The evaluation of the coupled cluster vector function is carried out via relativistic configuration interaction expansions. The implementation is based on a large-scale configuration interaction technique, which may efficiently treat long determinant expansions of more than 10⁸ terms. We demonstrate the capabilities of the new method in calculations of complete potential energy curves of the HBr molecule. The inclusion of spin–orbit interaction and higher excitations than coupled cluster double excitations, either by multi-reference model spaces or the inclusion of full iterative triple excitations, lead to highly accurate results for spectral constants of HBr. An erratum to this article can be found at     

Combination of LC-ICP-MS, LC-MS and NMR for investigation of the oxidative degradation of selenomethionine

Selenomethionine (SeMet) was oxidized by heating an acidic solution with hydrogen peroxide. Samples were taken before and during the oxidation process. The oxidation products were separated by cation exchange chromatography followed by ICP-MS detection to identify the selenium containing compounds as well as electrospray ionization MS detection to determine the masses of the degradation products. Furthermore, the samples were analyzed by ⁷⁷Se-NMR. The first appearing degradation product was selenomethionine selenoxide, which was converted via the deaminated selenoxide to methane seleninic acid and selenite.     

The puromycin route to assess stereo- and regiochemical constraints on peptide bond formation in eukaryotic ribosomes

We synthesized a series of puromycin analogues to probe the chemical specificity of the ribosome in an intact eukaryotic translation system. These studies reveal that both d-enantiomers and beta-amino acid analogues can be incorporated into protein, and provide a quantitative means to rank natural and unnatural residues. Modeling of a d-amino acid analogue into the 50S ribosomal subunit indicates that steric clash may provide part of the chiral discrimination. The data presented provide one metric of the chiral and regiospecificity of mammalian ribosomes.     

In situ NMR spectroscopy of combustion

The first successful in situ studies of free combustion processes by one- and two-dimensional NMR spectroscopy are reported, and the feasibility of this concept is demonstrated. In this proof-of-principle work, methane combustion over a nanoporous material is investigated using hyperpolarized (hp)-xenon-129 NMR spectroscopy. Different inhomogeneous regions within the combustion cell are identified by the xenon chemical shift, and the gas exchange between these regions during combustion is revealed by two-dimensional exchange spectra (EXSY). The development of NMR spectroscopy as an analytical tool for combustion processes is of potential importance for catalyzed reactions within opaque media that are difficult to investigate by other techniques.