Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments

Hybrid FTMS instruments, such as the LTQ-FT and LTQ-Orbitrap, are capable of generating high duty cycle linear ion trap MS/MS data along with high resolution information without compromising the overall throughput of measurements. Combined with online LC separations, these instruments provide powerful capabilities for proteomics research. In the present work, we explore three alternative strategies for high throughput proteomics measurements using hybrid FTMS instruments. Our accurate mass and time tag (AMT tag) strategy enables identification of thousands of peptides in a single LC-FTMS analysis by comparing accurate molecular mass and LC elution time information from the analysis to a reference database. An alternative strategy considered here, termed accurate precursor mass filter (APMF), employs linear ion trap (low resolution) MS/MS identifications generated by an appropriate search engine, such as SEQUEST, refined with high resolution precursor ion data obtained from FTMS mass spectra. The APMF results can be additionally filtered using the LC elution time information from the AMT tag database, which constitutes a precursor mass and time filter (PMTF), the third approach implemented in this study. Both the APMF and the PMTF approaches are evaluated for coverage and confidence of peptide identifications and contrasted with the AMT tag strategy. The commonly used decoy database method and an alternative method based on mass accuracy histograms were used to reliably quantify identification confidence, revealing that both methods yielded similar results. Comparison of the AMT, APMF and PMTF approaches indicates that the AMT tag approach is preferential for studies desiring a highest achievable number of identified peptides. In contrast, the APMF approach does not require an AMT tag database and provides a moderate level of peptide coverage combined with acceptable confidence values of approximately 99%. The PMTF approach yielded a significantly better peptide identification confidence, >99.9%, that essentially excluded any false peptide identifications. Since AMT tag databases that exclude incorrect identifications are desirable, this study points to the value of a multipass APMF approach to generate AMT tag databases, which are then validated using the PMTF approach. The resulting compact, high quality databases can then be used for subsequent high-throughput, high peptide coverage AMT tag studies.     

Identification of a cellular receptor for subgroup E avian leukosis virus

Genetic studies in chickens and receptor interference experiments have indicated that avian leukosis virus (ALV)-E may utilize a cellular receptor related to the receptor for ALV-B and ALV-D. Recently, we cloned CAR1, a tumor necrosis factor receptor (TNFR)-related protein, that serves as a cellular receptor for ALV-B and ALV-D. To determine whether the cellular receptor for ALV-E is a CAR1-like protein, a cDNA library was made from turkey embryo fibroblasts (TEFs), which are susceptible to ALV-E infection, but not to infection by ALV-B and ALV-D. The cDNA library was screened with a radioactively labeled CAR1 cDNA probe, and clones that hybridized with the probe were isolated. A 2.3-kb cDNA clone was identified that conferred susceptibility to ALV-E infection, but not to ALV-B infection, when expressed in transfected human 293 cells. The functional cDNA clone is predicted to encode a 368 amino acid protein with significant amino acid similarity to CAR1. Like CAR1, the TEF protein is predicted to have two extracellular TNFR-like cysteine-rich domains and a putative death domain similar to those of TNFR I and Fas. Flow cytometric analysis and immunoprecipitation experiments demonstrated specific binding between the TEF CAR1-related protein and an immunoadhesin composed of the surface (SU) envelope protein of subgroup E (RAV-0) virus fused to the constant region of a rabbit immunoglobulin. These two activities of the TEF CAR1-related protein, specific binding to ALV-E SU and permitting entry only of ALV-E, have unambiguously identified this protein as a cellular receptor specific for subgroup E ALV.     

Congenital cholesteatomas in the tympanic membrane

The etiology of congenital middle ear (ME) cholesteatomas is unclear. One etiologic possibility of ME cholesteatoma may be progression of a congenital tympanic membrane (TM) cholesteatoma. We recently have encountered three cases of congenital tympanic membrane cholesteatoma. Each child, ages 1, 3, and 14 years, presented with cholesteatoma of the tympanic membrane extending into the middle ear. These children have not had previous otologic surgery including myringotomy, nor had they had repeated middle ear infections, perforation, or trauma. Neither the 3-year-old nor 14-year-old child complained of hearing loss. Audiograms demonstrated only a mild conductive loss. Each child underwent excision with tympanoplasty. Although the middle ear component of the cholesteatoma was always more extensive than the pearl seen, the point of attachment was the TM and not the middle ear. This demonstrates one possible source for congenital cholesteatomas.     

Urethral cultures in female patients with a spinal cord injury

This paper tends to evaluate the effects of comprehensive prevention and treatment in COPD and cor pulmonale in the communities. A Randomized cohort with stratified design was undertaken in the rural areas with hundred thousand population in Beijing municipality, Lianning and Hubei Provinces, from spring 1992 to spring 1995. RESULTS: (1) the rates to all stratified populations under management were 85.6% among those with high risk, 87.8% among COPD and 83.6% among cor pulmonale, respectively. (2) The levels of KAB were raised more significantly in most intervention group than in control group which up +9.6% to +33.6% and -5.8% to +32.6%, respectively. (3) Comparisons between the two groups revealed: 1. Number of cigarette smokers who smoked more than before increased (20.1% vs 17.8%) but with no statistical significance. 2. The rate of smoking cessation went higher (15.5% vs. 11.3%, P < 0.01). 3. New high risk subjects were reduced (2.8% vs 3.9%, P < 0.01). 4. Number of new cor pulmonale patients decreased (19.9% vs 22.6%, P > 0.05) and mortality rate lowered (4.34% vs 4.78%, P > 0.05). CONCLUSION: preliminary results indicates that the active intervention is effective in reducing COPD and cor pulmonale among population at high risk in communities. However, it is necessary to point out that COPD and cor pulmonale are both having chronic nature which calls for patient and continuous efforts.     

Do personalised letters in Vietnamese increase cervical cancer screening among Vietnamese women?

In Australia, Vietnamese women are at greater risk of cervical cancer than other Australian women. To increase their participation in cervical screening, the Vietnamese community was exposed to a media campaign about the advantages of cervical smear screening which was delivered in Vietnamese through Vietnamese newspapers and radio. In addition, 689 Vietnamese (18-67 years) were selected from the electoral roll. They were randomly assigned to either receive a personal letter written in Vietnamese promoting cervical screening, or not. We report on the effect of the letter on smear rates. Being randomised to be sent such a letter was not associated with any increase in screening (relative rate of appropriate screening in the intervention versus the control group was 0.85, 95% CI 0.55-1.3). It is important to carefully evaluate untested health promotion interventions.     

Fludarabine. An update of its pharmacology and use in the treatment of haematological malignancies

Fludarabine is an antineoplastic agent which has been studied in patients with a variety of lymphoproliferative malignancies. Clinical evidence from comparative studies in chronic lymphocytic leukaemia (CLL) suggests that fludarabine is at least as effective as CAP (cyclophosphamide, doxorubicin and prednisone) or CHOP (cyclophosphamide, vincristine, doxorubicin and prednisone) in previously treated or chemotherapy-naive patients and significantly more effective than chlorambucil in terms of response rate and duration and survival in chemotherapy-naive patients. Promising results have also been reported with fludarabine-based combination therapy in the treatment of patients with CLL. In addition, sequential therapy with fludarabine and cytarabine has demonstrated good efficacy in the treatment of acute leukaemias, as has fludarabine monotherapy and combination therapy in low grade non-Hodgkin's lymphoma. A favourable cytoreductive response has been reported in patients with lymphoplasmacytoid lymphoma and in a smaller number of patients with cutaneous T cell lymphomas, CLL of T cell origin or prolymphocytic leukaemia. Recent data also support the use of fludarabine, either as a component of a nonmyeloablative conditioning regimen or in the attainment of minimal residual disease, in patients undergoing peripheral blood stem cell or bone marrow transplantation. The tolerability profile of fludarabine is similar to that of CAP, with the most common adverse events being granulocytopenia, thrombocytopenia, anaemia and infection. Alopecia and nausea/vomiting appear to be less frequent with fludarabine therapy than with CAP although the development of immune cytopenias is more frequent with fludarabine. Severe neurotoxicity has been reported with fludarabine but this is mostly confined to the use of high doses. Clinical experience therefore indicates that fludarabine is an effective and generally well-tolerated antineoplastic agent for the second-line treatment of advanced CLL. Recent data from comparative studies also support the earlier use of fludarabine in the treatment of chemotherapy-naive patients with CLL. Furthermore, results of available studies are increasingly highlighting an important future role for fludarabine in the treatment of acute leukaemias and low grade NHL and possibly other lymphoproliferative disorders, particularly when used as a component of combination chemotherapy.     

Allogeneic bone marrow transplantation in patients who relapse after autologous transplantation

Increasing numbers of patients have received autologous stem cell transplants (ASCT) for hematologic malignancies. Since only a fraction of these patients are cured, physicians are more frequently faced with the dilemma of how to manage relapse post-transplant. Potential advantages of allogeneic transplantation (alloBMT) over ASCT include lack of graft tumor contamination and presence of a graft-versus-tumor effect. For this reason, patients who relapse after ASCT are often considered candidates for allogeneic bone marrow transplantation. However, there is limited knowledge on the outcome of alloBMT in patients who relapse after ASCT. We retrospectively analyzed the outcome of 20 patients with malignant lymphoma (n = 14) and AML (n = 6) who underwent alloBMT after failing an ASCT. The median age was 30 (17-41) years and the interval from ASCT to alloBMT was 10.5 (2-25) months. Seventeen patients died between 0.3 to 11 months (median 2.0) after alloBMT, all due to BMT-related toxicities. Three patients remain alive and free of disease at 1.1, 1.2 and 2.5 years after alloBMT. Sixteen of the 18 evaluable patients (89%) developed grade II-IV acute GVHD. Patients undergoing alloBMT after ASCT have a very high treatment-related mortality and incidence of grade II-IV acute GVHD. Alternative treatments with salvage chemotherapy, radiation or investigational approaches should be considered in patients who relapse after ASCT.     

"Clinical comparability of the standard MMPI and the MMPI-168": Correction to Hart, McNeill, Lutz, and Adkins.

Reports an error in "Clinical comparability of the standard MMPI and the MMPI-168" by Ronald R. Hart, John W. McNeill, David J. Lutz and Thomas G. Adkins (Professional Psychology: Research and Practice, 1986[Jun], Vol 17[3], 269-272). In this article, the copyright information was incorrect. The corrected copyright information is included in the erratum. (The following abstract of the original article appeared in record 1986-26219-001.) Examined the clinical correspondence of the full-scale Minnesota Multiphasic Personality Inventory (MMPI) and the MMPI-168 on a psychiatric screening sample of 210 men (mean age 43.27 yrs). The present results fail to replicate previous optimistic findings regarding the worth of the MMPI-168 and accent the need for caution in any further use of this abbreviated instrument. (10 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Enantioselective Hydrogenation of Olefins using Commercially Available Pd/C. Chiral Heterogeneous Catalyst Applicable for High-Throughput Screening

Cinchonidine-modified Pd/C applicable for the high-throughput-guided study was developed. Commercial Pd/C catalysts were employed for the enantioselective hydrogenation of phenylcinnamic acid after the pretreatment, and some of the catalysts were found to result in the sufficient enantioselectivity. The Pd/C catalysts suitable for the cinchonidine modification were characterized by TEM and XAFS to have highly dispersed metal, 2.2 nm of the mean particles size for the best catalyst. The pre-modified Pd/C could be stored in a suspension accompanying with gradual decease in the product ee. The pre-modified catalyst was applicable for the high-throughput screening by using a parallel reactor in the 1/5-scale reactions.     

Dispersion control in magnetostatic wave delay lines

A major impediment to the realization of practical magnetostatic wave (MSW) devices is the inherent non-linear delay versus frequency characteristics of MSW delay lines. Most device applications require either nondispersive (delay vs. frequency slope=0) or linearly dispersive (delay vs. frequency slope = constant) characteristics. There are four basic approaches to the elimination and/or linearization of MSW dispersion: (1) modification of the magnetic film properties as a function of film thickness, (2) modification of the ground plane geometry, (3) modification of the bias field uniformity, and (4) perturbation of the propagation path surface with metal electrode reflective arrays. In principle all four approaches can yield either linearly dispersive or nondispersive characteristics with a suitable choice of bias field orientation and critical design parameters. These dispersion control techniques are reviewed, and data from recent experiments demonstrating the strengths and weaknesses of the various approaches are discussed. To date the most extensive experimental work has been done with the multiple layer (magnetic properties varied as a function of film thickness) and ground-plane spacing techniques. At present the ground-plane spacing technique produces results acceptable for some systems applications, while the multiple-layer approach is still under development.Research supported in part by Air Force Office of Scientific Research (AFSC), United States Air Force, under contract Number F49620-82-C-0081 and Rome Air Development Center (RADC), United States Air Force, under Contract Number F19628-82-C-0098. The United States Government is authorized to-reproduce and distribute reprints for governmental purposes notwithstanding any copyright notation herein.