Tandem mass spectrometry data quality assessment by self-convolution

<p>Abstract</p> <p>Background</p> <p>Many algorithms have been developed for deciphering the tandem mass spectrometry (MS) data sets. They can be essentially clustered into two classes. The first performs searches on theoretical mass spectrum database, while the second based itself on <it>de novo </it>sequencing from raw mass spectrometry data. It was noted that the quality of mass spectra affects significantly the protein identification processes in both instances. This prompted the authors to explore ways to measure the quality of MS data sets before subjecting them to the protein identification algorithms, thus allowing for more meaningful searches and increased confidence level of proteins identified.</p> <p>Results</p> <p>The proposed method measures the qualities of MS data sets based on the symmetric property of b- and y-ion peaks present in a MS spectrum. Self-convolution on MS data and its time-reversal copy was employed. Due to the symmetric nature of b-ions and y-ions peaks, the self-convolution result of a good spectrum would produce a highest mid point intensity peak. To reduce processing time, self-convolution was achieved using Fast Fourier Transform and its inverse transform, followed by the removal of the "DC" (Direct Current) component and the normalisation of the data set. The quality score was defined as the ratio of the intensity at the mid point to the remaining peaks of the convolution result. The method was validated using both theoretical mass spectra, with various permutations, and several real MS data sets. The results were encouraging, revealing a high percentage of positive prediction rates for spectra with good quality scores.</p> <p>Conclusion</p> <p>We have demonstrated in this work a method for determining the quality of tandem MS data set. By pre-determining the quality of tandem MS data before subjecting them to protein identification algorithms, spurious protein predictions due to poor tandem MS data are avoided, giving scientists greater confidence in the predicted results. We conclude that the algorithm performs well and could potentially be used as a pre-processing for all mass spectrometry based protein identification tools.</p

Modular Mass Spectrometric Tool for Analysis of Composition and Phosphorylation of Protein Complexes

The combination of high accuracy, sensitivity and speed of single and multiple-stage mass spectrometric analyses enables the collection of comprehensive sets of data containing detailed information about complex biological samples. To achieve these properties, we combined two high-performance matrix-assisted laser desorption ionization mass analyzers in one modular mass spectrometric tool, and applied this tool for dissecting the composition and post-translational modifications of protein complexes. As an example of this approach, we here present studies of the Saccharomyces cerevisiae anaphase-promoting complexes (APC) and elucidation of phosphorylation sites on its components. In general, the modular concept we describe could be useful for assembling mass spectrometers operating with both matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) ion sources into powerful mass spectrometric tools for the comprehensive analysis of complex biological samples

Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome

YesHuman identification from biological material is largely dependent on the ability to characterize genetic polymorphisms in DNA. Unfortunately, DNA can degrade in the environment, sometimes below the level at which it can be amplified by PCR. Protein however is chemically more robust than DNA and can persist for longer periods. Protein also contains genetic variation in the form of single amino acid polymorphisms. These can be used to infer the status of non-synonymous single nucleotide polymorphism alleles. To demonstrate this, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 66 European-American subjects. A total of 596 single nucleotide polymorphism alleles were correctly imputed in 32 loci from 22 genes of subjects’ DNA and directly validated using Sanger sequencing. Estimates of the probability of resulting individual non-synonymous single nucleotide polymorphism allelic profiles in the European population, using the product rule, resulted in a maximum power of discrimination of 1 in 12,500. Imputed non-synonymous single nucleotide polymorphism profiles from European–American subjects were considerably less frequent in the African population (maximum likelihood ratio = 11,000). The converse was true for hair shafts collected from an additional 10 subjects with African ancestry, where some profiles were more frequent in the African population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). This study demonstrates that quantifiable measures of identity discrimination and biogeographic background can be obtained from detecting genetically variant peptides in hair shaft protein, including hair from bioarchaeological contexts.The Technology Commercialization Innovation Program (Contracts #121668, #132043) of the Utah Governors Office of Commercial Development, the Scholarship Activitie

The Contribution of Viral Genotype to Plasma Viral Set-Point in HIV Infection

Disease progression in HIV-infected individuals varies greatly, and while the environmental and host factors influencing this variation have been widely investigated, the viral contribution to variation in set-point viral load, a predictor of disease progression, is less clear. Previous studies, using transmission-pairs and analysis of phylogenetic signal in small numbers of individuals, have produced a wide range of viral genetic effect estimates. Here we present a novel application of a population-scale method based in quantitative genetics to estimate the viral genetic effect on set-point viral load in the UK subtype B HIV-1 epidemic, based on a very large data set. Analyzing the initial viral load and associated pol sequence, both taken before anti-retroviral therapy, of 8,483 patients, we estimate the proportion of variance in viral load explained by viral genetic effects to be 5.7% (CI 2.8-8.6%). We also estimated the change in viral load over time due to selection on the virus and environmental effects to be a decline of 0.05 log10 copies/mL/year, in contrast to recent studies which suggested a reported small increase in viral load over the last 20 years might be due to evolutionary changes in the virus. Our results suggest that in the UK epidemic, subtype B has a small but significant viral genetic effect on viral load. By allowing the analysis of large sample sizes, we expect our approach to be applicable to the estimation of the genetic contribution to traits in many organisms

Extension to the Home Care User Experience Survey: Initial Feedback to Councils

All councils with social services responsibilities (CSSRs) were required to conduct a user experience survey (UES) for home care service users by April 2003. The extension to this survey sought to add value to the UES for a sample of participating councils by enhancing comparability across dimensions not included in the four compulsory questions. All councils with social services responsibilities were invited to participate in the extended survey using the slightly amended full version of the questionnaire that had been developed by ONS in collaboration with SPRU. In addition to collating in-depth and comparable data the study aims to assess the four questions devised by ONS for their suitability as performance indicators. The other principal objective is to enable authorities to compare the quality of home care providers in their authorities and with providers used by other authorities. Thirty-four CSSRs undertook the extended UES. They included one London borough, eight metropolitan authorities, fourteen shire counties and eleven unitary authorities. In total information was collected from over 20, 000 home care users. This report provides an overview of the survey results for all 34 participating authorities

Social care regulation: resource use. Final report

This paper reports on the findings of a study investigating the resource use of the NCSC. Our aim was to identify the resource requirements of the NCSC given current workloads and practice. The timing of the study means that the results need to be treated with some caution (see Appendix A). We start by briefly describing the method and response rates and then set the context in terms of the overall levels of regulatory responsibilities and activity during the first year of the NCSC. In section 4 we describe the work undertaken by inspectors and managers in terms of their caseloads and overall time use. We then turn to the individual regulatory activities in order to identify the resource use in terms of time input to the regulatory process, compare with the results of the previous studies and explore factors associated with variations in time taken. We end by identifying the unit cost of staff time and the estimated costs of each of the measured regulatory activities

The costs of community-based psychiatric care for first-ever patients: a case register study

Background. Analysing costs measures in conjunction with psychiatric case register (PCR) data can provide important epidemiologically-based information on resource utilization. Costing the service use patterns of first-ever patients can indicate the shape and likely resource consequences for mental health services operating within a community-based system of care. Methods. Yearly costs were calculated for the 299 first-ever patients and 768 longer-term patients who contacted the South-Verona Psychiatric Case Register between 1 January 1992 and 31 December 1993. Bivariate and multivariate analyses were used to compare costs between these groups and to test the associations between costs and the sociodemographic and diagnostic data recorded on the PCR. Results. For all diagnostic groups identified, first-ever patients were found to be less costly to support than longer-term patients, even after adjustment for various factors, including whether patients were single consulters. When multivariate analyses were employed, between 20% and 69% of the cost variation for first-ever patients could be explained by patient and other characteristics, and the effect of the contact (first or subsequent) variable was reduced. Conclusion. This study considered only the costs to the specialist psychiatric services but the methodology allows the likely annual resource implications of supporting new patients to be predicted from data collected at first contact. Such information can help ensure that services are adequately funded and that the resources are deployed appropriately between client groups

Using `Vector' in SPSS-x

The VECTOR command, introduced with SPSS-X, is a powerful but I suspect little-used tool in our SPSS data manipulation kit. Essentially it is simply a means of grouping a set of variables together under one name which can then be referred to in subscripted form. This provides greatly increased flexibility in data transformations, frequently avoiding the need for bespoke external programs. The paper outlines the syntax of the command and illustrates some of the uses to which VECTOR can be put with four practical examples