Processing methods for differential analysis of LC/MS profile data

BACKGROUND: Liquid chromatography coupled to mass spectrometry (LC/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i.e. broad screening of biomolecular components across multiple samples in order to elucidate the observed phenotypes and discover biomarkers. One of the major challenges in this domain remains development of better solutions for processing of LC/MS data. RESULTS: We present a software package MZmine that enables differential LC/MS analysis of metabolomics data. This software is a toolbox containing methods for all data processing stages preceding differential analysis: spectral filtering, peak detection, alignment and normalization. Specifically, we developed and implemented a new recursive peak search algorithm and a secondary peak picking method for improving already aligned results, as well as a normalization tool that uses multiple internal standards. Visualization tools enable comparative viewing of data across multiple samples. Peak lists can be exported into other data analysis programs. The toolbox has already been utilized in a wide range of applications. We demonstrate its utility on an example of metabolic profiling of Catharanthus roseus cell cultures. CONCLUSION: The software is freely available under the GNU General Public License and it can be obtained from the project web page at:

Alle kouluikäisten lasten seksuaalisen toiminnan salliminen ja siihen puuttuminen vanhempien järkeilemänä

Suhtautumisessa lapsen seksuaalisuuteen voi tunnistaa kaksi ajankohtaista, osin toistensa kanssa kilpailevaa näkökulma: suojelun ja toimijuuden näkökulmat. Suojelun näkökulmassa lapsen sisäisinä ominaisuuksina nähdään viattomuus ja haavoittuvuus. Aikuisen tehtävä on suojella lapsen seksuaalisuutta liian varhaisilta ja vääränlaisilta vaikutteilta. Erityisesti pedofilialta suojeleminen on 2000-luvun lasten suojelun keskeinen tehtävä. Uudemmassa, toimijuuden näkökulmassa lapsi nähdään aktiivisena toimijana, jolla on oikeus ilmaista mielipiteensä itseään koskevissa asioissa. Lapsi on myös seksuaalinen kansalainen, mikä tarkoittaa, että lapsella on oikeus saada tietoa seksuaalisuudesta ja oikeus itsemääräämiseen. Lapsen seksuaalisoikeuksien toteutuminen on yhteiskunnallinen tehtävä ja tavoite. Lapsen suojelu tapahtuu antamalla lapselle tietoja ja taitoja hallita omaa seksuaalisuuttaan ja käyttää itsemääräämistään seksuaalisuuden alueella. Tämän tutkimuksen tavoite on selvittää, miten vanhemmat järkeilevät 0-6-vuotiaiden seksuaalisen toiminnan sallimista ja siihen puuttumista. Tutkimuskysymykseni ovat 1) millaisten diskurssien kautta vanhemmat järkeilevät lapsen seksuaaliseen toimintaan puuttumista ja sen sallimista sekä 2) miten vanhemman ja lapsen positiot diskursseissa rakentuvat? Aineistoni on Väestöliiton Laseke-tutkimushakkeessa 0-6-vuotiaiden lasten vanhemmilta kerätty kyselyaineisto. Tutkimusmenetelmäni on diskurssianalyysi, joka mahdollistaa merkityskokonaisuuksien rakentumisen kielen avulla. Diskurssit ovat aikakausisidonnaisia selontekoja, joilla tehdään ymmärrettäväksi kulttuurisia ihanteita. Löysin aineistostani viisi diskurssia, joiden kautta vanhempien järkeily tapahtuu. Diskurssit vahvimmasta heikoimpaan ovat 1) luonnollisuuden varjelemisen, 2) normaalistamisen, 3) suojelun, 4) yksityisyyden ja 5) itsemääräämisen tukemisen diskurssi. Neljä ensimmäistä diskurssia mukailevat lapsen suojelun näkökulmaa: lapsen seksuaalisuus määrittyy kehittymässä olevaksi seksuaalisuudeksi, joka on hauras ja herkkä. Lapsen seksuaalinen toiminta on aikuisten kasvatustoimenpiteiden kohteena ja lapsen seksuaalista toimintaa rajoitetaan yksityisyysnormien mukaan. Itsemääräämisen tukemisen diskurssi on yhtäläinen toimijuuden näkökulman kanssa. Lapsen seksuaalisuus nähdään ensisijaisesti lapsen oikeuksien ja lapsen itsemääräämisen kautta. Lapsen itsemäärääminen omasta seksuaalisuudestaan ylittää vanhemman oikeuden puuttua lapsen toimintaan. Itsemääräämisen tukemisen diskurssiin kuuluvat myös turvataitojen opettaminen lapselle. Taitojen avulla lapsi pystyy harjoittamaan omia seksuaalioikeuksiaan. Lapsen seksuaalisen kansalaisuuden toteutumisen edistämiseksi lasten seksuaalisuutta pitäisi käsitteellistää omana, kompleksisena kokonaisuutenaan, eikä antaa sille merkityksiä aikuisseksuaalisuudesta käsin. Lapsen toimintakulttuurille ominaista on leikillisyys, toiminnallisuus ja huumori. Vastustaminen ja auktoriteetin kyseenalaistaminen lapsella on tärkeä toimijuuden ilmaus. Tärkeää onkin pohtia, miten lasten kanssa toimiessa voidaan paremmin huomioida lasten tapa tarkastella asioita. Lapsen seksuaalisuuden alueella se tarkoittaa seksuaalisuuden monimuotoisuuden hyväksymistä ja sen tunnustamista, että emme tarkkaan tunne lapsen seksuaalisuutta, mutta voimme olla avoimia sille, mitä tulee esiin

LICSS - a chemical spreadsheet in microsoft excel

Abstract Background Representations of chemical datasets in spreadsheet format are important for ready data assimilation and manipulation. In addition to the normal spreadsheet facilities, chemical spreadsheets need to have visualisable chemical structures and data searchable by chemical as well as textual queries. Many such chemical spreadsheet tools are available, some operating in the familiar Microsoft Excel environment. However, within this group, the performance of Excel is often compromised, particularly in terms of the number of compounds which can usefully be stored on a sheet. Summary LICSS is a lightweight chemical spreadsheet within Microsoft Excel for Windows. LICSS stores structures solely as Smiles strings. Chemical operations are carried out by calling Java code modules which use the CDK, JChemPaint and OPSIN libraries to provide cheminformatics functionality. Compounds in sheets or charts may be visualised (individually or en masse), and sheets may be searched by substructure or similarity. All the molecular descriptors available in CDK may be calculated for compounds (in batch or on-the-fly), and various cheminformatic operations such as fingerprint calculation, Sammon mapping, clustering and R group table creation may be carried out. We detail here the features of LICSS and how they are implemented. We also explain the design criteria, particularly in terms of potential corporate use, which led to this particular implementation. Conclusions LICSS is an Excel-based chemical spreadsheet with a difference: • It can usefully be used on sheets containing hundreds of thousands of compounds; it doesn't compromise the normal performance of Microsoft Excel • It is designed to be installed and run in environments in which users do not have admin privileges; installation involves merely file copying, and sharing of LICSS sheets invokes automatic installation • It is free and extensible LICSS is open source software and we hope sufficient detail is provided here to enable developers to add their own features and share with the community.</p

Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis.

BACKGROUND: Lipids are an important and highly diverse class of molecules having structural, energy storage and signaling roles. Modern analytical technologies afford screening of many lipid molecular species in parallel. One of the biggest challenges of lipidomics is elucidation of important pathobiological phenomena from the integration of the large amounts of new data becoming available. RESULTS: We present computational and informatics approaches to study lipid molecular profiles in the context of known metabolic pathways and established pathophysiological responses, utilizing information obtained from modern analytical technologies. In order to facilitate identification of lipids, we compute the scaffold of theoretically possible lipids based on known lipid building blocks such as polar head groups and fatty acids. Each compound entry is linked to the available information on lipid pathways and contains the information that can be utilized for its automated identification from high-throughput UPLC/MS-based lipidomics experiments. The utility of our approach is demonstrated by its application to the lipidomic characterization of the fatty liver of the genetically obese insulin resistant ob/ob mouse model. We investigate the changes of correlation structure of the lipidome using multivariate analysis, as well as reconstruct the pathways for specific molecular species of interest using available lipidomic and gene expression data. CONCLUSION: The methodology presented herein facilitates identification and interpretation of high-throughput lipidomics data. In the context of the ob/ob mouse liver profiling, we have identified the parallel associations between the elevated triacylglycerol levels and the ceramides, as well as the putative activated ceramide-synthesis pathways.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments.

The options available for processing quantitative data from isotope coded affinity tag (ICAT) experiments have mostly been confined to software specific to the instrument of acquisition. However, recent developments with data format conversion have subsequently increased such processing opportunities. In the present study, data sets from ICAT experiments, analysed with liquid chromatography/tandem mass spectrometry (MS/MS), using an Applied Biosystems QSTAR Pulsar quadrupole-TOF mass spectrometer, were processed in triplicate using separate mass spectrometry software packages. The programs Pro ICAT, Spectrum Mill and SEQUEST with XPRESS were employed. Attention was paid towards the extent of common identification and agreement of quantitative results, with additional interest in the flexibility and productivity of these programs. The comparisons were made with data from the analysis of a specifically prepared test mixture, nine proteins at a range of relative concentration ratios from 0.1 to 10 (light to heavy labelled forms), as a known control, and data selected from an ICAT study involving the measurement of cytokine induced protein expression in human lymphoblasts, as an applied example. Dissimilarities were detected in peptide identification that reflected how the associated scoring parameters favoured information from the MS/MS data sets. Accordingly, there were differences in the numbers of peptides and protein identifications, although from these it was apparent that both confirmatory and complementary information was present. In the quantitative results from the three programs, no statistically significant differences were observed.</p

Highly sensitive feature detection for high resolution LC/MS

<p>Abstract</p> <p>Background</p> <p>Liquid chromatography coupled to mass spectrometry (LC/MS) is an important analytical technology for e.g. metabolomics experiments. Determining the boundaries, centres and intensities of the two-dimensional signals in the LC/MS raw data is called feature detection. For the subsequent analysis of complex samples such as plant extracts, which may contain hundreds of compounds, corresponding to thousands of features – a reliable feature detection is mandatory.</p> <p>Results</p> <p>We developed a new feature detection algorithm <it>centWave </it>for high-resolution LC/MS data sets, which collects regions of interest (partial mass traces) in the raw-data, and applies continuous wavelet transformation and optionally Gauss-fitting in the chromatographic domain. We evaluated our feature detection algorithm on dilution series and mixtures of seed and leaf extracts, and estimated recall, precision and F-score of seed and leaf specific features in two experiments of different complexity.</p> <p>Conclusion</p> <p>The new feature detection algorithm meets the requirements of current metabolomics experiments. <it>centWave </it>can detect close-by and partially overlapping features and has the highest overall recall and precision values compared to the other algorithms, <it>matchedFilter </it>(the original algorithm of <it>XCMS</it>) and the centroidPicker from <it>MZmine</it>. The <it>centWave </it>algorithm was integrated into the Bioconductor R-package <it>XCMS </it>and is available from <url>http://www.bioconductor.org/</url></p

Parameter selection for peak alignment in chromatographic sample profiling: objective quality indicators and use of control samples

In chromatographic profiling applications, peak alignment is often essential as most chromatographic systems exhibit small peak shifts over time. When using currently available alignment algorithms, there are several parameters that determine the outcome of the alignment process. Selecting the optimum set of parameters, however, is not straightforward, and the quality of an alignment result is at least partly determined by subjective decisions. Here, we demonstrate a new strategy to objectively determine the quality of an alignment result. This strategy makes use of a set of control samples that are analysed both spiked and non-spiked. With this set, not only the system and the method can be checked but also the quality of the peak alignment can be evaluated. The developed strategy was tested on a representative metabolomics data set using three software packages, namely Markerlynx™, MZmine and MetAlign. The results indicate that the method was able to assess and define the quality of an alignment process without any subjective interference of the analyst, making the method a valuable contribution to the data handling process of chromatography-based metabolomics data

Prospects for a Statistical Theory of LC/TOFMS Data

The critical importance of employing sound statistical arguments when seeking to draw inferences from inexact measurements is well-established throughout the sciences. Yet fundamental statistical methods such as hypothesis testing can currently be applied to only a small subset of the data analytical problems encountered in LC/MS experiments. The means of inference that are more generally employed are based on a variety of heuristic techniques and a largely qualitative understanding of their behavior. In this article, we attempt to move towards a more formalized approach to the analysis of LC/TOFMS data by establishing some of the core concepts required for a detailed mathematical description of the data. Using arguments that are based on the fundamental workings of the instrument, we derive and validate a probability distribution that approximates that of the empirically obtained data and on the basis of which formal statistical tests can be constructed. Unlike many existing statistical models for MS data, the one presented here aims for rigor rather than generality. Consequently, the model is closely tailored to a particular type of TOF mass spectrometer although the general approach carries over to other instrument designs. Looking ahead, we argue that further improvements in our ability to characterize the data mathematically could enable us to address a wide range of data analytical problems in a statistically rigorous manner

High-resolution extracted ion chromatography, a new tool for metabolomics and lipidomics using a second-generation orbitrap mass spectrometer

Most analytical methods in metabolomics are based on one of two strategies. The first strategy is aimed at specifically analysing a limited number of known metabolites or compound classes. Alternatively, an unbiased approach can be used for profiling as many features as possible in a given metabolome without prior knowledge of the identity of these features. Using high-resolution mass spectrometry with instruments capable of measuring m/z ratios with sufficiently low mass measurement uncertainties and simultaneous high scan speeds, it is possible to combine these two strategies, allowing unbiased profiling of biological samples and targeted analysis of specific compounds at the same time without compromises. Such high mass accuracy and mass resolving power reduces the number of candidate metabolites occupying the same retention time and m/z ratio space to a minimum. In this study, we demonstrate how targeted analysis of phospholipids as well as unbiased profiling is achievable using a benchtop orbitrap instrument after high-speed reversed-phase chromatography. The ability to apply both strategies in one experiment is an important step forward in comprehensive analysis of the metabolome. Copyright © 2009 John Wiley & Sons, Ltd