Integrated data management and validation platform for phosphorylated tandem mass spectrometry data

MS/MS is a widely used method for proteome-wide analysis of protein expression and PTMs. The thousands of MS/MS spectra produced from a single experiment pose a major challenge for downstream analysis. Standard programs, such as MASCOT, provide peptide assignments for many of the spectra, including identification of PTM sites, but these results are plagued by false-positive identifications. In phosphoproteomic experiments, only a single peptide assignment is typically available to support identification of each phosphorylation site, and hence minimizing false positives is critical. Thus, tedious manual validation is often required to increase confidence in the spectral assignments. We have developed phoMSVal, an open-source platform for managing MS/MS data and automatically validating identified phosphopeptides. We tested five classification algorithms with 17 extracted features to separate correct peptide assignments from incorrect ones using over 2600 manually curated spectra. The naïve Bayes algorithm was among the best classifiers with an AUC value of 97% and PPV of 97% for phosphotyrosine data. This classifier required only three features to achieve a 76% decrease in false positives as compared with MASCOT while retaining 97% of true positives. This algorithm was able to classify an independent phosphoserine/threonine data set with AUC value of 93% and PPV of 91%, demonstrating the applicability of this method for all types of phospho-MS/MS data. PhoMSVal is available at http://csbi.ltdk.helsinki.fi/phomsval.National Science Foundation (U.S.). Graduate Research Fellowship Progra

Lack of hybridization between Yersinia enterocolitica and HLA-B27 DNA

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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

PRELI is a mitochondrial regulator of human primary T-helper cell apoptosis, STAT6, and Th2-cell differentiation

The identification of novel factors regulating human T helper (Th)–cell differentiation into functionally distinct Th1 and Th2 subsets is important for understanding the mechanisms behind human autoimmune and allergic diseases. We have identified a protein of relevant evolutionary and lymphoid interest (PRELI), a novel protein that induces oxidative stress and a mitochondrial apoptosis pathway in human primary Th cells. We also demonstrated that PRELI inhibits Th2-cell development and down-regulates signal transducer and activator of transcription 6 (STAT6), a key transcription factor driving Th2 differentiation. Our data suggest that calpain, an oxidative stress–induced cysteine protease, is involved in the PRELI-induced down-regulation of STAT6. Moreover, we observed that a strong T-cell receptor (TCR) stimulus induces expression of PRELI and inhibits Th2 development. Our results suggest that PRELI is involved in a mechanism wherein the strength of the TCR stimulus influences the polarization of Th cells. This study identifies PRELI as a novel factor influencing the human primary Th-cell death and differentiation

Ruskean rasvakudoksen toiminta ja merkitys

Ihmisen ruskea rasvakudos on herättänyt viime vuosina mielenkiintoa, koska sen määrän on osoitettu olevan yhteydessä kehon insuliiniherkkyyteen sekä pienempiin veren triglyseridipitoisuuksiin ja vyötärön ympärysmittaan. Siitä on siksi toivottu apua tyypin 2 diabeteksen ja lihavuuden hoitoon. Ruskea rasvakudos pystyy muuntamaan varastoitua energiaa lämmöksi, ja on arvioitu, että säännöllisesti aktivoituna se kuluttaa energiaa muutaman rasvakilon verran vuodessa. Lisäksi sillä voi olla merkitystä aineenvaihdunnan säätelyssä. Kilpirauhashormonien ja endokannabinoidien tiedetään osallistuvan ruskean rasvakudoksen toiminnan säätelyyn. Viime vuonna myös havaittiin, että ruskea rasvakudos aktivoituu ihmisillä ruokailun yhteydessä. Olemme osoittaneet, että hiirillä ruuansulatushormoni sekretiinin aktivoiman ruskean rasvakudoksen lämmöntuotanto hillitsee ruokahalua. Mikäli näin tapahtuu myös ihmisillä, se voisi osaltaan selittää, miksi ruskea rasvakudos on aineenvaihdunnalle hyödyllistä.</p

Maternal asthma is associated with increased risk of perinatal mortality

Background Asthma is the most common chronic disease during pregnancy and it may have influence on pregnancy outcome. Objectives Our goal was to assess the association between maternal asthma and the perinatal risks as well as possible effects of asthma medication. Methods The study was based on a nationwide Finnish register-based cohort between the years 1996 and 2012 in the Drug and Pregnancy Database. The register data comprised 962 405 singleton live and stillbirths, 898 333 (93.3%) pregnancies in mothers with neither confirmed asthma nor use of asthma medication (controls), and 26 674 (2.8%) pregnancies with confirmed maternal asthma. 71% of mothers with asthma used asthma medication. The diagnosis of asthma was based on the mothers' right for subsidised medication which is carefully evaluated by strict criteria including pulmonary function testing. Odds ratio was used in comparison. Premature birth (PB), low birth weight, small for gestational age (SGA), neonatal death were the main outcome measures. Results Maternal asthma was associated with adjusted odds ratios (aORs) for perinatal mortality 1.24 (95% CI 1.05 to 1.46), preterm birth 1.18 (1.11 to 1.25), low birth weight 1.29 (1.21 to 1.37), fetal growth restriction (SGA) 1.32, (1.24 to 1.40), and asphyxia 1.09 (1.02 to 1.17). Asthma treatment reduced the increased risk of preterm birth aOR 0.85 (95% CI 0.76 to 0.96) but mothers with treated asthma had higher risks of fetal growth restriction (SGA) aOR 1.26 (1.10 to 1.45), and asphyxia aOR 1.37 (1.17 to 1.61) than mothers with untreated asthma. Conclusion Asthma is associated with increased risks of perinatal mortality, preterm birth, low birth weight, fetal growth restriction (SGA), and asphyxia. Asthma treatment reduces the risk of preterm delivery, but it does not seem to reduce other complications such as perinatal mortality.Peer reviewe

Kohti yksilöllistä hoitoa - proteomiikan näkymät diagnostiikassa

Sairaudet aiheuttavat muutoksia proteiinien ilmentymisessä, ja monet diagnostiset testit perustuvat proteiinien mittaamiseen näytteestä. Valtaosalla testeistä mitataan yksittäisiä proteiineja, vaikka sairauksien aiheuttamat muutokset elimistössä ovat usein moninaisia ja vaikuttavat useiden proteiinien ilmentymiseen. Proteomiikan hyödyntäminen diagnostiikassa mahdollistaisi lukuisien eri proteiinien, esimerkiksi tiettyyn signalointireittiin kuuluvien proteiinien, samanaikaisen mittaamisen näytteestä. Kattavammat testit voisivat tarjota tarkemman diagnoosin sekä yksilöllistä tietoa esimerkiksi sairauden vaiheesta ja mahdollisista liitännäissairauksista. Proteomiikassa käytetään nykyään yleisimmin massaspektrometriaan perustuvia menetelmiä, jotka mahdollistavat tuhansien proteiinien samanaikaisen mittaamisen näytteestä. Menetelmiä on käytetty menestyksekkäästi erilaisissa biomarkkeritutkimuksissa, ja ensimmäiset massaspektrometriaan perustuvat kliiniset proteomiikkatestit on otettu käyttöön. Proteomiikan menetelmät tarjoavat lukuisia ratkaisuja ja mahdollisuuksia käytännön lääketieteeseen

Plasma cell-free DNA methylation marks for episodic memory impairment : a pilot twin study

Decline in episodic memory performance usually causes the first clinical symptoms of Alzheimer's disease. At present, Alzheimer's disease can only be diagnosed at a very late stage when neurodegeneration and cognitive impairment is already irreversible. New early disease markers are needed for earlier and more efficient Alzheimer's disease intervention. To identify early disease markers, we implemented a genome-wide bisulphite sequencing method for the analysis of plasma cell-free DNA methylation profiles and compared differences associated with episodic memory performance in Finnish twin pairs. A noticeable amount of cell-free DNA was present in plasma, however, the amounts as well as the genomic coverage of these fragments varied substantially between individuals. We found no significant markers associated with episodic memory performance in the twins' plasma cell-free DNA methylation profiles. Furthermore, our results indicate that due to the low genomic coverage of cell-free DNA fragments and the variety in these fragments between individuals, the implemented genome-wide bisulphite sequencing method is not optimal for comparing cell-free DNA methylation differences between large groups of individuals.Peer reviewe

The RhoA transcriptional program in pre-T cells

The GTPase RhoA is essential for the development of pre-T cells in the thymus. To investigate the mechanisms used by RhoA to control thymocyte development we have used Affymetrix gene profiling to identify RhoA regulated genes in T cell progenitors. The data show that RhoA plays a specific and essential role in pre-T cells because it is required for the expression of transcription factors of the Egr-1 and AP-1 families that have critical functions in thymocyte development. Loss of RhoA function in T cell progenitors causes a developmental block that pheno-copies the consequence of losing pre-TCR expression in Recombinase gene 2 (Rag2) null mice. Transcriptional profiling reveals both common and unique gene targets for RhoA and the pre-TCR indicating that RhoA participates in the pre-TCR induced transcriptional program but also mediates pre-TCR independent gene transcription

Circulating metabolic signatures of rapid and slow progression to type 1 diabetes in islet autoantibody-positive children

Aims/hypothesisAppearance of multiple islet cell autoantibodies in early life is indicative of future progression to overt type 1 diabetes, however, at varying rates. Here, we aimed to study whether distinct metabolic patterns could be identified in rapid progressors (RP, disease manifestation within 18 months after the initial seroconversion to autoantibody positivity) vs. slow progressors (SP, disease manifestation at 60 months or later from the appearance of the first autoantibody).MethodsLongitudinal samples were collected from RP (n=25) and SP (n=41) groups at the ages of 3, 6, 12, 18, 24, or ≥ 36 months. We performed a comprehensive metabolomics study, analyzing both polar metabolites and lipids. The sample series included a total of 239 samples for lipidomics and 213 for polar metabolites.ResultsWe observed that metabolites mediated by gut microbiome, such as those involved in tryptophan metabolism, were the main discriminators between RP and SP. The study identified specific circulating molecules and pathways, including amino acid (threonine), sugar derivatives (hexose), and quinic acid that may define rapid vs. slow progression to type 1 diabetes. However, the circulating lipidome did not appear to play a major role in differentiating between RP and SP.Conclusion/interpretationOur study suggests that a distinct metabolic profile is linked with the type 1 diabetes progression. The identification of specific metabolites and pathways that differentiate RP from SP may have implications for early intervention strategies to delay the development of type 1 diabetes