Surface-enhanced Laser Desorption/ionization Time-of-flight Research Articles

Selymatra: A web application for protein-profiling analysis of mass spectra.

Surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry is a variant of the matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. It is used in many cases especially for the analysis of protein profiling and for preliminary screening of biomarkers in complex samples. Unfortunately, these analyses are time consuming and protein identification is generally strictly limited. SELDI-TOF analysis of mass spectra (SELYMATRA) is a web application (WA) developed to reduce these limitations by (i) automating the identification processes and (ii) introducing the possibility to predict proteins in complex mixtures from cells and tissues. The WA architectural pattern is the model-view-controller, commonly used in software development. The WA compares the mass value between two mass spectra (sample vs. control) to extract differences, and, according to the set parameters, it queries a local database to predict most likely proteins based on their masses and different expression amplification. The WA was validated in a cellular model overexpressing a tagged NURR1 receptor, being able to recognize the tagged protein in the profiling of transformed cells. A help page, including a description of parameters for WA use, is available on the website.

Cold-modulated small proteins abundance in winter triticale (x Triticosecale, Wittm.) seedlings tolerant to the pink snow mould (Microdochium nivale, Samuels and Hallett) infection.

Two winter triticale (x Triticosecale Wittmack) model cultivars: Hewo (tolerant to pink snow mould) and Magnat (sensitive) were used to test the effect of cold-hardening (4 weeks at 4°C) on soluble ≤50 kDa protein profiles of the seedling leaves. The presence and abundance of individual proteins were analysed via two-dimensional gel electrophoresis (2-DE) and Surface-Enhanced Laser Desorption/Ionization Time-of-Flight (SELDI-TOF). Up to now, no proteomics analysis of triticale response to hardening has been performed. Thus, the present paper is the first in the series describing the obtained results. In our experiments, the exposure to the low temperature-induced only quantitative changes in the leaves of both cultivars, causing either an increase or decrease of 4-50 kDa protein abundance. Among proteins which were cold-accumulated in cv. Hewo's leaves, we identified two thioredoxin peroxidases (chloroplastic thiol-specific antioxidant proteins) as well as mitochondrial- β-ATP synthase subunit and ADP-binding resistance protein. On the contrary, in hardened seedlings of this genotype, we observed the decreased level of chloroplastic RuBisCO small subunit PW9 and epidermal peroxidase 10. Simultaneous SELDI-TOF analysis revealed several low mass proteins better represented in cold-hardened plants of tolerant genotype in comparison to the sensitive one and the impact of both genotype and temperature on their level. Based on those results, we suggest that indicated proteins might be potential candidates for molecular markers of cold-induced snow mould resistance of winter triticale and their role is worth to be investigated in the further inoculation experiments.

MALDI-TOF DAN SELDI-TOF MASS SPECTROMETRY DENGAN THROUGHPUT TINGGI UNTUK ANALISIS PROTEOMIK PROFIL PROTEIN DARI PETANDA BIOLOGIS

In recent years, proteomic approach has been widely used for diagnosing the diseases and matrix assisted laser desorption /ionization- time of the flight (MALDI-TOF) mass spectrometry and its modification, surface enhanced laser desorption /ionization-timeof flight (SELDI-TOF) mass spectrometry have became very promising diagnostic tools. High throughputs and relative simplicity of thesetechnologies attracted the researchers to know the biomarkers of specific diseases by analyzing specimens of serum/plasma and otherbody fluids. Analyzing plasma specimens by MALDI/SELDI TOF mass spectrometry provides new information especially about smallprotein and peptides in high abundance. Protein profilings, resulting by these technologies provide higher sensitivity and specificity valuesthan current biomarkers. Knowing how these principle tools work and its promising application to early detection of specific diseases isthe aim of writing this paper.

Immunoproteomics technologies in the discovery of autoantigens in autoimmune diseases.

Proteomics technologies are often used for the identification of protein targets of the immune system. Here, we discuss the immunoproteomics technologies used for the discovery of autoantigens in autoimmune diseases where immune system dysregulation plays a central role in disease onset and progression. These autoantigens and associated autoantibodies can be used as potential biomarkers for disease diagnostics, prognostics and predicting/monitoring drug responsiveness (theranostics). Here, we compare a variety of methods such as mass spectrometry (MS)-based [serological proteome analysis (SERPA), antibody mediated identification of antigens (AMIDA), circulating immune complexome (CIC) analysis, surface enhanced laser desorption/ionization-time of flight (SELDI-TOF)], nucleic acid based serological analysis of antigens by recombinant cDNA expression cloning (SEREX), phage immunoprecipitation sequencing (PhIP-seq) and array-based immunoscreening (proteomic microarrays), luciferase immunoprecipitation systems (LIPS), nucleic acid programmable protein array (NAPPA) methods. We also review the relevance of immunoproteomic data generated in the last 10 years, with a focus on the aforementioned MS based methods.

Characterization of Amyloid-β Deposits in Bovine Brains.

Amyloid-β (Aβ) deposits are seen in aged individuals of many mammalian species that possess the same aminoacid sequence as humans. This study describes Aβ deposition in 102 clinically characterized cattle brains from animals aged 0 to 20 years. Extracellular and intracellular Aβ deposition was detected with 4G8 antibody in the cortex, hippocampus, and cerebellum. X-34 staining failed to stain Aβ deposits, indicating the non β-pleated nature of these deposits. Western blot analysis and surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry revealed in Tris, Triton, and formic acid fractions the presence of different Aβ peptides, characterized mainly by C-terminally truncated forms. Exploration of the genetic variability of APOE, PSEN1, and PSEN2 genes involved in Alzheimer’s disease pathogenesis revealed several previously unreported polymorphisms. This study demonstrates certain similarities between Aβ deposition patterns exhibited in cattle brains and those in the human brain in early stages of aging. Furthermore, the identification of the same Aβ peptides reported in humans, but unable to form aggregates, supports the hypothesis that cattle may be protected against amyloid plaque formation.

Application of SELDI-TOF in N-glycopeptides profiling of the urine from patients with endometrial, ovarian and cervical cancer

Purpose: Endometrial (ECa), ovarian (OCa) and cervical (CCa) cancers are among 10 of the most common cancers affecting women worldwide. Cancers are known to cause some proteins to be differentially glycosylated or aberrantly excreted in the urine, which can be used as biomarkers. Since ECa, OCa and CCa are difficult to diagnose at the early stage, the aim of the present study was to identify a panel of new biomarkers for early detection of the cancers using surface-enhanced laser desorption/ionization-time-of-flight (SELDI-TOF) technology. Identification of early biomarkers that are specific and efficient can increase the survival rate of the patients. Experimental design: Digested urinary proteins from patients with ECa, OCa and CCa were incubated on the champedak mannose-binding (CMB) lectin-immobilized PS10 chip. The lectin-captured glycopeptides were detected with SELDI-TOF mass spectrometry and followed by biomarker wizard analysis. Results: Peaks m/z 1201 and 1449 were detected as potential group discriminators. The peak m/z 1201 could distinguish OCa from CCa and ECa and its sensitivity and specificity were 100%. For m/z 1449, it was able to differentiate ECa from the other two types of cancer. Conclusions: The findings of this study suggest urinary glycopeptides m/z 1201 and 1449 may serve as potential biomarkers for the early detection of ECa, OCa and CCa, although this requires further extensive validation on clinically representative populations.

Ubiquitin: a potential cerebrospinal fluid progression marker in Huntington's disease.

Finding early and dynamic biomarkers in Huntington's disease is a key to understanding the early pathology of Huntington's disease and potentially to tracking disease progression. This would benefit the future evaluation of potential neuroprotective and disease-modifying therapies, as well as aid in identifying an optimal time point for initiating a potential therapeutic intervention. This explorative proteomics study evaluated cerebrospinal fluid from 94 Huntington's disease gene-expansion carriers (39 premanifest and 55 manifest) and 27 Huntington's disease gene-expansion negative individuals using surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry. Differences in peak intensity from SELDI-TOF spectra were evaluated. Levels of 10 peaks were statistically significantly different between manifest gene-expansion carriers and controls. One of them identified as ubiquitin was shown to be dependent on the Unified Huntington Disease Rating Scale Total Functional Capacity, a pseudo-measure of disease severity (P=0.001), and the Symbol Digit Modalities Test (0.04) in manifest and CAG-age product score (P=0.019) in all gene-expansion carriers. Multiple studies have shown that the ubiquitin-proteasome system is involved in Huntington's disease pathogenesis and understanding of this involvement may have therapeutic potential in humans. This is the first study on cerebrospinal fluid to confirm the involvement of the ubiquitin-proteasome system in Huntington's disease. Furthermore it is shown that ubiquitin increases with disease progression and CAG-age product score and therefore may have the potential as a Huntington's disease progression marker, also prior to motor onset.

Novel serum protein biomarker panel revealed by mass spectrometry and its prognostic value in breast cancer.

IntroductionSerum profiling using proteomic techniques has great potential to detect biomarkers that might improve diagnosis and predict outcome for breast cancer patients (BC). This study used surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS) to identify differentially expressed proteins in sera from BC and healthy volunteers (HV), with the goal of developing a new prognostic biomarker panel.MethodsTraining set serum samples from 99 BC and 51 HV subjects were applied to four adsorptive chip surfaces (anion-exchange, cation-exchange, hydrophobic, and metal affinity) and analyzed by time-of-flight MS. For validation, 100 independent BC serum samples and 70 HV samples were analyzed similarly. Cluster analysis of protein spectra was performed to identify protein patterns related to BC and HV groups. Univariate and multivariate statistical analyses were used to develop a protein panel to distinguish breast cancer sera from healthy sera, and its prognostic potential was evaluated.ResultsFrom 51 protein peaks that were significantly up- or downregulated in BC patients by univariate analysis, binary logistic regression yielded five protein peaks that together classified BC and HV with a receiver operating characteristic (ROC) area-under-the-curve value of 0.961. Validation on an independent patient cohort confirmed the five-protein parameter (ROC value 0.939). The five-protein parameter showed positive association with large tumor size (P = 0.018) and lymph node involvement (P = 0.016). By matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, immunoprecipitation and western blotting the proteins were identified as a fragment of apolipoprotein H (ApoH), ApoCI, complement C3a, transthyretin, and ApoAI. Kaplan-Meier analysis on 181 subjects after median follow-up of >5 years demonstrated that the panel significantly predicted disease-free survival (P = 0.005), its efficacy apparently greater in women with estrogen receptor (ER)-negative tumors (n = 50, P = 0.003) compared to ER-positive (n = 131, P = 0.161), although the influence of ER status needs to be confirmed after longer follow-up.ConclusionsProtein mass profiling by MS has revealed five serum proteins which, in combination, can distinguish between serum from women with breast cancer and healthy control subjects with high sensitivity and specificity. The five-protein panel significantly predicts recurrence-free survival in women with ER-negative tumors and may have value in the management of these patients.

Epidemiological tools for effective surveillance of porcine cysticercosis in Africa

Porcine cysticercosis is widely distributed in developing countries. Many tools were developed for effective control of the tapeworm in endemic countries. Tongue examination, meat inspection and Ag-ELISA were widely used in epidemiological survey. Both tongue examination and meat inspection are highly specific but less sensitive. To improve performance of AgELISA, unambiguous test based on nanobodies was performed. Immunodiagnostic tests based on PCR, flows through assay (FTA), Surface Enhanced Laser Desorption–Ionization Time of Flight (SELDI-TOF) were also developed. Less data were reported using spatial statistical analysis hence multiples approaches were available for effective epidemiological survey of porcine cysticercosis.

Identification of diagnostic and prognostic biomarkers to improve the management of diabetes-related ulcers

IntroductionDiabetes-related ulcers are a common and severe complication of diabetes which is expected to increase in prevalence in line with projected global growth in rates of diabetes. Caring for these chronic wounds imposes a multi-billion dollar burden on the health care systems. These ulcers can prove lethal if untreated or not recognised and can lead to critical health complications. MethodsTo investigate underlying causes of wound chronicity, proteomic analyses of swab samples collected weekly from healing and non-healing diabetic foot ulcers was performed. Protein profiling was conducted based on Surface Enhanced Laser Desorption Ionisation Time of Flight (SELDI-TOF) mass spectrometry and statistical softwares were used to short list potential biomarkers. In addition, bottom-up proteomics was performed on healing and non-healing samples by SDS-PAGE and LC-MS/MS analysis using an AB SCIEX Triple TOF ® 5600 System. Trans-proteomic pipeline was used for data analyses and X! Tandem was used to search the database. Label-free quantitative proteomic analyses were performed using a computational tool called Abacus. Results(1) Statistical analyses of healing and non healing samples analysed on SELDI-TOF revealed 5 and 7 potential biomarkers (m/z) for samples with Texas score A1 and C1 respectively. (2) Bottom-up proteomics approach from both healing and non-healing samples identified 15 unique (healing) and 16 unique (non-healing) potential biomarkers. (3) Quantitative proteomic analyses resulted in 24 and 45 up-regulated healing candidates and 67 and 43 up-regulated nonhealing candidates for Texas score A1 and C1 wounds. (4) Relative quantification of 23 proteins related to oxidative stress has been identified through Abacus and 5/23 proteins have been validated using ELISA. ConclusionsWe are investigating these potential biomarkers using various biochemical, bioinformatics and statistical tools. A thorough investigation and study of the patterns may generate new protein candidates that can be used as potential prognostic and diagnostic biomarkers to improve the management of diabetic ulcers.

The diagnostic performance of the Mass Restricted (MR) score in the identification of microbial invasion of the amniotic cavity or intra-amniotic inflammation is not superior to amniotic fluid interleukin-6

Objective: Intra-amniotic infection/inflammation are major causes of spontaneous preterm labor and delivery. However, diagnosis of intra-amniotic infection is challenging because most are subclinical and amniotic fluid (AF) cultures take several days before results are available. Several tests have been proposed for the rapid diagnosis of microbial invasion of the amniotic cavity (MIAC) or intra-amniotic inflammation. The aim of this study was to examine the diagnostic performance of the AF Mass Restricted (MR) score in comparison with interleukin-6 (IL-6) and matrix metalloproteinase-8 (MMP-8) for the identification of MIAC or inflammation.Methods: AF samples were collected from patients with singleton gestations and symptoms of preterm labor (n = 100). Intra-amniotic inflammation was defined as >100 white blood cells/mm3 (WBCs) in AF; MIAC was defined as a positive AF culture. AF IL-6 and MMP-8 were determined using ELISA. The MR score was obtained using the Surface-Enhanced Laser Desorption Ionization Time of Flight (SELDI-TOF) mass spectrometry. Sensitivity and specificity were calculated and logistic regression models were fit to construct receiver-operating characteristic (ROC) curves for the identification of each outcome. The McNemar’s test and paired sample non-parametric statistical techniques were used to test for differences in diagnostic performance metrics.Results: (1) The prevalence of MIAC and intra-amniotic inflammation was 34% (34/100) and 40% (40/100), respectively; (2) there were no significant differences in sensitivity of the three tests under study (MR score, IL-6 or MMP-8) in the identification of either MIAC or intra-amniotic inflammation (using the following cutoffs: MR score >2, IL-6 >11.4 ng/mL, and MMP-8 >23 ng/mL); (3) there was no significant difference in the sensitivity among the three tests for the same outcomes when the false positive rate was fixed at 15%; (4) the specificity for IL-6 was not significantly different from that of the MR score in identifying either MIAC or intra-amniotic inflammation when using previously reported thresholds; and (5) there were no significant differences in the area under the ROC curve when comparing the MR score, IL-6 or MMP-8 in the identification of these outcomes.Conclusions: IL-6 and the MR score have equivalent diagnostic performance in the identification of MIAC or intra-amniotic inflammation. Selection from among these three tests (MR score, IL-6 and MMP-8) for diagnostic purposes should be based on factors such as availability, reproducibility, and cost. The MR score requires a protein chip and a SELDI-TOF instrument which are not widely available or considered “state of the art”. In contrast, immunoassays for IL-6 can be performed in the majority of clinical laboratories.

SELDI-TOF analysis of glioblastoma cyst fluid is an approach for assessing cellular protein expression

Objectives:In about 10% of glioblastoma patients, preoperative MRI discloses the presence of tumor cysts. Whereas the impact of cystic appearance on prognosis has been discussed extensively, only little is known about the tumor cyst fluid. In this study, we tested the feasibility of the surface enhanced laser desorption ionization time of flight (SELDI-TOF) technique to detect cyst fluid proteins.Methods:Cyst fluid was collected from 21 glioblastoma patients for SELDI-TOF analysis and compared to control cerebrospinal fluids from 15 patients with spinal stenosis. Resulting protein peaks with significant differences between groups were further described, using the molecular weight in an internet search of protein databases and publications. Two potential cyst fluid proteins, basigin and ferritin light chain, were selected for immunohistological detection in the histologic slides of the patients, metallothionein (MT) served as negative control.Results:As supposed from the results of the SELDI-TOF analysis, basigin and ferritin were detected immunohistochemically in the cyst wall, whereas MT was more equally distributed between the cyst wall and the surrounding tumor tissue. Median survival time of the patients was 20 months (range 2 to 102 months) and correlated with age, but not with expression of the three proteins.Discussion:The SELDI-TOF approach reveals a number of proteins, potentially present in glioblastoma cyst fluid. Identification of these proteins in tumor cells may help understand the pathogenetic pathways and the prognostic value of cystic changes.

The Human Urinary Proteome Fingerprint Database UPdb

The use of human urine as a diagnostic tool has many advantages, such as ease of sample acquisition and noninvasiveness. However, the discovery of novel biomarkers, as well as biomarker patterns, in urine is hindered mainly by a lack of comparable datasets. To fill this gap, we assembled a new urinary fingerprint database. Here, we report the establishment of a human urinary proteomic fingerprint database using urine from 200 individuals analysed by SELDI-TOF (surface enhanced laser desorption ionisation-time of flight) mass spectrometry (MS) on several chip surfaces (SEND, HP50, NP20, Q10, CM10, and IMAC30). The database currently lists 2490 unique peaks/ion species from 1172 nonredundant SELDI analyses in the mass range of 1500 to 150000. All unprocessed mass spectrometric scans are available as “.xml” data files. Additionally, 1384 peaks were included from external studies using CE (capillary electrophoresis)-MS, MALDI (matrix assisted laser desorption/ionisation), and CE-MALDI hybrids. We propose to use this platform as a global resource to share and exchange primary data derived from MS analyses in urinary research.

Urine screening by Seldi-Tof, followed by biomarker identification, in a Brazilian cohort of patients with Renal Cell Carcinoma (RCC)

To screen proteins/peptides in urine of Renal Cell Carcinoma (RCC) patients by SELDI-TOF (Surface Enhanced Laser Desorption Ionization - Time of Flight) in search of possible biomarkers. Sixty-one urines samples from Clear Cell RCC and Papillary RCC were compared to 29 samples of control urine on CM10 chip. Mass analysis was performed in a ProteinChip Reader PCS 4,000 (Ciphergen Biosystems, Fremont, CA) with the software Ciphergen Express 3.0. All chips were read at low and at high laser energy. For statistical analysis the urine samples were clustered according to the histological classification (Clear Cell and Papillary Carcinoma). For identification urine was loaded on a SDS PAGE gel and bands of most interest were excised, trypsinized and identified by MS/MS. Databank searches were performed in Swiss-Prot database using the MASCOT search algorithm and in Profound. Proteins that were identified from urine of controls included immunoglobulin light chains, albumin, secreted and transmembrane 1 precursor (protein K12), mannan-binding lectin-associated serine protease-2 (MASP-2) and vitelline membrane outer layer 1 isoform 1. Identification of immunoglobulins and isoforms of albumin are quite common by proteomics and therefore cannot be considered as possible molecular markers. K12 and MASP-2 play important physiological roles, while vitellite membrane outer layer 1 role is unknown since it was never purified in humans. The down expression of Protein K-12 and MASP-2 make them good candidates for RCC urine marker and should be validated in a bigger cohort including the other less common histological RCC subtypes.

Alterations in the Tear Proteome of Dry Eye Patients—A Matter of the Clinical Phenotype

Previous studies demonstrated alterations in the tear proteome of dry eye patients. The aim of the present study was to analyze tear protein patterns of dry eye patients considering different clinical phenotypes in order to examine their influence on tear film protein composition. We applied a surface-enhanced laser desorption/ ionization-time-of-flight (SELDI-TOF)/matrix-assisted laser desorption/ ionization-time-of-flight (MALDI-TOF)/TOF mass spectrometry (MS)-based strategy to detect/identify candidate biomarkers. Tear samples of 169 patients, enrolled in two independent studies, were analyzed. Patients were subdivided into healthy controls(CTRL: N = 39), aqueous-deficient dry eye (DRYaq: N = 40), lipid-deficient dry eye (DRYlip: N = 40), and a combination of the two (DRYaqlip: N = 40). We uncovered six peptide/protein markers matching the stringent criteria applied for selection of reliable markers (P < 5.0E-03 in both studies). For example, proline-rich protein 4 was found to be diminished in DRYaq and DRYaqlip patients when compared to healthy subjects. Mammaglobin B and lipophilin A were found to be increased in these patients, as well as calgranulin S100A8. Remarkably, DRYlip patients revealed only slight alterations; these patients strongly deviated from the DRYaq or DRYaqlip group. With regard to classification of patients, we achieved discrimination from healthy subjects with a sensitivity and specificity ≈100% for DRYaq and DRYaqlip patients (receiver operating characteristic curve [ROC curve]: area under the curve [AUC] = 1) through use of the six-biomarker set. This study demonstrates that different clinical phenotypes of dry eye are reflected by specific alterations of the tear film proteome. Especially a deficiency of the aqueous phase of the tear film seems to strongly influence the expression patterns of several proteins.

Pre-analytical factors influencing the stability of cerebrospinal fluid proteins

Cerebrospinal fluid (CSF) is a potential source for new biomarkers due to its proximity to the brain. This study aimed to clarify the stability of the CSF proteome when undergoing pre-analytical factors.We investigated the effects of repeated freeze/thaw cycles, protease inhibitors and delayed storage for 4h, 24h or 14 days at −20°C, 4°C and room temperature (RT) after centrifugation compared with our standard practice of two hours at RT before placing the samples in an −80°C environment. The results were obtained using immunoassays for amyloid-beta 1–42 (Aβ42), tau, phosphorylated tau (P-tau) and cystatin C and using surface-enhanced laser desorption/ionisation time-of-flight (SELDI-TOF) mass spectrometry for proteomic profiling.Tau and P-tau were susceptible to repeated freeze/thaw cycles while SELDI-TOF analysis produced eight significant peaks and additional artefact peaks from samples with added protease inhibitors. Delayed storage for different durations and in different temperatures produced six significant SELDI-TOF peaks. Aβ42 and tau were susceptible to increased temperatures and the duration before storage, whereas P-tau and cystatin C were not. Transthyretin and several of its isoforms were found using SELDI-TOF and were susceptible to freeze/thaw cycles and to increased temperature and length of time prior to storage.We recommend that CSF should be collected and centrifuged immediately after sampling and prior to storage at −80°C without the addition of protease inhibitors. Freeze/thawing should be avoided because of the instability of tau, P-tau and transthyretin. Standardised CSF sampling, handling and storage for biomarker research are essential for accurately comparing the results obtained by different studies and institutions.

Attempted Validation of Surface Enhanced Laser Desorption Ionization-Time of Flight Derived Kinesin Biomarkers in Malignant Mesothelioma

Surface-enhanced Laser Desorption/Ionization Time-of-flight (SELDI-TOF) mass spectrometry allows researchers to search proteomes for biomarkers of disease. Validating SELDI-TOF results using traditional methodologies has yielded mixed results. Real-time PCR, ELISA and Western blot assays were utilized in an attempt to confirm the link between asbestos related cancers and kinesin family proteins, KIF5A and KIF18A. These proteins had been identified using SELDI-TOF and Classification and Regression Tree Analysis (CART) in serum of patients with asbestos related cancers. When well-characterized asbestos fibers were used to challenge mesothelial cell lines, mixed results in KIF5A and KIF18A RNA expression were observed. Western blot analysis comparing protein levels in mesothelioma cell lines versus transformed mesothelial cells yielded inconclusive results, as did Western blot analyses of human mesothelioma and non-cancerous peritoneum that had been obtained from the same patients. These results suggest that kinesin family proteins detected by SELDI-TOF CART are unlikely to be of use as biomarkers for malignant mesothelioma.

Biomarker Selection and Classification of “-Omics” Data Using a Two-Step Bayes Classification Framework

Identification of suitable biomarkers for accurate prediction of phenotypic outcomes is a goal for personalized medicine. However, current machine learning approaches are either too complex or perform poorly. Here, a novel two-step machine-learning framework is presented to address this need. First, a Naïve Bayes estimator is used to rank features from which the top-ranked will most likely contain the most informative features for prediction of the underlying biological classes. The top-ranked features are then used in a Hidden Naïve Bayes classifier to construct a classification prediction model from these filtered attributes. In order to obtain the minimum set of the most informative biomarkers, the bottom-ranked features are successively removed from the Naïve Bayes-filtered feature list one at a time, and the classification accuracy of the Hidden Naïve Bayes classifier is checked for each pruned feature set. The performance of the proposed two-step Bayes classification framework was tested on different types of -omics datasets including gene expression microarray, single nucleotide polymorphism microarray (SNParray), and surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) proteomic data. The proposed two-step Bayes classification framework was equal to and, in some cases, outperformed other classification methods in terms of prediction accuracy, minimum number of classification markers, and computational time.

Proteomic analysis of midtrimester amniotic fluid to identify novel biomarkers for preterm delivery

Objective: The aim of this study was to identify possible biomarkers for preterm delivery by analyzing midtrimester amniotic fluid. Methods: Thirty-two amniotic fluid samples were studied; 16 patients had a spontaneous preterm delivery and 16 patients delivered at term. The proteomic technique consisted of surface-enhanced laser desorption ionization time-of-flight (SELDI-TOF) using different types of solid chromatographic chips (Q10, CM10 and IMAC30). Results: Mass spectrometry tracings were obtained from the amniotic fluids of both patients who delivered preterm and patients who delivered at term. Seven potential markers were identified to be differentially expressed in patients who delivered preterm. Conclusions: Proteomic analysis of amniotic fluid obtained in the midtrimester reveals the presence of a set of proteins in patients at risk for preterm delivery.

Salivary proteome modifications associated with periodontitis in obese patients

To identify changes in the salivary protein/peptide profiles by differential proteomics in obese patients with or without periodontitis. Periodontal examinations and whole saliva samples were obtained from 38 obese patients (mean age: 45.1±7.3years, mean BMI: 49.3±9kg/m(2) ) including 13 periodontitis and 25 non-periodontitis subjects, and 19 healthy controls (mean age: 44.2±6.4years, mean BMI: 21.5±2.1kg/m(2) ). Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS) was used to compare the whole saliva polypeptide profiles. The SELDI-TOF-MS analysis detected eight putative markers. Six of them were increased and identified in obese subjects versus controls (albumin, α and β haemoglobin chains, α-defensins 1, 2 and 3). Alpha-defensins were less abundant in saliva of periodontitis obese patients (36.47±19.84μA) versus non-periodontitis obese patients (43.44±30.34 μA), whereas α-defensins were more abundant in obese patients (40.99±26.66 μA) versus controls (27.1±23.98 μA). Periodontal status modifies the salivary proteome in obese patients. Alpha-defensins may play a role in gingival inflammation, and be involved in the higher susceptibility of obese patients to periodontal diseases.