Machine learning approaches to lung cancer prediction from mass spectra

We addressed the problem of discriminating between 24 diseased and 17 healthy specimens on the basis of protein mass spectra. To prepare the data, we performed mass to charge ratio (m/z) normalization, baseline elimination, and conversion of absolute peak height measures to height ratios. After preprocessing, the major difficulty encountered was the extremely large number of variables (1676 m/z values) versus the number of examples (41). Dimensionality reduction was treated as an integral part of the classification process; variable selection was coupled with model construction in a single ten-fold cross-validation loop. We explored different experimental setups involving two peak height representations, two variable selection methods, and six induction algorithms, all on both the original 1676-mass data set and on a prescreened 124-mass data set. Highest predictive accuracies (1-2 off-sample misclassifications) were achieved by a multilayer perceptron and Na?ve Bayes, with the latter displaying more consistent performance (hence greater reliability) over varying experimental conditions. We attempted to identify the most discriminant peaks (proteins) on the basis of scores assigned by the two variable selection methods and by neural network based sensitivity analysis. These three scoring schemes consistently ranked four peaks as the most relevant discriminators: 11683, 1403, 17350 and 66107.     

Combinatorial approaches to materials discovery

Using a mixture of scientific intuition, iteration and serendipity, combinatorial materials science is an approach to the discovery and study of new materials that combines high-speed chemical synthesis, high-throughput screening and high-capacity information processing to create, analyse and interpret large numbers of new and diverse material compositions. Technology has now been developed that makes this powerful integration possible. The classes of materials under investigation include catalysts, luminescent, optical, magnetic and dielectric materials, and structural polymers.     

Combinatorial approaches to synthetic receptors

Combinatorial chemistry can be efficiently used for the synthesis and evaluation of binding properties of libraries of synthetic receptors. This approach has been applied particularly to 'tweezer' and other 'multi-armed' receptors, and has been used for the identification of receptors for peptides in aqueous media, and for the development of new sensors and sensor arrays.     

Combinatorial approaches to functional models for galactose oxidase

The copper enzyme galactose oxidase (GOase, EC 1.1.3.9) catalyses the oxidation of D-galactose and other primary alcohols in air to the corresponding aldehydes and hydrogen peroxide. The current mechanistic hypothesis for this two-electron redox reaction involves a Cu(I)/Cu(II) couple and the reversible oxidation of a ligating phenolate (tyrosine residue of the Tyr272-Cys228 conjugate) to a phenoxyl radical. Our approaches to functional models for galactose oxidase comprise both the use of low-molecular-weight copper complexes of a Schiff-base and sulfonamide ligands, and the synthesis/screening of combinatorial libraries. With regard to the latter, we have synthesized (by the IRORI-directed synthesis approach) peptide libraries carrying either His or the redox-active amino acids Tyr, mod-Cys (a model for the Tyr272-Cys228 conjugate) or TOAC (a TEMPO-derived alpha-amino acid) at four variable positions. After incubation with copper ions, the catalytically active library members were identified by specially designed screening methods.     

Combinatorial approaches to affinity chromatography

A new armoury of protein purification tools is required to support rapid advances in high-throughput genomics and proteomics, which are predicted to lead to the discovery, isolation, characterisation and manufacture of a number of new biopharmaceutical proteins. Computer-aided molecular design, combinatorial (bio)chemistry and high-throughput screening techniques are now being exploited to identify highly selective ligands for use in the purification of these proteins by affinity chromatography.     

Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly

Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.     

Screening for transglutaminase-catalyzed modifications by peptide mass finger printing using multipoint recalibration on recognized peaks for high mass accuracy.

Detection of posttranslational modifications is expected to be one of the major future experimental challenges for proteomics. We describe herein a mass spectrometric procedure to screen for protein modifications by peptide mass fingerprinting that is based on post-data acquisition improvement of the mass accuracy by exporting the peptide mass values into analytical software for multipoint recalibration on recognized peaks. Subsequently, the calibrated peak mass data set is used in searching for modified peptides, i.e., peptides possessing specific mass deviations. In order to identify the location of Lys- and Gln-residues available for transglutaminase-catalyzed isopeptide bond formation, mammalian small heat shock proteins (sHsps) were screened for labeling with the two hexapeptide probes GQDPVR and GNDPVK in presence of transglutaminase. Peptide modification due to cross-linking of the GQDPVR hexa-peptide probe was detected for C-terminal Lys residues. Novel transglutaminase-susceptible Gln sites were identified in two sHsps (Q31/Q27 in Hsp20 and HspB2, respectively), by cross-linking of the GNDPVK hexapeptide probe. Deamidation of specific Gln residues was also detected, as well an isopeptide derived from intramolecular Gln-Lys isopeptide bond formation. We conclude that peptide mass fingerprinting can be an efficient way of screening for various posttranslational modifications. Basically any instrumentation for MALDI mass spectrometry can be used, provided that post-data acquisition recalibration is applied.     

Mini-review: Combinatorial approaches for the design of novel coating systems

Abstract

Combinatorial and high throughput experimental methods are being applied to the design and development of novel polymers and coatings used in a number of application areas. Methods have been developed for polymer synthesis and screening and for the development of polymer thin film and coating libraries and the screening of these libraries for key properties such as surface energy and modulus. Combinatorial and high throughput methods enable the efficient exploration of a large number of compositional variables over a wide range. In the development of coatings for use in the marine environment, the key challenge is in the development of screening methods that can predict good performance. A number of assays are under development that will permit the rapid screening of the interaction of coatings with representative marine organisms.     

Combinatorial approaches to protein stability and structure.

Why do proteins adopt the conformations that they do, and what determines their stabilities? While we have come to some understanding of the forces that underlie protein architecture, a precise, predictive, physicochemical explanation is still elusive. Two obstacles to addressing these questions are the unfathomable vastness of protein sequence space, and the difficulty in making direct physical measurements on large numbers of protein variants. Here, we review combinatorial methods that have been applied to problems in protein biophysics over the last 15 years. The effects of hydrophobic core composition, the most important determinant of structure and stability, are still poorly understood. Particular attention is given to core composition as addressed by library methods. Increasingly useful screens and selections, in combination with modern high-throughput approaches borrowed from genomics and proteomics efforts, are making the empirical, statistical correlation between sequence and structure a tractable problem for the coming years.     

Combinatorial approaches towards the discovery of new tryptase inhibitors

The synthesis and evaluation as tryptase inhibitors of a library of 2,5-diketopiperazine derivatives containing guanidine or amidine functional groups is reported. Among the compounds evaluated, derivatives 6{CG4-CG8} and 6{CG4-CG9} are the most active compounds and have marked selectivity towards tryptase in front of trypsin.     

Combinatorial computational approaches to identify tetracycline derivatives as flavivirus inhibitors

Limited structural information of drug targets, cellular toxicity possessed by lead compounds, and large amounts of potential leads are the major issues facing the design-oriented approach of discovering new leads. In an attempt to tackle these issues, we have developed a process of virtual screening based on the observation that conformational rearrangements of the dengue virus envelope protein are essential for the mediation of viral entry into host cells via membrane fusion. Screening was based solely on the structural information of the Dengue virus envelope protein and was focused on a target site that is presumably important for the conformational rearrangements necessary for viral entry. To circumvent the issue of lead compound toxicity, we performed screening based on molecular docking using structural databases of medical compounds. To enhance the identification of hits, we further categorized and selected candidates according to their novel structural characteristics. Finally, the selected candidates were subjected to a biological validation assay to assess inhibition of Dengue virus propagation in mammalian host cells using a plaque formation assay. Among the 10 compounds examined, rolitetracycline and doxycycline significantly inhibited plaque formation, demonstrating their inhibitory effect on dengue virus propagation. Both compounds were tetracycline derivatives with IC(50)s estimated to be 67.1 microM and 55.6 microM, respectively. Their docked conformations displayed common hydrophobic interactions with critical residues that affected membrane fusion during viral entry. These interactions will therefore position the tetracyclic ring moieties of both inhibitors to bind firmly to the target and, subsequently, disrupt conformational rearrangement and block viral entry. This process can be applied to other drug targets in which conformational rearrangement is critical to function.     

Targeted mass spectrometry approaches for protein biomarker verification

The search for protein biomarkers has been a highly pursued topic in the proteomics community in the last decade. This relentless search is due to the constant need for validated biomarkers that could facilitate disease risk stratification, disease diagnosis, prognosis, monitoring as well as drug development, which ultimately would improve our quality of life. The recent development of proteomic technologies including the advancement of mass spectrometers with high sensitivity and speed has greatly advanced the discovery of potential biomarkers. One of the bottlenecks lies in the development of well-established verification assays to screen the biomarker candidates identified in the discovery stage. Recently, absolute quantitation using multiple-reaction monitoring mass spectrometry (MRM-MS) in combination with isotope-labeled internal standards has been extensively investigated as a tool for high-throughput protein biomarker verification. In this review, we describe and discuss recent developments and applications of MRM-MS methods for biomarker verification.     

基于质谱技术的神经肽研究进展

神经肽是一类重要的内源活性物质,在神经系统中发挥重要的作用,并连接大脑和其他神经器官。基于质谱技术的神经肽组学研究旨在对神经肽进行大规模研究,在分子水平上得到重要信息,进一步加深对神经系统调控机制以及神经疾病致病机理的理解。文中综述了利用质谱技术进行神经肽研究的基本策略,包括样品处理、定性定量方法以及质谱成像等研究进展。     

Electron and photon spectra for three gadolinium-based cancer therapy approaches

Some recent neutron capture therapy research has focused on using compounds containing the element gadolinium, which produces internal conversion and Auger cascade electrons. The low-energy, short-range Auger electrons are absorbed locally and increase cell killing dramatically as the gadolinium compounds are introduced into the cell nucleus and bind to the DNA. Detailed electron and photon spectra are needed for biophysical modeling and Monte Carlo calculations of damage to DNA. This paper presents calculated electron and photon spectra for three cases: thermal neutron absorption by (157)Gd, the beta-particle decay of (159)Gd, and the K-shell photoelectric event in gadolinium. The Monte Carlo sampling of atomic and nuclear transitions for each of the three cases was used to calculate a large number of representative decays. The sampled decays were used to determine average emissions and energy deposited in small spheres of tissue. The kinetic energy nuclear recoil from gamma-ray and electron emissions was calculated and found to be more than 10 eV for 26% of all (157)Gd neutron capture reactions.     

Temporal recalibration of vision

Our sense of relative timing is malleable. For instance, visual signals can be made to seem synchronous with earlier sounds following prolonged exposure to an environment wherein auditory signals precede visual ones. Similarly, actions can be made to seem to precede their own consequences if an artificial delay is imposed for a period, and then removed. Here, we show that our sense of relative timing for combinations of visual changes is similarly pliant. We find that direction reversals can be made to seem synchronous with unusually early colour changes after prolonged exposure to a stimulus wherein colour changes precede direction changes. The opposite effect is induced by prolonged exposure to colour changes that lag direction changes. Our data are consistent with the proposal that our sense of timing for changes encoded by distinct sensory mechanisms can adjust, at least to some degree, to the prevailing environment. Moreover, they reveal that visual analyses of colour and motion are sufficiently independent for this to occur.     

Combinatorial approaches to probe the sequence determinants of protein aggregation and amyloidogenicity

Elucidation of the molecular determinants that drive proteins to aggregate is important both to advance our fundamental understanding of protein folding and misfolding, and as a step towards successful intervention in human disease. Combinatorial strategies enable unbiased and model-free approaches to probe sequence/structure relationships. Through the use of combinatorial methods, it is possible (i) to probe the sequence determinants of natural amyloid proteins by screening libraries of amino acid substitutions (mutations) to identify those that prevent amyloid formation; and (ii) to test new hypotheses about the mechanism of formation of amyloid fibrils by using these hypotheses to guide the design of combinatorial libraries of de novo amyloid-like proteins. Here, we review how these two approaches have been used to study the molecular determinants of protein aggregation and amyloidogenicity.     

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

Summary: DeconMSn accurately determines the monoisotopic massand charge state of parent ions from high-resolution tandemmass spectrometry data, offering significant improvement forLTQ_FT and LTQ_Orbitrap instruments over the commercially deliveredThermo Fisher Scientific's extract_msn tool. Optimal parention mass tolerance values can be determined using accurate massinformation, thus improving peptide identifications for high-massmeasurement accuracy experiments. For low-resolution data fromLCQ and LTQ instruments, DeconMSn incorporates a support-vector-machine-basedcharge detection algorithm that identifies the most likely chargeof a parent species through peak characteristics of its fragmentationpattern. Availability: http://ncrr.pnl.gov/software/ or http://www.proteomicsresource.org/ Contact: rds{at}pnl.gov Supplementary information: PowerPoint presentation/Poster onhttp://ncrr.pnl.gov/software/. Associate Editor: Alfonso Valencia     

利用MALDI-TOF MS对血流感染病原菌快速鉴定的研究进展

基质辅助激光解析电离飞行时间质谱(MALDI-TOF MS)是近年来发展起来的一种非常重要的病原微生物鉴定方法,在临床微生物实验室的应用具有划时代的意义.除了有较高的准确性外,它的最大优点是能在很短时间内完成病原微生物的鉴定.在临床血流感染的诊断中,结果报告的准确性和及时性至关重要,MALDI-TOF MS具有高效准确,快速简便的特点,有可能成为传统血流感染病原菌检测的替代或补充方法.随着质谱数据库和分析软件的完善,MALDI-TOF MS目前能鉴定超过80％的阳性血培养病原菌.然而它还需要不断改进,包括建立前处理程序的标准化,详尽全面的数据库以及分析软件的优化.不远将来,它将更加简便、快速、准确,为血培养中病原菌的诊断提供更有力支持.     

Interpreting peptide mass spectra by VEMS

Most existing Mass Spectra (MS) analysis programs are automatic and provide limited opportunity for editing during the interpretation. Furthermore, they rely entirely on publicly available databases for interpretation. VEMS (Virtual Expert Mass Spectrometrist) is a program for interactive analysis of peptide MS/MS spectra imported in text file format. Peaks are annotated, the monoisotopic peaks retained, and the b-and y-ion series identified in an interactive manner. The called peptide sequence is searched against a local protein database for sequence identity and peptide mass. The report compares the calculated and the experimental mass spectrum of the called peptide. The program package includes four accessory programs. VEMStrans creates protein databases in FASTA format from EST or cDNA sequence files. VEMSdata creates a virtual peptide database from FASTA files. VEMSdist displays the distribution of masses up to 5000 Da. VEMSmaldi searches singly charged peptide masses against the local database.