Target Decoy Research Articles

Two-Dimensional Target Decoy Strategy for Shotgun Proteomics

The target-decoy approach to estimating and controlling false discovery rate (FDR) has become a de facto standard in shotgun proteomics, and it has been applied at both the peptide-to-spectrum match (PSM) and protein levels. Current bioinformatics methods control either the PSM- or the protein-level FDR, but not both. In order to obtain the most reliable information from their data, users must employ one method when the number of tandem mass spectra exceeds the number of proteins in the database and another method when the reverse is true. Here we propose a simple variation of the standard target-decoy strategy that estimates and controls PSM and protein FDRs simultaneously, regardless of the relative numbers of spectra and proteins. We demonstrate that even if the final goal is a list of PSMs with a fixed low FDR and not a list of protein identifications, the proposed two-dimensional strategy offers advantages over a pure PSM-level strategy.

Proteomic Profiling of Adipose Tissue from Zmpste24−/− Mice, a Model of Lipodystrophy and Premature Aging, Reveals Major Changes in Mitochondrial Function and Vimentin Processing

Lipodystrophy is a major disease involving severe alterations of adipose tissue distribution and metabolism. Mutations in genes encoding the nuclear envelope protein lamin A or its processing enzyme, the metalloproteinase Zmpste24, cause diverse human progeroid syndromes that are commonly characterized by a selective loss of adipose tissue. Similarly to humans, mice deficient in Zmpste24 accumulate prelamin A and display phenotypic features of accelerated aging, including lipodystrophy. Herein, we report the proteome and phosphoproteome of adipose tissue as well as serum metabolome in lipodystrophy by using Zmpste24(-/-) mice as experimental model. We show that Zmpste24 deficiency enhanced lipolysis, fatty acid biogenesis and β-oxidation as well as decreased fatty acid re-esterification, thus pointing to an increased partitioning of fatty acid toward β-oxidation and away from storage that likely underlies the observed size reduction of Zmpste24-null adipocytes. Besides the mitochondrial proteins related to lipid metabolism, other protein networks related to mitochondrial function, including those involved in tricarboxylic acid cycle and oxidative phosphorylation, were up-regulated in Zmpste24(-/-) mice. These results, together with the observation of an increased mitochondrial response to oxidative stress, support the relationship between defective prelamin A processing and mitochondrial dysfunction and highlight the relevance of oxidative damage in lipoatrophy and aging. We also show that absence of Zmpste24 profoundly alters the processing of the cytoskeletal protein vimentin and identify a novel protein dysregulated in lipodystrophy, High-Mobility Group Box-1 Protein. Finally, we found several lipid derivates with important roles in energy balance, such as Lysophosphatidylcholine or 2-arachidonoylglycerol, to be dysregulated in Zmpste24(-/-) serum. Together, our findings in Zmpste24(-/-) mice may be useful to unveil the mechanisms underlying adipose tissue dysfunction and its overall contribution to body homeostasis in progeria and other lipodystrophy syndromes as well as to develop novel strategies to prevent or ameliorate these diseases.

Regulation of Gene Expression in Plants through miRNA Inactivation

Eukaryotic organisms possess a complex RNA-directed gene expression regulatory network allowing the production of unique gene expression patterns. A recent addition to the repertoire of RNA-based gene regulation is miRNA target decoys, endogenous RNA that can negatively regulate miRNA activity. miRNA decoys have been shown to be a valuable tool for understanding the function of several miRNA families in plants and invertebrates. Engineering and precise manipulation of an endogenous RNA regulatory network through modification of miRNA activity also affords a significant opportunity to achieve a desired outcome of enhanced plant development or response to environmental stresses. Here we report that expression of miRNA decoys as single or heteromeric non-cleavable microRNA (miRNA) sites embedded in either non-protein-coding or within the 3′ untranslated region of protein-coding transcripts can regulate the expression of one or more miRNA targets. By altering the sequence of the miRNA decoy sites, we were able to attenuate miRNA inactivation, which allowed for fine regulation of native miRNA targets and the production of a desirable range of plant phenotypes. Thus, our results demonstrate miRNA decoys are a flexible and robust tool, not only for studying miRNA function, but also for targeted engineering of gene expression in plants. Computational analysis of the Arabidopsis transcriptome revealed a number of potential miRNA decoys, suggesting that endogenous decoys may have an important role in natural modulation of expression in plants.

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model. On proteome data, Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. Furthermore, it can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. The algorithms of Andromeda are provided. Andromeda can function independently or as an integrated search engine of the widely used MaxQuant computational proteomics platform and both are freely available at www.maxquant.org. The combination enables analysis of large data sets in a simple analysis workflow on a desktop computer. For searching individual spectra Andromeda is also accessible via a web server. We demonstrate the flexibility of the system by implementing the capability to identify cofragmented peptides, significantly improving the total number of identified peptides.

The Protein-disulfide Isomerase DsbC Cooperates with SurA and DsbA in the Assembly of the Essential β-Barrel Protein LptD

The assembly of the β-barrel proteins present in the outer membrane (OM) of Gram-negative bacteria is poorly characterized. After translocation across the inner membrane, unfolded β-barrel proteins are escorted across the periplasm by chaperones that reside within this compartment. Two partially redundant chaperones, SurA and Skp, are considered to transport the bulk mass of β-barrel proteins. We found that the periplasmic disulfide isomerase DsbC cooperates with SurA and the thiol oxidase DsbA in the folding of the essential β-barrel protein LptD. LptD inserts lipopolysaccharides in the OM. It is also the only β-barrel protein with more than two cysteine residues. We found that surAdsbC mutants, but not skpdsbC mutants, exhibit a synthetic phenotype. They have a decreased OM integrity, which is due to the lack of the isomerase activity of DsbC. We also isolated DsbC in a mixed disulfide complex with LptD. As such, LptD is identified as the first substrate of DsbC that is localized in the OM. Thus, electrons flowing from the cytoplasmic thioredoxin system maintain the integrity of the OM by assisting the folding of one of the most important β-barrel proteins.

Statistical potential for assessment and prediction of protein structures

Protein structures in the Protein Data Bank provide a wealth of data about the interactions that determine the native states of proteins. Using the probability theory, we derive an atomic distance-dependent statistical potential from a sample of native structures that does not depend on any adjustable parameters (Discrete Optimized Protein Energy, or DOPE). DOPE is based on an improved reference state that corresponds to noninteracting atoms in a homogeneous sphere with the radius dependent on a sample native structure; it thus accounts for the finite and spherical shape of the native structures. The DOPE potential was extracted from a nonredundant set of 1472 crystallographic structures. We tested DOPE and five other scoring functions by the detection of the native state among six multiple target decoy sets, the correlation between the score and model error, and the identification of the most accurate non-native structure in the decoy set. For all decoy sets, DOPE is the best performing function in terms of all criteria, except for a tie in one criterion for one decoy set. To facilitate its use in various applications, such as model assessment, loop modeling, and fitting into cryo-electron microscopy mass density maps combined with comparative protein structure modeling, DOPE was incorporated into the modeling package MODELLER-8.

Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations

Researchers have several options when designing proteomics experiments. Primary among these are choices of experimental method, instrumentation and spectral interpretation software. To evaluate these choices on a proteome scale, we compared triplicate measurements of the yeast proteome by liquid chromatography tandem mass spectrometry (LC-MS/MS) using linear ion trap (LTQ) and hybrid quadrupole time-of-flight (QqTOF; QSTAR) mass spectrometers. Acquired MS/MS spectra were interpreted with Mascot and SEQUEST algorithms with and without the requirement that all returned peptides be tryptic. Using a composite target decoy database strategy, we selected scoring criteria yielding 1% estimated false positive identifications at maximum sensitivity for all data sets, allowing reasonable comparisons between them. These comparisons indicate that Mascot and SEQUEST yield similar results for LTQ-acquired spectra but less so for QSTAR spectra. Furthermore, low reproducibility between replicate data acquisitions made on one or both instrument platforms can be exploited to increase sensitivity and confidence in large-scale protein identifications.

A quantitative study of Luneberg-lens reflectors

Luneberg-lens reflectors, which provide passive wideband and wide-angle radar-signature augmentation, have been widely used in small military target drones, decoys, and marine vessels. Due to the difficulty of fabricating inhomogeneous dielectrics with a continuously varying index, Luneberg lenses are usually constructed with multilayered step-index dielectrics. This paper presents a quantitative study of a practical design of a three-layer Luneberg-lens reflector for C- and X-band operations. Extensive wideband and wide-angle measurements were carried out for this lens with three different cap reflectors, as well as for the lens alone without any reflector. A comprehensive numerical analysis, using the finite-element method combined with boundary integral equations, was also conducted. This was done to support the measured data and to provide additional insight for a better understanding of the performance and the limitations of the Luneberg-lens reflector than could be achieved with the traditional ray-optics method. The effect of reflector size is discussed, and the limitation of three-layer design is demonstrated. It has also been shown that very accurate material parameters must be ascertained so as to achieve the level of accuracy commonly desired in the computational electromagnetic codes applied to inhomogeneous dielectrics. The excellent agreement between the numerical and measured data indicates that this full-wave Maxwell solver can be used to explore the design limits and optimize designs for this type of lens reflector.

The insulin-like growth factor system as a treatment target in breast cancer.

Advances in breast cancer treatment have come from the recognition that pathways relevant to cancer cell biology could be identified and targeted. There is abundant in vitro, animal model, and epidemiologic evidence to suggest that the insulin-like growth factors (IGFs) play a role in regulating the malignant phenotype in breast cancer. Insulin-like growth factor action has been implicated in malignant transformation, cellular proliferation, protection from apoptosis, and metastasis. Because IGFs interact with specific cell surface receptors to affect intracellular signaling pathways, blockade of receptor activation could be a successful method to interrupt IGF-driven processes. In contrast to other transmembrane growth factor receptors, the IGF receptor requires activation by ligand. Thus, neutralization of ligand by a "target decoy" could be a useful method to inhibit IGF action. Use of an IGF-binding protein to inhibit activation of IGF receptors will be discussed.

Irrational choices in hummingbird foraging behaviour

It is conventionally assumed that, when animals evaluate alternative options, the value assigned to an option is absolute and independent of the other options available. It follows that animal choices should exhibit the rational property of regularity whereby the proportion of choices for an option cannot be increased by the addition of further options to the choice set. However, violations of regularity occur in human decision making, suggesting that humans may use comparative evaluation mechanisms whereby the value of an option is computed relative to the other options available. For example, in the asymmetrically dominated decoy effect the preference for a target option over a competitor is altered by the addition of a decoy option that is inferior to the target and competitor on one attribute, but lies between them on a second. We tested whether foraging wild rufous hummingbirds, Selasphorus rufus, would demonstrate violations of regularity in response to an asymmetrically dominated decoy. Sixteen birds chose between three artificial flower types (Target: 15μl, 40% sucrose; Competitor: 45μl, 30%; Decoy: 10μl, 35%) in Binary (Target versus Competitor) and Trinary (Target versus Competitor versus Decoy) treatments. We predicted higher preference for the Target in the Trinary treatment. The birds ranked the three options in the same order in the Binary and Trinary treatments (Competitor>Target>Decoy). Seven birds showed violations of regularity, six increasing their absolute preference for the Competitor in the Trinary treatment. Overall, relative preference for the Competitor over the Target was higher in the Trinary than in the Binary treatment. These changes in preference are incompatible with an absolute evaluation mechanism.

The insulin-like growth factor system as a treatment target in breast cancer

Advances in breast cancer treatment have come from the recognition that pathways relevant to cancer cell biology could be identified and targeted. There is abundant in vitro, animal model, and epidemiologic evidence to suggest that the insulin-like growth factors (IGFs) play a role in regulating the malignant phenotype in breast cancer. Insulin-like growth factor action has been implicated in malignant transformation, cellular proliferation, protection from apoptosis, and metastasis. Because IGFs interact with specific cell surface receptors to affect intracellular signaling pathways, blockade of receptor activation could be a successful method to interrupt IGF-driven processes. In contrast to other transmembrane growth factor receptors, the IGF receptor requires activation by ligand. Thus, neutralization of ligand by a “target decoy” could be a useful method to inhibit IGF action. Use of an IGF-binding protein to inhibit activation of IGF receptors will be discussed. Semin Oncol 29 (suppl 11):86-95. Copyright 2002, Elsevier Science (USA). All rights reserved.

4907169 Adaptive tracking vision and guidance system

An adaptive dual-control guidance algorithm is presented for intercepting a moving target in the presence of an interfering target (decoy) in a stochastic environment. Two sequences of measurements are obtained at discrete points in time; however, it is not certain which sequence came from the target of interest and which from the decoy. Associated with each track, the interceptor also receives noisy, state-dependent feature measurements. The optimum control for the interceptor which is given by the solution of the stochastic dynamic programming equation is not numerically feasible to obtain. An approximate solution of this equation is obtained by evaluating the value of the future information gathering. This is done through the use of preposterior analysis—approximate prior probability densities are obtained and used to describe the future learning and control. In this way, the interceptor control is used for information gathering in order to reduce the future target and decoy intertial measurement errors and enhance the observable target/decoy feature differences for subsequent discrimination between the true target and the decoy. Simulation studies have shown the effectiveness of the scheme.

Dual control guidance for simultaneous identification and interception

An adaptive dual-control guidance algorithm is presented for intercepting a moving target in the presence of an interfering target (decoy) in a stochastic environment. Two sequences of measurements are obtained at discrete points in time; however, it is not certain which sequence came from the target of interest and which from the decoy. Associated with each track, the interceptor also receives noisy, state-dependent feature measurements. The optimum control for the interceptor which is given by the solution of the stochastic dynamic programming equation is not numerically feasible to obtain. An approximate solution of this equation is obtained by evaluating the value of the future information gathering. This is done through the use of preposterior analysis—approximate prior probability densities are obtained and used to describe the future learning and control. In this way, the interceptor control is used for information gathering in order to reduce the future target and decoy intertial measurement errors and enhance the observable target/decoy feature differences for subsequent discrimination between the true target and the decoy. Simulation studies have shown the effectiveness of the scheme.

Dual Control for Identification and Guidance

An adaptive dual control guidance algorithm is presented for intercepting a moving target in tile presence of an interfering target (decoy) in a stochastic environment. Two sequences of measurements are obtained at discrete points in time; however, it is not certain, which sequencecame from the target of interest and which from the decoy. Associated with each track, the interceptor also receives noisy, state dependent feature measurements. The optimum control for the interceptor which is given by the solution of the stochastic dynamic programming equation is not numerically feasible to obtain. An approximate solution of this equation is obtained by evaluating the value of the future information gathering. This is done through the use of preposterior analysis-approximate prior probability densities are obtained and used to describe the future learning and control. In this way, the interceptor control is used for information gathering in order to reduce the future target and decoy inertial measurement errors and enhance the observable target/decoy feature differences for subsequent dis crimination between the true target and the decoy.

DESCRIPTION OF A NEW SPECIES,CRANGON HANDI, AND NEW GENUS,LISSOCRANGON, OF CRANGONID SHRIMPS (CRUSTACEA: CARIDEA) FROM THE CALIFORNIA COAST, WITH NOTES ON ADAPTATION IN BODY SHAPE AND COLORATION

1. Crangon handi, new species. is described and compared with five other California crangonid shrimps; it occurs from the littoral zone to 55 m from Sonoma County to Bahia Colnett. northern Baja California. Crangon handi is a specialist for shallow-water coarse sand substrates and here exhibits remarkable crypsis. Crangon handi eats small gammarid amphipods and has in turn been found in the stomach of the thornback skate.2. Lissocrangon, new genus, is proposed to accomodate C. stylirostris, a species lacking gastric spination; Crangon is restricted to shrimp with one gastric spine; Steiracrangon Kinahan, is revived for shrimp with bicarinate sixth abdominal segments; and Neocrangon Zarenkov is revised and amended to include shrimp with two gastric spines and bicarinate sixth abdominal segments.3. Morphological analyses and relative growth are presented and discussed for all six crangonids considered. Crangon handi and L. stylirostris are squat shrimps in restricted habitats probably adapted for short quick bursts of movement followed by rapid reburial: the remaining four species are relatively elongate and habitat generalists.4. Crangon species normally occurring on finer mud and sand bottoms are unable to achieve the degree of crypsis of the coarse-grained species, Crangon handi. Crangon handi from dark coarse-grained sediments is only partially able to adapt to light coarse-grained sediments.5. Crangon nigromaculata is the only species with a lateral color spot, and it is suggested that this may serve as a predator shock signal or target decoy analogous to similar markings in some fish.6. Fish, such as cottids, and macrocrustaceans, including C. handi and the sphaeromatid isopod, Tecticeps convexus, sympatric with it on coarse sand bottoms, exhibit a wide range of mechanisms apparently to escape detection and avoid predation. Tecticeps alone has at least six such mechanisms. This suggests that predation pressure in such habitats may be relatively high.