Increasing confidence in proteomic spectral deconvolution through mass defect

MOTIVATION

Confident deconvolution of proteomic spectra is critical for several applications such as de novo sequencing, cross-linking mass spectrometry and handling chimeric mass spectra.

RESULTS

In general, all deconvolution algorithms may eventually report mass peaks that are not compatible with the chemical formula of any peptide. We show how to remove these artifacts by considering their mass defects. We introduce Y.A.D.A. 3.0, a fast deconvolution algorithm that can remove peaks with unacceptable mass defects. Our approach is effective for polypeptides with less than 10 kDa, and its essence can be easily incorporated into any deconvolution algorithm.

AVAILABILITY AND IMPLEMENTATION

Y.A.D.A. 3.0 is freely available for academic use at http://patternlabforproteomics.org/yada3.

SUPPLEMENTARY INFORMATION

Supplementary information is available at Bioinformatics online.

Molecular Architecture of the Antiophidic Protein DM64 and its Binding Specificity to Myotoxin II From Bothrops asper Venom

DM64 is a toxin-neutralizing serum glycoprotein isolated from Didelphis aurita, an ophiophagous marsupial naturally resistant to snake envenomation. This 64 kDa antitoxin targets myotoxic phospholipases A2, which account for most local tissue damage of viperid snakebites. We investigated the noncovalent complex formed between native DM64 and myotoxin II, a myotoxic phospholipase-like protein from Bothrops asper venom. Analytical ultracentrifugation (AUC) and size exclusion chromatography indicated that DM64 is monomeric in solution and binds equimolar amounts of the toxin. Attempts to crystallize native DM64 for X-ray diffraction were unsuccessful. Obtaining recombinant protein to pursue structural studies was also challenging. Classical molecular modeling techniques were impaired by the lack of templates with more than 25% sequence identity with DM64. An integrative structural biology approach was then applied to generate a three-dimensional model of the inhibitor bound to myotoxin II. I-TASSER individually modeled the five immunoglobulin-like domains of DM64. Distance constraints generated by cross-linking mass spectrometry of the complex guided the docking of DM64 domains to the crystal structure of myotoxin II, using Rosetta. AUC, small-angle X-ray scattering (SAXS), molecular modeling, and molecular dynamics simulations indicated that the DM64-myotoxin II complex is structured, shows flexibility, and has an anisotropic shape. Inter-protein cross-links and limited hydrolysis analyses shed light on the inhibitor's regions involved with toxin interaction, revealing the critical participation of the first, third, and fifth domains of DM64. Our data showed that the fifth domain of DM64 binds to myotoxin II amino-terminal and beta-wing regions. The third domain of the inhibitor acts in a complementary way to the fifth domain. Their binding to these toxin regions presumably precludes dimerization, thus interfering with toxicity, which is related to the quaternary structure of the toxin. The first domain of DM64 interacts with the functional site of the toxin putatively associated with membrane anchorage. We propose that both mechanisms concur to inhibit myotoxin II toxicity by DM64 binding. The present topological characterization of this toxin-antitoxin complex constitutes an essential step toward the rational design of novel peptide-based antivenom therapies targeting snake venom myotoxins.

Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition

MOTIVATION

Chemical cross-linking coupled to mass spectrometry (XLMS) emerged as a powerful technique for studying protein structures and large-scale protein-protein interactions. Nonetheless, XLMS lacks software tailored toward dealing with multiple conformers; this scenario can lead to high-quality identifications that are mutually exclusive. This limitation hampers the applicability of XLMS in structural experiments of dynamic protein systems, where less abundant conformers of the target protein are expected in the sample.

RESULTS

We present QUIN-XL, a software that uses unsupervised clustering to group cross-link identifications by their quantitative profile across multiple samples. QUIN-XL highlights regions of the protein or system presenting changes in its conformation when comparing different biological conditions. We demonstrate our software's usefulness by revisiting the HSP90 protein, comparing three of its different conformers. QUIN-XL's clusters correlate directly to known protein 3D structures of the conformers and therefore validates our software.

AVAILABILITYAND IMPLEMENTATION

QUIN-XL and a user tutorial are freely available at http://patternlabforproteomics.org/quinxl for academic users.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment

MOTIVATION

We present a high-performance software integrating shotgun with top-down proteomic data. The tool can deal with multiple experiments and search engines. Enable rapid and easy visualization, manual validation and comparison of the identified proteoform sequences including the post-translational modification characterization.

RESULTS

We demonstrate the effectiveness of our approach on a large-scale Escherichia coli dataset; ProteoCombiner unambiguously shortlisted proteoforms among those identified by the multiple search engines.

AVAILABILITY AND IMPLEMENTATION

ProteoCombiner, a demonstration video and user tutorial are freely available at https://proteocombiner.pasteur.fr, for academic use; all data are thus available from the ProteomeXchange consortium (identifier PXD017618).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Leveraging the partition selection bias to achieve a high-quality clustering of mass spectra

In proteomics, the identification of peptides from mass spectral data can be mathematically described as the partitioning of mass spectra into clusters (i.e., groups of spectra derived from the same peptide). The way partitions are validated is just as important, having evolved side by side with the clustering algorithms themselves and given rise to many partition assessment measures. An assessment measure is said to have a selection bias if, and only if, the probability that a randomly chosen partition scoring a high value depends on the number of clusters in the partition. In the context of clustering mass spectra, this might mislead the validation process to favor clustering algorithms that generate too many (or few) spectral clusters, regardless of the underlying peptide sequence. A selection bias toward the number of peptides is desirable for proteomics as it estimates the number of peptides in a complex protein mixture. Here, we introduce an assessment measure that is purposely biased toward the number of peptide ion species. We also introduce a partition assessment framework for proteomics, called the Partition Assessment Tool, and demonstrate its importance by evaluating the performance of eight clustering algorithms on seven proteomics datasets while discussing the trade-offs involved. SIGNIFICANCE: Clustering algorithms are widely adopted in proteomics for undertaking several tasks such as speeding up search engines, generating consensus mass spectra, and to aid in the classification of proteomic profiles. Choosing which algorithm is most fit for the task at hand is not simple as each algorithm has advantages and disadvantages; furthermore, specifying clustering parameters is also a necessary and fundamental step. For example, deciding on whether to generate "pure clusters" or fewer clusters but accepting noise. With this as motivation, we verify the performance of several widely adopted algorithms on proteomic datasets and introduce a theoretical framework for drawing conclusions on which approach is suitable for the task at hand.

Field distribution patterns of pests are asymmetrically affected by the presence of other herbivores

Because plant phenotypes can change in response to attacks by herbivores in highly variable ways, the distribution of herbivores depends on the occurrence of other herbivore species on the same plant. We carried out a field study to evaluate the co-occurrence of three coconut pests, the mites Aceria guerreronis (Acari: Eriophyidae), Steneotarsonemus concavuscutum (Acari: Tarsonemidae) and the moth Atheloca bondari (Lepidoptera: Pyralidae). The eriophyid mite Ac. guerreronis is the most important coconut pest around the world, whereas S. concavuscutum and At. bondari are economically important only in some areas along the Brazilian coast. A previous study suggested that the necrosis caused by Ac. guerreronis facilitates the infestation of At. bondari larvae. Because all three species infest the area under the perianths on coconuts and S. concavuscutum also causes necrosis that could facilitate At. bondari, we evaluated the co-occurrence of all three species. We found that the occurrence of At. bondari was positively associated with Ac. guerreronis, but negatively associated with S. concavuscutum. In addition, the two mite species showed negative co-occurrence. Atheloca bondari was found on nuts of all ages, but more on nuts that had fallen than on those on the trees, suggesting that nuts infested by At. bondari tend to fall more frequently. We discuss the status of At. bondari as a pest and discuss experiments to test the causes of these co-occurrence patterns.

RawVegetable - A data assessment tool for proteomics and cross-linking mass spectrometry experiments

We present RawVegetable, a software for mass spectrometry data assessment and quality control tailored toward shotgun proteomics and cross-linking experiments. RawVegetable provides four main modules with distinct features: (A) The charge state chromatogram that independently displays the ion current for each charge state; useful for optimizing the chromatography for highly charged ions and with lower XIC values such as those typically found in cross-linking experiments. (B) The XL-Artefact determination, which flags possible noncovalently associated peptides. (C) The TopN density estimation, for detecting retention time intervals of under or over-sampling, and (D) The chromatography reproducibility module, which provides pairwise comparisons between multiple experiments. RawVegetable, a tutorial, and the example data are freely available for academic use at: http://patternlabforproteomics.org/rawvegetable. SIGNIFICANCE: Chromatography optimization is a critical step for any shotgun proteomic or cross-linking mass spectrometry experiment. Here, we present a nifty solution with several key features, such as displaying individual charge state chromatograms, highlighting chromatographic regions of under- or over-sampling and checking for reproducibility.

Effects of Acaricides on the Functional and Numerical Responses of the Phytoseid Predator Neoseiulus idaeus (Acari: Phytoseiidae) to Spider Mite Eggs

Integrated control tactics are often necessary for pest management. This is especially true for organisms such as the two-spotted spider mite, Tetranychus urticae Koch. The management of this mite pest species relies on pesticide use, but its short life cycle associated with high selection pressure results in frequent problems of acaricide resistance and population outbreaks. Therefore, combining acaricides and natural enemies is an appealing strategy for managing this pest species. The predatory mite Neoseiulus idaeus Denmark & Muma (Phytoseiidae) is important in arid environments, where other natural enemies show low efficacy. Thus, we investigated the effects of representative acaricides used for managing spider mites around the world in several crops (i.e., abamectin, fenpyroximate, and azadirachtin), on the functional and numerical responses of the phytoseid predator N. idaeus to increasing egg densities of its prey. Acaricide exposure did not affect the type of N. idaeus functional response or attack rate (a). However, acaricide exposure decreased the amount of consumed prey and increased prey handling time (Th). All acaricides affected the numerical response of the predator, which reduced oviposition rates. Therefore, caution is required in attempts to integrate the control methods.

Bothrops alternatus Snake Venom Induces Cytokine Expression and Oxidative Stress on Renal Function

BACKGROUND

Envenomation caused by Bothrops alternatus is common in Southern Brazil. Acute Kidney Injury occurs after Bothrops snakebite and more information is necessaryrequired to understand its mechanism.

OBJECTIVE

The objective was to evaluate the effect of Bothrops alternatus venom (BaV) on renal cells and rat isolated kidney function.

METHODS

Wistar rats (n = 6, weighing 260-320 g) were perfused with a Krebs-Henseleit solution containing 6 g 100 mL-1 of bovine serum albumin. After 30 minutes, the kidneys were perfused with BaV to a final concentration of 1 and 3 μgmL-1; and subsequently were evaluated for Perfusion Pressure (PP), Renal Vascular Resistance (RVR), Urinary Flow (UF), Glomerular Filtration Rate (GFR), and percentage of electrolyte tubular transport. Renal histological analysis, cytokine release, oxidative stress and cytotoxicity in renal proximal tubular cells were assessed.

RESULTS

BaV reduced PP, RVR, GFR, UF, total and proximal sodium transport (%TNa+), and chloride (%TCl-) in the isolated kidney perfusion model. Histological analysis of perfused kidneys disclosed the presence of proteinaceous material in the glomeruli and renal tubules, vacuolar tubular epithelial cell degeneration, Bowman's capsule degeneration, swelling of glomerular epithelial cells, glomerular atrophy and degeneration, and the presence of intratubular protein. Cytokine release (TNF-α, IL-1β, IL-10) and oxidative stress were increased in the kidneys. The viability of LLC-MK2 cells (IC50: 221.3 μg/mL) was decreased by BaV and necrosis was involved in cell death.

CONCLUSION

These findings indicate that BaV modifies functional parameters in an isolated perfused kidney model and has cytotoxic effects on renal lineage cells.

A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics

We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sample type. We validate our algorithm using an M. tuberculosis dataset obtained from two biological conditions; we used three dimethyl labels, one serving as an internal control for labeling a mixture of samples from both biological conditions. This internal control certified the proper functioning of our software. Availability: http://patternlabforproteomics.org, freely available for academic use.

Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra

Motivation

We present the first tool for unbiased quality control of top-down proteomics datasets. Our tool can select high-quality top-down proteomics spectra, serve as a gateway for building top-down spectral libraries and, ultimately, improve identification rates.

Results

We demonstrate that a twofold rate increase for two E. coli top-down proteomics datasets may be achievable.

Availability and implementation

http://patternlabforproteomics.org/tdgc, freely available for academic use.

Supplementary information

Supplementary data are available at Bioinformatics online.

Data on antigen recognition hindrance by antibodies covalently immobilized to Protein G magnetic beads by dimethyl pimelimidate (DMP) cross-linking

The data presented herein is related to the article entitled "Trypanosoma cruzi immunoproteome: calpain-like CAP5.5 differentially detected throughout distinct stages of human Chagas disease cardiomyopathy" [1]. Electrophoretic analyses under denaturing and reducing conditions indicate that covalent immobilization of human IgG to Protein G magnetic beads by cross-linking with 50 mM dimethyl pimelimidate hinders the recognition of T. cruzi antigens in immunoprecipitation assays.

Fertility Life Table of Tetranychus palmarum Flechtmann & Noronha (Acari: Tetranychidae) in Oil Palm

Some species of spider mites belonging to the Tetranychidae family are known to associate with oil palm (Elaeis guineensis Jacq. - Arecaceae). The occurrence of Tetranychus palmarum Flechtmann & Noronha (Acari, Tetranychidae) was verified on oil palm seedlings under greenhouse conditions in the State of Pará in Northern Brazil. Plants with colonies of T. palmarum presented yellowish spots on leaflets and leaves with chlorosis. The objective of this study was to access the biology and fertility life table of T. palmarum in E. guineensis leaves. The experiment was conducted under four constant temperatures, 22, 25, 28, and 31°C, at 70 ± 10% RH under a 12:12 LD photoperiod. The duration of the egg-to-adult period was 18.4 and 9.8 days, at 22 and 31°C, respectively. The parameters of the fertility life table showed that 28°C is most suitable for the development and reproduction of T. palmarum, with higher values for reproductive parameters (R _o , r _m , and λ) and lower values for duplicating the population (TD). Therefore, it is apparent that the best temperature conditions for the development of T. palmarum are found in the warmer regions of Brazil, such as those observed in northern Brazil.

Predator performance is impaired by the presence of a second prey species

The simultaneous infestation of a plant by several species of herbivores may affect the attractiveness of plants to the natural enemies of one of the herbivores. We studied the effect of coconut fruits infested by the pests Aceria guerreronis and Steneotarsonemus concavuscutum, which are generally found together under the coconut perianth. The predatory mite Neoseiulus baraki produced lower numbers of offspring on fruits infested with S. concavuscutum and on fruits infested with both prey than on fruits with A. guerreronis only. The predators were attracted by odours emanating from coconuts with A. guerreronis, but not by odours from coconuts with S. concavuscutum, even when A. guerreronis were present on the same fruit. Fewer N. baraki were recaptured on fruits with both prey or with S. concavuscutum than on fruits with only A. guerreronis. Furthermore, the quality of A. guerreronis from singly and multiply infested coconuts as food for N. baraki did not differ. Concluding, our results suggest that N. baraki does not perform well when S. concavuscutum is present on the coconuts, and the control of A. guerreronis by N. baraki may be negatively affected by the presence of S. concavuscutum.

An Evaluation of the Crystal Structure of C-terminal Truncated Apolipoprotein A-I in Solution Reveals Structural Dynamics Related to Lipid Binding

Apolipoprotein (apo) A-I mediates many of the anti-atherogenic functions attributed to high density lipoprotein. Unfortunately, efforts toward a high resolution structure of full-length apoA-I have not been fruitful, although there have been successes with deletion mutants. Recently, a C-terminal truncation (apoA-I(Δ185-243)) was crystallized as a dimer. The structure showed two helical bundles connected by a long, curved pair of swapped helical domains. To compare this structure to that existing under solution conditions, we applied small angle x-ray scattering and isotope-assisted chemical cross-linking to apoA-I(Δ185-243) in its dimeric and monomeric forms. For the dimer, we found evidence for the shared domains and aspects of the N-terminal bundles, but not the molecular curvature seen in the crystal. We also found that the N-terminal bundles equilibrate between open and closed states. Interestingly, this movement is one of the transitions proposed during lipid binding. The monomer was consistent with a model in which the long shared helix doubles back onto the helical bundle. Combined with the crystal structure, these data offer an important starting point to understand the molecular details of high density lipoprotein biogenesis.

Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0

PatternLab for proteomics is an integrated computational environment that unifies several previously published modules for the analysis of shotgun proteomic data. The contained modules allow for formatting of sequence databases, peptide spectrum matching, statistical filtering and data organization, extracting quantitative information from label-free and chemically labeled data, and analyzing statistics for differential proteomics. PatternLab also has modules to perform similarity-driven studies with de novo sequencing data, to evaluate time-course experiments and to highlight the biological significance of data with regard to the Gene Ontology database. The PatternLab for proteomics 4.0 package brings together all of these modules in a self-contained software environment, which allows for complete proteomic data analysis and the display of results in a variety of graphical formats. All updates to PatternLab, including new features, have been previously tested on millions of mass spectra. PatternLab is easy to install, and it is freely available from http://patternlabforproteomics.org.

Evidence of Amblyseius largoensis and Euseius alatus as biological control agent of Aceria guerreronis

Amblyseius largoensis (Muma) (Acari: Phytoseiidae) and Euseius alatus De Leon (Acari: Phytoseiidae) are predatory mites that are mostly found on leaves and on the exposed fruit surface of coconut plants. Their morphology hampers the access to the microhabitat occupied by Aceria guerreronis Keifer (Acari: Eriophyidae), the most important pest of coconut fruits throughout the world. However, it was suggested that they can prey on A. guerreronis under natural conditions when this pest leaves its refuge to disperse. Since the trophic interactions between A. largoensis or E. alatus and A. guerreronis are unknown, we compare the frequencies of occurrence of A. largoensis and E. alatus under the bracts of coconut fruits and on coconut leaflets. In addition, because phytoseiids feed by liquid ingestion, we used molecular analysis to confirm the potential role of A. largoensis or E. alatus as predators of A. guerreronis and to assess how fast the A. guerreronis DNA fragment is degradated in the A. largoensis digestive tract. Our study demonstrated that E. alatus was only present on coconut leaflets whereas A. largoensis was found mostly on leaflets and, to a much lesser extent, under the bracts of coconuts. Species-specific ITS primers designed for A. guerreronis were shown to have a high degree of specificity for A. guerreronis DNA and did not produce any PCR product from DNA templates of the other insects and mites associated with the coconut agroecosystem. Based on molecular analysis, we confirmed that the predatory mites, A. largoensis and E. alatus, had preyed on the coconut mite in the field. Overall the predatory mites collected in the field exhibited low levels of predation (26.7% of A. largoensis and 8.9% of E. alatus tested positive for A. guerreronis DNA). The fragment of A. guerreronis DNA remained intact for a very short time (no more than 6 h after feeding) in the digestive tract of A. largoensis.

Acaricide-impaired functional predation response of the phytoseiid mite Neoseiulus baraki to the coconut mite Aceria guerreronis

Acaricides may interfere with a myriad of interactions among arthropods, particularly predator-prey interactions. The coconut mite, Aceria guerreronis Keifer (Acari: Eriophyidae), and its phytoseiid predator, Neoseiulus baraki (Athias-Henriot) (Acari: Phytoseiidae), provide an opportunity to explore such interference because the former is a key coconut pest species that requires both predation and acaricide application for its management. The objective of the present study was to assess the effect of the acaricides abamectin, azadirachtin and fenpyroximate on the functional response of N. baraki to A. guerreronis densities. The following prey densities were tested: 5, 10, 20, 40 and 80 preys. The type of functional response and prey handling time (Th) were not altered by the acaricides. However, the attack rate (a') was modified by abamectin and fenpyroximate, and the consumption peak was reduced by abamectin. All of the acaricides allowed for the maintenance of the predator in the field, but exposure to abamectin and fenpyroximate compromised prey consumption.

SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis

Chemical cross-linking has emerged as a powerful approach for the structural characterization of proteins and protein complexes. However, the correct identification of covalently linked (cross-linked or XL) peptides analyzed by tandem mass spectrometry is still an open challenge. Here we present SIM-XL, a software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). Our software introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. Moreover, our search engine is the first to capitalize on reporter ions for selecting tandem mass spectra derived from cross-linked peptides. It also makes available a 2D interaction map and a spectrum-annotation tool unmatched by any of its kind. We show SIM-XL to be more sensitive and faster than a competing tool when analyzing a data set obtained from the human HSP90. The software is freely available for academic use at http://patternlabforproteomics.org/sim-xl. A video demonstrating the tool is available at http://patternlabforproteomics.org/sim-xl/video. SIM-XL is the first tool to support XL data in the mzIdentML format; all data are thus available from the ProteomeXchange consortium (identifier PXD001677). This article is part of a Special Issue entitled: Computational Proteomics.

Host finding behaviour of the coconut mite Aceria guerreronis

For the coconut mite, Aceria guerreronis Keifer, its host plant, the coconut palm, is not merely a source of food, but more generally a habitat to live in for several generations. For these minute organisms, finding a new plant is difficult and risky, especially because their main mode of dispersal is passive drifting with the wind and because they are highly specialized on their host plant. Consequently, the probability of landing on a suitable host is very low, let alone to land in their specific microhabitat within the host. How coconut mites manage to find their microhabitat within a host plant is still underexplored. We tested the hypothesis that they use volatile chemical information emanating from the plant to find a specific site within their host plants and/or use non-volatile plant chemicals to stay at a profitable site on the plant. This was investigated in a Y-tube olfactometer (i.e. under conditions of a directed wind flow) and on cross-shaped arenas (i.e. under conditions of turbulent air) that either allowed contact with odour sources or not. The mites had to choose between odours from specific parts (leaflet, spikelet or fruit) of a non-infested coconut plant and clean air as the alternative. In the olfactometer experiments, no mites were found to reach the upwind end of the Y-tube: <5 % of the mites were able to pass the bifurcation of the "Y". On the cross-shaped arenas, however, a large number of coconut mites was found only when the arm of the arena contained discs of fruit epidermis and contact with these discs was allowed. The results suggest that coconut mites on palm trees are not attracted to specific sites on the plant by volatile plant chemicals, but that they arrested once they contact the substrate of specific sites. Possibly, they perceive non-volatile chemicals, but these remain to be identified.

Behaviour of coconut mites preceding take-off to passive aerial dispersal

For more than three decades the coconut mite Aceria guerreronis Keifer is one of the most important pests of coconut palms and has recently spread to many coconut production areas worldwide. Colonization of coconut palms is thought to arise from mites dispersing aerially after take-off from other plants within the same plantation or other plantations. The underlying dispersal behaviour of the mite at take-off, in the airborne state and after landing is largely unknown and this is essential to understand how they spread from tree to tree. In this article we studied whether take-off to aerial dispersal of coconut mites is preceded by characteristic behaviour, whether there is a correlation between the body position preceding aerial dispersal and the direction of the wind, and whether the substrate (outer surface of coconut bracts or epidermis) and the wind speed matter to the decision to take-off. We found that take-off can sometimes be preceded by a raised body stance, but more frequently take-off occurs while the mite is walking or resting on its substrate. Coconut mites that become airborne assumed a body stance that had no relation to the wind direction. Take-off was suppressed on a substrate providing food to coconut mites, but occurred significantly more frequently on the outer surface of coconut bracts than on the surface of the fruit. For both substrates, take-off frequency increased with wind speed. We conclude that coconut mites have at least some degree of control over take-off for aerial dispersal and that there is as yet no reason to infer that a raised body stance is necessary to become airborne.

PepExplorer: a similarity-driven tool for analyzing de novo sequencing results

Peptide spectrum matching is the current gold standard for protein identification via mass-spectrometry-based proteomics. Peptide spectrum matching compares experimental mass spectra against theoretical spectra generated from a protein sequence database to perform identification, but protein sequences not present in a database cannot be identified unless their sequences are in part conserved. The alternative approach, de novo sequencing, can make it possible to infer a peptide sequence directly from a mass spectrum, but interpreting long lists of peptide sequences resulting from large-scale experiments is not trivial. With this as motivation, PepExplorer was developed to use rigorous pattern recognition to assemble a list of homologue proteins using de novo sequencing data coupled to sequence alignment to allow biological interpretation of the data. PepExplorer can read the output of various widely adopted de novo sequencing tools and converge to a list of proteins with a global false-discovery rate. To this end, it employs a radial basis function neural network that considers precursor charge states, de novo sequencing scores, peptide lengths, and alignment scores to select similar protein candidates, from a target-decoy database, usually obtained from phylogenetically related species. Alignments are performed using a modified Smith-Waterman algorithm tailored for the task at hand. We verified the effectiveness of our approach using a reference set of identifications generated by ProLuCID when searching for Pyrococcus furiosus mass spectra on the corresponding NCBI RefSeq database. We then modified the sequence database by swapping amino acids until ProLuCID was no longer capable of identifying any proteins. By searching the mass spectra using PepExplorer on the modified database, we were able to recover most of the identifications at a 1% false-discovery rate. Finally, we employed PepExplorer to disclose a comprehensive proteomic assessment of the Bothrops jararaca plasma, a known biological source of natural inhibitors of snake toxins. PepExplorer is integrated into the PatternLab for Proteomics environment, which makes available various tools for downstream data analysis, including resources for quantitative and differential proteomics.

Limits to ambulatory displacement of coconut mites in absence and presence of food-related cues

Ambulatory movement of plant-feeding mites sets limits to the distances they can cover to reach a new food source. In absence of food-related cues these limits are determined by survival, walking activity, walking path tortuosity and walking speed, whereas in presence of food the limits are also determined by the ability to orient and direct the path towards the food source location. For eriophyoid mites such limits are even more severe because they are among the smallest mites on earth, because they have only two pairs of legs and because they are very sensitive to desiccation. In this article we test how coconut mites (Aceria guerreronis Keifer) are constrained in their effective displacement by their ability to survive in absence of food (meristematic tissue under the coconut perianth) and by their ability to walk and orient in absence or presence of food-related cues. We found that the mean survival time decreased with increasing temperature and decreasing humidity. Under climatic conditions representative for the Tropics (27 °C and 75 % relative humidity) coconut mites survived on average for 11 h and covered 0.4 m, representing the effective linear displacement away from the origin. Within a period of 5 h, coconut mites collected from old fruits outside the perianth moved further away from the origin than mites collected under the perianth of young fruits. However, in the presence of food-related cues coconut mites traveled over 30 % larger distances than in absence of these cues. These results show that ambulatory movement of eriophyoid mites may well bring them to other coconuts within the same bunch and perhaps also to other bunches on the same coconut palm, but it is unlikely to help them move from palm to palm, given that palms usually do not touch each other.

Comparative proteomic analysis of the aging soleus and extensor digitorum longus rat muscles using TMT labeling and mass spectrometry

Sarcopenia describes an age-related decline in skeletal muscle mass, strength, and function that ultimately impairs metabolism and leads to poor balance, frequent falling, limited mobility, and a reduction in quality of life. Here we investigate the pathogenesis of sarcopenia through a proteomic shotgun approach. In brief, we employed tandem mass tags to quantitate and compare the protein profiles obtained from young versus old rat slow-twitch type of muscle (soleus) and a fast-twitch type of muscle (extensor digitorum longus, EDL). Our results disclose 3452 and 1848 proteins identified from soleus and EDL muscles samples, of which 78 and 174 were found to be differentially expressed, respectively. In general, most of the proteins were structural related and involved in energy metabolism, oxidative stress, detoxification, or transport. Aging affected soleus and EDL muscles differently, and several proteins were regulated in opposite ways. For example, pyruvate kinase had its expression and activity different in both soleus and EDL muscles. We were able to verify with existing literature many of our differentially expressed proteins as candidate aging biomarkers and, most importantly, disclose several new candidate biomarkers such as the glioblastoma amplified sequence, zero β-globin, and prolargin.

Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics

Mass-spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. Here we describe a new module integrated into PatternLab for Proteomics that allows the pinpointing of differentially expressed domains. This is accomplished by inferring functional domains through our cloud service, using HMMER3 and Pfam remotely, and then mapping the quantitation values into domains for downstream analysis. In all, spotting which functional domains are changing when comparing biological states serves as a complementary approach to facilitate the understanding of a system's biology. We exemplify the new module's use by reanalyzing a previously published MudPIT dataset of Cryptococcus gattii cultivated under iron-depleted and replete conditions. We show how the differential analysis of functional domains can facilitate the interpretation of proteomic data by providing further valuable insight.

Enteric parasites and HIV infection: occurrence in AIDS patients in Rio de Janeiro, Brazil

The occurrence of intestinal parasites, its relation with the transmission mechanism of HIV, and the clinical state of the AIDS patients, were analyzed in 99 Group IV patients (CDC, 1986), treated at "Hospital Universitário Pedro Ernesto" (HUPE), between 1986 and 1988. The group consisted of 79 (79.8%) patients whose HIV transmission mechanism took place through sexual contact and of 16 (20.2%) who were infected through blood. Feces samples from each patient were examined by four distincts methods (Faust et al., Kato-Katz, Baermann-Moraes and Baxby et al.). The most occurring parasites were: Cryptosporidium sp., Entamoeba coli and Endolimax nana (18.2%), Strongyloides stercoralis and Giardia lamblia (15.2%), E. histolytica and/or E. hartmanni (13.1%), Ascaris lumbricoides (11.1%) and Isospora belli (10.1%). Furthermore, 74.7% of the patients carried at least one species. Intestinal parasites were found in 78.5% of the patients who acquired the HIV through sexual intercourse and in 56.3% of those infected by blood contamination. The difference, was not statistically significant (p greater than 0.05). In the group under study, the increase of the occurrence of parasitic infections does not seem to depend on the acquisition of HIV through sexual contact. It appears that in developing countries, the dependency is more related to the classic mechanisms of parasites transmission and its endemicity.