SearchGUI: An open‐source graphical user interface for simultaneous OMSSA and X!Tandem searches

Vaudel, Marc; Barsnes, Harald; Berven, Frode S.; Sickmann, Albert; Martens, Lennart

doi:10.1002/pmic.201000595

Cited by 327 publications

(277 citation statements)

References 14 publications

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“…A similar database containing the T. muris genome, the cRAP and the Mus musculus genome was used for the analysis of the EV mass spectrometry data. Database search was performed using X!Tandem, MS-GF+, OMSSA and Tide search engines using SearchGUI [25]. Parameters were set as follows: tryptic specificity allowing two missed cleavages, MS tolerance of 50 ppm and 0.2 Da tolerance for MS/MS ions.…”

Section: Methodsmentioning

confidence: 99%

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Eichenberger

Talukder

Field

et al. 2018

J of Extracellular Vesicle

107

145

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Whipworms are parasitic nematodes that live in the gut of more than 500 million people worldwide. Owing to the difficulty in obtaining parasite material, the mouse whipworm Trichuris muris has been extensively used as a model to study human whipworm infections. These nematodes secrete a multitude of compounds that interact with host tissues where they orchestrate a parasitic existence. Herein we provide the first comprehensive characterization of the excretory/secretory products of T. muris. We identify 148 proteins secreted by T. muris and show for the first time that the mouse whipworm secretes exosome-like extracellular vesicles (EVs) that can interact with host cells. We use an Optiprep® gradient to purify the EVs, highlighting the suitability of this method for purifying EVs secreted by a parasitic nematode. We also characterize the proteomic and genomic content of the EVs, identifying >350 proteins, 56 miRNAs (22 novel) and 475 full-length mRNA transcripts mapping to T. muris gene models. Many of the miRNAs putatively mapped to mouse genes are involved in regulation of inflammation, implying a role in parasite-driven immunomodulation. In addition, for the first time to our knowledge, colonic organoids have been used to demonstrate the internalization of parasite EVs by host cells. Understanding how parasites interact with their host is crucial to develop new control measures. This first characterization of the proteins and EVs secreted by T. muris provides important information on whipworm–host communication and forms the basis for future studies.

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Section: Methodsmentioning

confidence: 99%

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Eichenberger

Talukder

Field

et al. 2018

J of Extracellular Vesicle

107

145

View full text Add to dashboard Cite

show abstract

“…The tolerances of peptides and fragment ions were set at 10 ppm and 0.02 Daltons respectively. SearchGUI (30) was used for MyriMatch and OMSSA searching. BuildSummary (31) was used to generate a confident protein list for both peptide and protein with a false discovery rate Յ 0.01.…”

Section: Methodsmentioning

confidence: 99%

Preprocessing Significantly Improves the Peptide/Protein Identification Sensitivity of High-resolution Isobarically Labeled Tandem Mass Spectrometry Data

Sheng

Dai

et al. 2015

Molecular & Cellular Proteomics

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Isobaric labeling techniques coupled with high-resolution mass spectrometry have been widely employed in proteomic workflows requiring relative quantification. For each high-resolution tandem mass spectrum (MS/MS), isobaric labeling techniques can be used not only to quantify the peptide from different samples by reporter ions, but also to identify the peptide it is derived from. Because the ions related to isobaric labeling may act as noise in database searching, the MS/MS spectrum should be preprocessed before peptide or protein identification. In this article, we demonstrate that there are a lot of high-frequency, high-abundance isobaric related ions in the MS/MS spectrum, and removing isobaric related ions combined with deisotoping and deconvolution in MS/MS preprocessing procedures significantly improves the peptide/protein identification sensitivity. The userfriendly software package TurboRaw2MGF (v2.0) has been implemented for converting raw TIC data files to mascot generic format files and can be downloaded for free Mass spectrometry-based proteomics has been widely applied to investigate protein mixtures derived from tissue, cell lysates, or from body fluids (1, 2). Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) 1 is the most popular strategy for protein/peptide mixtures analysis in shotgun proteomics (3). Large-scale protein/peptide mixtures are separated by liquid chromatography followed by online detection by tandem mass spectrometry. The capabilities of proteomics rely greatly on the performance of the mass spectrometer. With the improvement of MS technology, proteomics has benefited significantly from the high-resolution and excellent mass accuracy (4). In recent years, based on the higher efficiency of higher energy collision dissociation (HCD), a new "high-high" strategy (high-resolution MS as well as MS/MS(tandem MS)) has been applied instead of the "highlow" strategy (high-resolution MS, i.e. in Orbitrap, and lowresolution MS/MS, i.e. in ion trap) to obtain high quality tandem MS/MS data as well as full MS in shotgun proteomics. Both full MS scans and MS/MS scans can be performed, and the whole cycle time of MS detection is very compatible with the chromatographic time scale (5).High-resolution measurement is one of the most important features in mass spectrometric application. In this high-high strategy, high-resolution and accurate spectra will be achieved in tandem MS/MS scans as well as full MS scans, which makes isotopic peaks distinguishable from one another, thus enabling the easy calculation of precise charge states and monoisotopic mass. During an LC-MS/MS experiment, a multiply charged precursor ion (peptide) is usually isolated and fragmented, and then the multiple charge states of the fragment ions are generated and collected. After full extraction of peak lists from original tandem mass spectra, the commonly used search engines (i.e. Mascot (6), Sequest (7)) have no capability to distinguish isotopic peaks and recognize charge states, so all of the product ion...

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“…Tandem Vengeance (2015.12.15.2) (58), and MS-GFϩ version Beta (v10282) (59). The search was conducted using SearchGUI version 2.8.5 (60). Protein identification was conducted against a concatenated target/ decoy version of the T. urticae protein database holding 17,907 target sequences (version of December 16th 2014, see supplemental Data S1) and the common Repository of Adventitious Proteins (cRAP) database (available at http://www.thegpm.org/crap/).…”

Section: Establishment Of T Urticae Lines On Different Host Plants-tmentioning

confidence: 99%

The Salivary Protein Repertoire of the Polyphagous Spider Mite Tetranychus urticae: A Quest for Effectors

Jonckheere

Dermauw

Zhurov

et al. 2016

Molecular & Cellular Proteomics

123

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The two-spotted spider mite Tetranychus urticae is an extremely polyphagous crop pest. Alongside an unparalleled detoxification potential for plant secondary metabolites, it has recently been shown that spider mites can attenuate or even suppress plant defenses. Salivary constituents, notably effectors, have been proposed to play an important role in manipulating plant defenses and might determine the outcome of plant-mite interactions.Here, the proteomic composition of saliva from T. urticae lines adapted to various host plants-bean, maize, soy, and tomato-was analyzed using a custom-developed feeding assay coupled with nano-LC tandem mass spectrometry. About 90 putative T. urticae salivary proteins were identified. Many are of unknown function, and in numerous cases belonging to multimembered gene families. RNAseq expression analysis revealed that many genes coding for these salivary proteins were highly expressed in the proterosoma, the mite body region that includes the salivary glands. A subset of genes encoding putative salivary proteins was selected for whole-mount in situ hybridization, and were found to be expressed in the anterior and dorsal podocephalic glands. Strikingly, host plant dependent expression was evident for putative salivary proteins, and was further studied in detail by micro-array based genome-wide expression profiling. This meta-analysis revealed for the first time the salivary protein repertoire of a phytophagous chelicerate. The availability of this salivary proteome will assist in unraveling the molecular interface between phytophagous mites and their host plants, and may ultimately facilitate the development of mite-resistant crops. Furthermore, the technique used in this study is a time-and resourceefficient method to examine the salivary protein composition of other small arthropods for which saliva or salivary glands cannot be isolated easily. The family of spider mites (Chelicerata: Acari: Tetranychidae) comprises well over 1000 species, including several that are important pests on crops, and about 0.9 billion euro is being spent annually for their control worldwide (1, 2). These minute herbivores-about 0.5 mm in size-use their stylets to pierce leaf mesophyll cells and to inject saliva, after which they suck out the cytoplasm. This results in cell death visible as chlorotic spots sometimes accompanied by necrosis, and ultimately in leaf abscission (3,4). Among the spider mites, the From the ‡Laboratory

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SearchGUI: An open‐source graphical user interface for simultaneous OMSSA and X!Tandem searches

Cited by 327 publications

References 14 publications

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Preprocessing Significantly Improves the Peptide/Protein Identification Sensitivity of High-resolution Isobarically Labeled Tandem Mass Spectrometry Data

The Salivary Protein Repertoire of the Polyphagous Spider Mite Tetranychus urticae: A Quest for Effectors

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