Parallel Tandem:  A Program for Parallel Processing of Tandem Mass Spectra Using PVM or MPI and X!Tandem

Duncan, Dexter T.; Craig, Robertson; Link, Andrew J.

doi:10.1021/pr050058i

Cited by 74 publications

(58 citation statements)

References 17 publications

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“…In addition, some samples were run on a similar Thermo Finnigan mass spectrometer at the Cancer Center at the Massachusetts Institute of Technology (MIT). Mass spectra were compared to tryptic digests of E. histolytica proteins predicted from whole-genome sequencing using SEQUEST, GPM (The Global Proteome Machine Organization [www.thegpm.org]) open source software, or Mascot software (13,22,23).…”

Section: Methodsmentioning

confidence: 99%

The Antiretroviral Lectin Cyanovirin-N Targets Well-Known and Novel Targets on the Surface of Entamoeba histolytica Trophozoites

et al. 2010

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Entamoeba histolytica, the protist that causes amebic dysentery and liver abscess, has a truncated Asn-linked glycan (N-glycan) precursor composed of seven sugars (Man 5 GlcNAc 2 ). Here, we show that glycoproteins with unmodified N-glycans are aggregated and capped on the surface of E. histolytica trophozoites by the antiretroviral lectin cyanovirin-N and then replenished from large intracellular pools. Cyanovirin-N cocaps the Gal/GalNAc adherence lectin, as well as glycoproteins containing O-phosphodiester-linked glycans recognized by an anti-proteophosphoglycan monoclonal antibody. Cyanovirin-N inhibits phagocytosis by E. histolytica trophozoites of mucin-coated beads, a surrogate assay for amebic virulence. For technical reasons, we used the plant lectin concanavalin A rather than cyanovirin-N to enrich secreted and membrane proteins for mass spectrometric identification. E. histolytica glycoproteins with occupied N-glycan sites include Gal/GalNAc lectins, proteases, and 17 previously hypothetical proteins. The latter glycoproteins, as well as 50 previously hypothetical proteins enriched by concanavalin A, may be vaccine targets as they are abundant and unique. In summary, the antiretroviral lectin cyanovirin-N binds to well-known and novel targets on the surface of E. histolytica that are rapidly replenished from large intracellular pools.Entamoeba histolytica causes amebic dysentery and liver abscess in the developing world (10,20,29). We are interested in E. histolytica glycoproteins containing Asn-linked glycans (Nglycans) for numerous reasons. E. histolytica makes an N-glycan precursor that contains 7 sugars (Man 5 GlcNAc 2 -PP-dolichol) rather than 14 sugars (Glc 3 Man 9 GlcNAc 2 -PP-dolichol) made by most animals, plants, and fungi (21,31,44). E. histolytica N-glycans are used for quality control of glycoprotein folding in the endoplasmic reticulum (ER) lumen, and there is positive selection for sites of N-linked glycosylation in secreted and membrane proteins of E. histolytica (5,11,53).Unprocessed Man 5 GlcNAc 2 , by far the most abundant E. histolytica N-glycan, is present on the plasma membrane and vesicular membranes (31). The antiretroviral lectin cyanovirin-N, which is specific for ␣-1,2-linked mannose present on unprocessed N-glycans, binds E. histolytica N-glycans and forms aggregates or caps on the surface of E. histolytica trophozoites (1,25,31,44,45). E. histolytica glycoproteins are also capped by the plant lectin concanavalin A (ConA), which has a broader carbohydrate specificity (mannose and glucose) than cyanovirin- N (3, 16, 18, 19). Heavy subunits of the Gal/GalNAc lectin, the most important E. histolytica vaccine candidate, have 7 to 10 potential sites for N-linked glycosylation (32,39,43). Inhibition of N-glycan synthesis results in Gal/GalNAc lectins that are unable to bind to sugars on host epithelial cells.Carbohydrates appear to be an important target on the surface of E. histolytica as anti-proteophosphoglycan (PPG) monoclonal antibodies bind to O-phosphodiester-linked glycans...

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Section: Methodsmentioning

confidence: 99%

The Antiretroviral Lectin Cyanovirin-N Targets Well-Known and Novel Targets on the Surface of Entamoeba histolytica Trophozoites

et al. 2010

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“…39,40 The spectral libraries for human and E. coli from National Institute of Standards and Technology (NIST) were used for the SpectraST searches. 41 11 It is beneficial to run a search engine on a cluster using MPI in terms of speed; this requires however the availability of an MPI enabled server/cluster to the scientist. Pratt et al 13 developed a cloud parallel peptide identification using parallel X!Tandem, 11 Hadoop, 43,44 and MapReduce.…”

Section: Data Sets Used For Testingmentioning

confidence: 99%

Cloud Parallel Processing of Tandem Mass Spectrometry Based Proteomics Data

et al. 2012

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Data analysis in mass spectrometry based proteomics struggles to keep pace with the advances in instrumentation and the increasing rate of data acquisition. Analyzing this data involves multiple steps requiring diverse software, using different algorithms and data formats. Speed and performance of the mass spectral search engines are continuously improving, although not necessarily as needed to face the challenges of acquired big data. Improving and parallelizing the search algorithms is one possibility; data decomposition presents another, simpler strategy for introducing parallelism. We describe a general method for parallelizing identification of tandem mass spectra using data decomposition that keeps the search engine intact and wraps the parallelization around it. We introduce two algorithms for decomposing mzXML files and recomposing resulting pepXML files. This makes the approach applicable to different search engines, including those relying on sequence databases and those searching spectral libraries. We use cloud computing to deliver the computational power and scientific workflow engines to interface and automate the different processing steps. We show how to leverage these technologies to achieve faster data analysis in proteomics and present three scientific workflows for parallel database as well as spectral library search using our data decomposition programs, X!Tandem and SpectraST.

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“…In their approach, the high-frequency vibrational motion corresponding to bonding interactions is treated analytically. Duncan et al [12] introduced "Parallel Tandem", a fast and accurate search algorithm, to reduce the computational time necessary for the analysis of MS spectra against a protein sequence database. Recently, Huang et al [13] showed the full power of ab initio quantum mechanics, which represented a full molecule by smaller "kernels" of atoms, to calculate the interaction of long chain molecules of biological and medicinal interest.…”

Section: Introductionmentioning

confidence: 99%

Parallel implementation of finite volume based method for isoelectric focusing

2009

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A message passing interface (MPI) based parallel simulation algorithm is developed to simulate protein behavior in non-linear isoelectric focusing (IEF). The mathematical model of IEF is formulated based on mass conservation, charge conservation, ionic dissociation-association relations of amphoteric molecules and the electroneutrality condition. First, the concept of parallelism is described for isoelectric focusing, and the isoelectric focusing model is implemented for 96 components: 94 ampholytes and 2 proteins. The parallelisms were implemented for two equations (mass conservation equation and electroneutrality equation). The CPU times are presented according to the increase of the number of processors (1, 2, 4 and 8 nodes). The maximum reduction of CPU time was achieved when four CPUs were employed, regardless of the input components in isoelectric focusing. The speed enhancement was defined for comparison of parallel efficiency. Computational speed was enhanced by maximum of 2.46 times when four CPUs were used with 96 components in isoelectric focusing.

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Parallel Tandem: A Program for Parallel Processing of Tandem Mass Spectra Using PVM or MPI and X!Tandem

Cited by 74 publications

References 17 publications

The Antiretroviral Lectin Cyanovirin-N Targets Well-Known and Novel Targets on the Surface of Entamoeba histolytica Trophozoites

The Antiretroviral Lectin Cyanovirin-N Targets Well-Known and Novel Targets on the Surface of Entamoeba histolytica Trophozoites

Cloud Parallel Processing of Tandem Mass Spectrometry Based Proteomics Data

Parallel implementation of finite volume based method for isoelectric focusing

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