iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations

Kunszt, Péter Z.; Blum, Lorenz C.; Hullár, Béla; Schmid, Emanuel; Srebniak, Adam; Wolski, Witold; Rinn, Bernd; Elmer, Franz-Josef; Ramakrishnan, Chandrasekhar; Quandt, Andreas; Malmström, Lars

doi:10.1002/cpe.3294

Cited by 46 publications

(39 citation statements)

References 18 publications

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“…Decoy assays were appended to the TraML file using the OpenSwathDecoyGenerator command (option: -method pseudo-reverse -append -exclude_similar). Data analysis using the tool OpenSwathWorkflow was performed on a computer cluster running CentOS release 6.7 through the iPortal40 workflow manager. The SWATH WIFF files were first converted to profile mzXML using msconvert as previously described18.…”

Section: Methodsmentioning

confidence: 99%

A multicenter study benchmarks software tools for label-free proteome quantification

et al. 2016

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The consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra), a method that uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test datasets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation windows setups. For consistent evaluation we developed LFQbench, an R-package to calculate metrics of precision and accuracy in label-free quantitative MS, and report the identification performance, robustness and specificity of each software tool. Our reference datasets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.

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Section: Methodsmentioning

confidence: 99%

A multicenter study benchmarks software tools for label-free proteome quantification

et al. 2016

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“…SWATH/DIA data were analyzed via targeted, peptide‐centric analysis, querying 204,545 precursors based on the combined human assay library (CAL; Rosenberger et al , ) in the SWATH fragment ion chromatograms, using a modified OpenSWATH (Röst et al , ), PyProphet (Reiter et al , ; Teleman et al , ), and TRIC (Röst et al , ) workflow and the iPortal framework (Kunszt et al , ). Specifically, a global PyProphet scoring function was trained on a master sample of the unfractionated HEK293 lysate with tryptic digest and SWATH/DIA data acquisition equivalent to the fractionated samples.…”

Section: Methodsmentioning

confidence: 99%

Complex‐centric proteome profiling by SEC ‐ SWATH ‐ MS

Heusel

Bludau

Rosenberger

et al. 2019

Molecular Systems Biology

128

114

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Proteins are major effectors and regulators of biological processes that can elicit multiple functions depending on their interaction with other proteins. The organization of proteins into macromolecular complexes and their quantitative distribution across these complexes is, therefore, of great biological and clinical significance. In this paper, we describe an integrated experimental and computational technique to quantify hundreds of protein complexes in a single operation. The method consists of size exclusion chromatography (SEC) to fractionate native protein complexes, SWATH/DIA mass spectrometry to precisely quantify the proteins in each SEC fraction, and the computational framework CCprofiler to detect and quantify protein complexes by error‐controlled, complex‐centric analysis using prior information from generic protein interaction maps. Our analysis of the HEK293 cell line proteome delineates 462 complexes composed of 2,127 protein subunits. The technique identifies novel sub‐complexes and assembly intermediates of central regulatory complexes while assessing the quantitative subunit distribution across them. We make the toolset CCprofiler freely accessible and provide a web platform, SECexplorer, for custom exploration of the HEK293 proteome modularity.

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“…3"). The analysis was performed in the swiss grid proteomics portal (Kunszt et al, 2015). The enzyme was set to trypsin, allowing 2 missed cleavages.…”

Section: Protein Identification and Quantificationmentioning

confidence: 99%

The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification

et al. 2019

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Krüppel‐associated box (KRAB)‐containing zinc finger proteins (KZFPs) are encoded in the hundreds by the genomes of higher vertebrates, and many act with the heterochromatin‐inducing KAP1 as repressors of transposable elements (TEs) during early embryogenesis. Yet, their widespread expression in adult tissues and enrichment at other genetic loci indicate additional roles. Here, we characterized the protein interactome of 101 of the ~350 human KZFPs. Consistent with their targeting of TEs, most KZFPs conserved up to placental mammals essentially recruit KAP1 and associated effectors. In contrast, a subset of more ancient KZFPs rather interacts with factors related to functions such as genome architecture or RNA processing. Nevertheless, KZFPs from coelacanth, our most distant KZFP‐encoding relative, bind the cognate KAP1. These results support a hypothetical model whereby KZFPs first emerged as TE‐controlling repressors, were continuously renewed by turnover of their hosts’ TE loads, and occasionally produced derivatives that escaped this evolutionary flushing by development and exaptation of novel functions.

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iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations

Cited by 46 publications

References 18 publications

A multicenter study benchmarks software tools for label-free proteome quantification

A multicenter study benchmarks software tools for label-free proteome quantification

Complex‐centric proteome profiling by SEC ‐ SWATH ‐ MS

The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification

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