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Download from ChemSpider using Accurate Mass (2)

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Created: 2007-11-26 | Last updated: 2008-02-05

Credits: Egon Willighagen

getInchIfromMassBankPeaklist_ChemSpider_wo... (2)

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uses InChI's retrieved from a MassBank peaklist query to get compound information about those compounds via querying ChemSpider for information and displaying those results with image

Created: 2008-06-05 | Last updated: 2008-06-16

Credits: Michael Gerlich

Download from ChemSpider using Accurate Ma... (1)

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updated version of Download from ChemSpider using Accurate Mass to make use of the new ChemSpider services

Created: 2008-06-11 | Last updated: 2008-06-11

Credits: Michael Gerlich Egon Willighagen

Attributions: Download from ChemSpider using Accurate Mass

MassBank to KEGG (1)

Workflow that queries MassBank DB to retrieve database identifiers (KEGG, PubChem, InChI) and continue search with them to retrieve pathways from KEGG for given compound identifier,searches PubChem via eutils and PUG, queries ChemSpider for compound information and image. Note: Usage of ChemSpider web services requires a valid security token - receive one by registering at ChemSpider (look at your profile to see your token)

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

getTimololFromMassBank (1)

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This workflow will retrieve a peaklist from a fixed entry (Timolol) from the MassBank spectral library. Note, the API is still in alpha, as of 10.11.2009.  

Created: 2009-11-10 | Last updated: 2009-11-10

Credits: http://sneumann.pip.verisignlabs.com/

In-silico Fragmentation of Naringenin (2)

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Created: 2010-02-08

Credits: http://sneumann.pip.verisignlabs.com/

LipidMaps Query (1)

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This workflow retrieves database entries from LipidMaps for given exact mass and tolerance inputs.

Created: 2010-02-16

Plasma Precipitation Analysis (1)

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ABOUT THE WORKFLOW This workflow was used to analyze the data in a manuscript by Mostovenko et al. (2012, submitted), comparing proteins in the precipitate with those left in solution after organic solvent precipitation. However, the workflow is generally applicable in comparisons of any binary fractionation method in proteomics, where the fractions are analyzed by liquid chromatography-tandem mass spectrometry. The workflow identifies proteins by SpectraST spectral library search and X!Ta...

Created: 2012-07-31 | Last updated: 2012-07-31

Credits: Magnus Palmblad Kate Mostovenko Yassene

de Bruin et al. Workflow 1 (1)

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This is "Workflow 1" from de Bruin et al., Mol. Cell. Proteomics 2012.

Created: 2012-08-01 | Last updated: 2012-08-01

Credits: Magnus Palmblad

de Bruin et al. Workflow 2 (1)

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This is "Workflow 2" from de Bruin et al., Mol. Cell. Proteomics 2012.

Created: 2012-08-01 | Last updated: 2012-08-01

Credits: Magnus Palmblad

de Bruin et al. Workflow 3 (1)

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This is "Workflow 3" from de Bruin et al., Mol. Cell. Proteomics 2012.

Created: 2012-08-01 | Last updated: 2012-08-01

Credits: Magnus Palmblad

de Bruin et al. Workflow 4 (1)

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This is "Workflow 4" from de Bruin et al., Mol. Cell. Proteomics 2012.

Created: 2012-08-01 | Last updated: 2012-08-01

Credits: Magnus Palmblad

Retention Time Prediction with X!Tandem (1)

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This workflow identifies peptides from tandem mass spectra using X!Tandem as in a standard installation of the Trans-Proteomic Pipeline (TPP, version 4.6, but earlier versions should also work). The peptide-spectrum matches are validates using PeptideProphet (also from a standard installation of TPP) and peptides with at least a probability 0.95 are used to train a linear retention time predictor (Palmblad et al., 2002), whereby retention coefficients are also derived. These indirectly provid...

Created: 2012-09-03 | Last updated: 2012-09-03

Credits: Magnus Palmblad Yassene Eleni

Attributions: rt3.c

Cloud Parallel Processing of Tandem Mass S... (1)

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A workflow for searching LC−MS/MS data using SpectraST on the cloud. The processor mzxmlDecomposer, pepxmlUnzip, and pepxmlComposer are identical to the one in the X!Tandem workflow (Figure 2). The only difference is that the Xtandem processor is exchanged with the Spectrast processor and the constant inputs are adjusted to SpectraST. This approach is also possible for other search engines as described in Data Decomposition and Recomposition Algorithms. More details can be found here:...

Created: 2012-09-10

Credits: Yassene

Cloud Parallel Processing of Tandem Mass S... (1)

An advanced scientific workflow for searching LC−MS data using SpectraST on the cloud. Uploading the libraries is optimized to achieve better performance, which makes this workflow more suitable for processing mzXML spectra files from human samples, as the corresponding NIST library needed by SpectraST is larger than 2 GB. Here we connect 3 nested workflows, in which the first 2, i.e., decomposeMzxml and uploadToCloud, run in parallel, while the third nested workflow, i.e. runSpectrastO...

Created: 2012-09-10 | Last updated: 2015-08-19

Credits: Yassene

Cloud Parallel Processing of Tandem Mass S... (1)

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A workflow for searching LC−MS/MS mass spectrometry data using X!Tandem on the cloud. The workflow consists of 5 processors. The objectLogic processor prepares all inputs in the right format, i.e. keeping or converting strings into file object according to the following processor. The mzxmlDecomposer and pepxmlComposer run the decomposing/recomposing algorithms. objectLogic, mzxmlDecomposer and pepxmlComposer are Beanshell processors and they run locally. Xtandem runs X!Tandem on a remo...

Created: 2012-09-10

Credits: Yassene

Calculate_Isotopic_Distribution (1)

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This small workflow takes as input a peptide sequence and calculates the elemental composition of the peptide (Calculate_Elemental_Composition). This is then transferred as a numerical vector to the Rshell Calculate_Isotopic_Distribution, that calculates the (integer mass) isotopic distribution using the FFT method. To shift to approximate real masses (or m/z values), transpose the distribution with the difference between the integer and real monoisotopic masses (both easily calculated using ...

Created: 2013-03-05

Credits: Magnus Palmblad

Simulate_Mass_Spectrum (1)

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This workflow takes as input a peptide sequence and calculates the elemental composition of the peptide (Calculate_Elemental_Composition). This is then transferred as a numerical vector to the Rshell Simulate_Mass_Spectrum, that calculates the isotopic distribution using the FFT method and convolutes the theoretical (infinite resolution) distribution with a Gaussian peak shape. The building blocks can be used in any other workflows using the isotopic distribution of peptides or other molecul...

Created: 2013-03-12

Credits: Magnus Palmblad

Optimization of retention time prediction (1)

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The workflow uses RTCalc from the TPP toolbox to perform two different retention time predictions. The third branch uses a linear retention time predictor (Palmblad et al., 2002). The workflow has a flag that switches on a specific branch.

Created: 2013-08-13 | Last updated: 2013-09-04

Credits: Sonja Holl Yassene Magnus Palmblad

Attributions: Retention Time Prediction with X!Tandem

Generate Spectral Library (1)

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This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License (CC BY-SA). Copyright© 2012 Yassene Mohammed Please send your feedback, questions, comments and suggestions for improvement to y.mohammed@lumc.nl 14 November 2012 Yassene

Created: 2013-08-16

Credits: Yassene Magnus Palmblad

Metabolic differences in ripening of Solan... (2)

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Updated data processing workflow for metabolomics LC-MS/MS data. This workflow depends on the stable community plug-in MassCascade and KNIME plug-ins Base Chemistry, Chemistry Types & Nodes, Math Expression, and XLS Support. The workflow was run under KNIME version 2.9.2.

Created: 2013-10-16 | Last updated: 2014-07-04

Credits: SBeisken

RTCalc Retention Time Prediction and Outli... (1)

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This workflow takes as input a pepXML file from PeptideProphet, applied RTCalc and outputs a filtered list of peptides based on the retention time Z-scores.

Created: 2014-02-06 | Last updated: 2014-02-06

Credits: Magnus Palmblad Sonja Holl

Quantitation of identified proteins from M... (1)

No description

Created: 2014-12-08 | Last updated: 2015-08-19

Credits: Arzu Tugce Guler

Scan range splitting for untargeted metabo... (1)

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This workflow analyzes untargeted HPLC-Orbitrap measurements split into separate or alternating scan ranges. The input nodes expect OpenMS consensusXML files that were exported using TextExporter. The workflow then combines the separate scan ranges, filters them utilizing blank and QC measurements, and performs a statistical analysis.Requirements:- KNIME Interactive R Statistics Integration

Created: 2016-01-14 | Last updated: 2016-01-14

Credits: Marc Rurik