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Category: Workflow Tag: mass spectrometry Licence: by-sa

Workflow Download from ChemSpider using Accurate Mass (2)

No description

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

Credits: User Egon Willighagen

Workflow 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: User Michael Gerlich

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

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: User Michael Gerlich User Egon Willighagen

Attributions: Workflow Download from ChemSpider using Accurate Mass

Workflow getInchIfromMassBankPeaklist_ChemSpider_wo... (2)

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: User Michael Gerlich

Workflow LipidMaps Query (1)

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

Created: 2010-02-16

Workflow In-silico Fragmentation of Naringenin (2)

This is the equivalent of the MetFrag Interface found on It takes a Speclipse Spectrum and a Bioclipse Molecule and runs MetFrag.  

Created: 2010-02-08

Credits: User

Workflow getTimololFromMassBank (1)

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: User


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

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: User Marc Rurik

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

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: User Magnus Palmblad User Sonja Holl


Workflow Generate Spectral Library (1)

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 14 November 2012 Yassene

Created: 2013-08-16

Credits: User Yassene User Magnus Palmblad

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