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Items tagged with "mass spectrometry" (16)

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Workflows (16)
Original Uploader

Workflow getInchIfromMassBankPeaklist_ChemSpider_wo... (2)

Created: 05/06/08 @ 16:00:38 | Last updated: 16/06/08 @ 11:40:46

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 137 times | Downloaded: 80 times

Tags (8):

Original Uploader

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

Created: 11/06/08 @ 12:13:36 | Last updated: 11/06/08 @ 12:15:21

Credits: User Michael Gerlich User Egon Willighagen

Attributions: Workflow Download from ChemSpider using Accurate Mass

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 105 times | Downloaded: 46 times

Tags (4):

Original Uploader

Workflow MassBank to KEGG (1)

Created: 30/03/09 @ 09:30:32 | Last updated: 30/03/09 @ 09:49:13

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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)

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 215 times | Downloaded: 0 times

Tags (21):

Original Uploader

Workflow getTimololFromMassBank (1)

Created: 10/11/09 @ 08:58:05 | Last updated: 10/11/09 @ 08:59:56

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.  

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 39 times | Downloaded: 35 times

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Workflow In-silico Fragmentation of Naringenin (2)

Created: 08/02/10 @ 12:19:23

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the equivalent of the MetFrag Interface found on http://msbi.ipb-halle.de/MetFrag/ It takes a Speclipse Spectrum and a Bioclipse Molecule and runs MetFrag.  

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 288 times | Downloaded: 64 times

Tags (3):

Original Uploader

Workflow LipidMaps Query (1)

Created: 16/02/10 @ 14:47:56

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 114 times | Downloaded: 33 times

Tags (3):

Original Uploader

Workflow Plasma Precipitation Analysis (1)

Created: 31/07/12 @ 16:04:54 | Last updated: 31/07/12 @ 16:16:40

Credits: User Magnus Palmblad User Kate Mostovenko User Yassene

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 50 times | Downloaded: 3 times

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Original Uploader

Workflow de Bruin et al. Workflow 1 (1)

Created: 01/08/12 @ 08:50:28 | Last updated: 01/08/12 @ 08:54:59

Credits: User Magnus Palmblad

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 31 times | Downloaded: 4 times

Tags (6):

Original Uploader

Workflow de Bruin et al. Workflow 2 (1)

Created: 01/08/12 @ 09:00:25 | Last updated: 01/08/12 @ 09:02:17

Credits: User Magnus Palmblad

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 11 times | Downloaded: 7 times

Tags (6):

Original Uploader

Workflow de Bruin et al. Workflow 3 (1)

Created: 01/08/12 @ 09:03:01 | Last updated: 01/08/12 @ 09:07:18

Credits: User Magnus Palmblad

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 15 times | Downloaded: 3 times

Tags (6):

Original Uploader

Workflow de Bruin et al. Workflow 4 (1)

Created: 01/08/12 @ 09:08:13 | Last updated: 01/08/12 @ 09:08:58

Credits: User Magnus Palmblad

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 30 times | Downloaded: 3 times

Tags (6):

Original Uploader

Workflow Retention Time Prediction with X!Tandem (1)

Created: 03/09/12 @ 10:43:31 | Last updated: 03/09/12 @ 10:44:33

Credits: User Magnus Palmblad User Yassene User Eleni

Attributions: Blob rt3.c

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 17 times | Downloaded: 0 times

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Original Uploader

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

Created: 10/09/12 @ 12:20:30

Credits: User Yassene

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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:...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 18 times | Downloaded: 1 time

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Original Uploader

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

Created: 10/09/12 @ 12:22:32 | Last updated: 10/09/12 @ 12:22:33

Credits: User Yassene

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 6 times | Downloaded: 0 times

Tags (3):

Original Uploader

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

Created: 10/09/12 @ 09:49:08

Credits: User Yassene

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 17 times | Downloaded: 1 time

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