myExperiment - Workflows

Taverna 2

Uploader

Yassene

Download

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

Taverna 2

Uploader

Sonja Holl

Optimization of retention time prediction (1)

Download

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

Taverna 2

Uploader

Magnus Palmblad

Simulate_Mass_Spectrum (1)

Download

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

Taverna 2

Uploader

Magnus Palmblad

Calculate_Isotopic_Distribution (1)

Download

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

Taverna 2

Uploader

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

Taverna 2

Uploader

Yassene

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

Download

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

Taverna 2

Uploader

Yassene

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

Download

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

Taverna 2

Uploader

Magnus Palmblad

Retention Time Prediction with X!Tandem (1)

Download

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...