KNIME
Old (TOPPAS)
- Targeted feature detection for label-free quantification
- Parallel execution of OpenMS tools in KNIME
- DNA heteroconjugate detection (Flett et al.)
- Non-targeted LC-MS-based lipidomics
- Basic Peptide Identification
- Consensus Peptide Identification
- Peptide Identification and Label-free Quantification
- Protein Inference
- SWATH Analysis
- Small Molecule Identification and Quantification
This KNIME workflow shows the very basics of peptide identification using OpenMS.
What it does:
It shows how to use a peptide search engine adapter (here: OMSSA) on multiple input files using the same database multiple times.
This workflow is part of the OpenMS tutorial and described in detail in the tutorial.
Preset parameter assumptions:
You have recorded MS/MS data in CID mode and medium resolution (comparable to an ion trap)
Important parameters:
OMSSAAdapter
| database | expects NCBI formatted FASTA files. The .psq filename should be given. |
| precursor_mass_tolerance | choose according to your acquisition settings |
| fragment_mass_tolerance | choose according to your acquisition settings |