I performed some comparitive proteomics between planktonic and biofilm membrane proteomes using tandem mass tags. The mass spectrometry generated HCID and CID data . I now need to identify all the peptides and proteins using a database I constructed . The data has been sitting for some years now because much of the analysis of the raw mass spec data and adjustments is a black box to me. I was wondering if there is a software pipeline out there that can take the raw files and provide me with quantification of the proteins ?
Hi,
You can try Thermo's Proteome Discoverer and can use the default processing and consensus workflow using quantitative node. It will fetch you the result from your raw files and would also allow you to know the labelling efficiency. You can give TMT-nplex in 'Static modification' section of the search algorithm node (SEQUEST or Mascot or both).
You can also use MaxQuant which is a free software using ANDROMEDA as the search algorithm.
Hope this helps!
- Badges
- Science topic
- Similar topics
- Chemistry
- General Biochemistry
- Proteomics