Question: free software or tools for analyzing mass spectrometry
3
gravatar for rob.costa1234
2.6 years ago by
rob.costa1234250
United States
rob.costa1234250 wrote:

Is there any free web based or online tool to analyze mass- spec protein data?

Thanks

proteomics • 1.8k views
ADD COMMENTlink modified 2.6 years ago by Hugo290 • written 2.6 years ago by rob.costa1234250

What have you tried?

ADD REPLYlink written 2.6 years ago by Michael Dondrup47k
1
gravatar for Jean-Karim Heriche
2.6 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche22k wrote:

What kind of MS data ? There's plenty of software for different types of data/tasks. You can start by having a look on OMICtools or at the list of MS software on wikipedia.

ADD COMMENTlink written 2.6 years ago by Jean-Karim Heriche22k
0
gravatar for Bastien Hervé
2.6 years ago by
Bastien Hervé4.6k
Karolinska Institutet, Sweden
Bastien Hervé4.6k wrote:

If you are not afraid to install some tools, you can take a look to open source software as OpenMS, OpenSwath. To process mzML data I used OpenSwathWorkflow and TOPPview for mzML visualisation. For general analysis you can take a look to TPP software (Trans-Proteomic Pipeline).

ADD COMMENTlink written 2.6 years ago by Bastien Hervé4.6k
0
gravatar for Leite
2.6 years ago by
Leite1000
São Paulo - Brazil - Unifesp
Leite1000 wrote:

Hey,

In my opinion, MaxQuant is the best and most used, it is quantitative proteomics software package designed for analyzing large-scale mass-spectrometric data sets.

Best regards,

Leite

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Leite1000
0
gravatar for Hugo
2.6 years ago by
Hugo290
Universidade de Vigo, Ourense (Spain)
Hugo290 wrote:

As it has been said, the software tools depend on the type of analyses you want to do. Maybe Mass-Up (http://www.sing-group.org/mass-up/; https://doi.org/10.1186/s12859-015-0752-4) can be useful to you if you want to preprocess raw spectra and perform clustering analysis or PCA in the peak lists.

ADD COMMENTlink written 2.6 years ago by Hugo290
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