Question

free software or tools for analyzing mass spectrometry

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6.4 years ago

rob.costa1234 ▴ 310

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

Thanks

proteomics • 3.6k views

ADD COMMENT • link updated 6.4 years ago by Hugo ▴ 380 • written 6.4 years ago by rob.costa1234 ▴ 310

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What have you tried?

ADD REPLY • link 6.4 years ago by Michael 54k

score 1 · Answer 1 · 2017-11-22

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6.4 years ago

Jean-Karim Heriche 27k

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 COMMENT • link 6.4 years ago by Jean-Karim Heriche 27k

score 0 · Answer 2 · 2017-11-22

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6.4 years ago

Bastien Hervé 5.3k

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 COMMENT • link 6.4 years ago by Bastien Hervé 5.3k

score 0 · Answer 3 · 2017-11-22

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6.4 years ago

Leite ★ 1.3k

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 COMMENT • link 6.4 years ago by Leite ★ 1.3k

score 0 · Answer 4 · 2017-11-22

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.