Hi!

What kind of MS data did you obtain from your tryptic in-gel digests; peptide mass fingerprints, or (also) MS/MS data?

I think the Matrix Science page could provide a starting point when it comes to different types of searches, it also has some tutorials.

https://www.matrixscience.com/search_form_select.html

Hope this helps!

Hi Gabriela,

It would be akin of asking a video tutorial to learn swimming or driving. the issue is much more complex than that. I would suggest you find an expert in the field to help you.

D.

Dear Gabriela,

the Matrix Science website (Mascot database) has some good pdf files for training, which could be helpful for you.

Here is the link:

https://www.matrixscience.com/training_webcast.html

Good luck,

Murat

Hola Gabriela,

I assume proteomics and bioinformatics might be a new field for you. Hence, I highly recommend this review paper on state of the art proteomics data analyis first: https://www.sciencedirect.com/science/article/abs/pii/S1874391918304263

EMBL made a nice theoretical introduction course as well:

https://www.ebi.ac.uk/training/online/courses/proteomics-an-introduction/

I like this tutorial as it is short yet gives you a good overview over the field. Once you got an overview, I would recommend to continue with some hands on tutorials.

#### Galaxy ####

The Galaxy website is a great and versatile web based tool for everyone who wants to use powerful bioinformatic tools without needing to know how to code. For proteomics analysis visit:

https://proteore.org/

or the EU based server at:

https://proteomics.usegalaxy.eu/

Don't be scared if you don't know what Galaxy is or how to use it. You will learn. They provide excellent introduction tutorials:

https://usegalaxy.eu/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html

Once you know a little bit about Galaxy you can continue with this tutorial on label-free MS data analysis using MaxQuant:

https://training.galaxyproject.org/training-material//topics/proteomics/tutorials/maxquant-label-free/tutorial.html

There are far more Galaxy tutorials out there for proteomics. See:

https://training.galaxyproject.org/training-material/topics/proteomics/

#### CompOmics ####

Another really excellent step by step tutorial for Proteomic data analysis is provided by the fellows from Lennart Martens CompOmics Group:

https://www.compomics.com/bioinformatics-for-proteomics/

Everything from setting up the software to load in the data and analyze it will be described in the tutorials step by step. You should start with Chapter 1:

https://www.compomics.com/bioinformatics-for-proteomics/identification/

Last but not least - yes, it is a very challenging and complex field. But don't get demotivated. Start somewhere and keep learning day by day. Keep asking questions and enjoy your learning adventure. We all started somewhere someday.

Good luck!