What Projects Would You Like to See?

[michaelmarty]

Post ideas here for future tutorials. It can be as specific or as vague as you want. If you have specific data, feel free to suggest it. Also, feel free to nominate other instructors for videos or make some yourself.

[schatzsc]

Access to the different instrument vendor original data files.

I managed to read ThermoFisher files but it was quite some effort to find a working API.

Main interest: extract combinatorial and kinetics data from HPLC/MS runs to aid projects like this: Electrospray Mass Spectrometry to Study Combinatorial iClick Reactions and Multiplexed Kinetics of [Ru(N3)(N∧N)(terpy)]PF6 with Alkynes of Different Steric and Electronic **Demand**

[michaelmarty]

Great idea! I'll put it on the list. We may need to lay some more intro groundwork first, but I have a number of ideas on how we could do this. Thanks!

[schatzsc]

The package I finally settled on was https://github.com/ethz-institute-of-microbiology/fisher_py but my main job is teaching chemistry and leading an experimental synthetic research group, so programming is only a part-time activity for me and I'm not exactly the best Python programmer in the world

[michaelmarty]

I like MultiplierZ from @BlaisProteomics, but there are a handful of options out there, and some work better or worse for different vendors.

[StreetResearch]

Processing and analyzing polymer MS data would also be nice (for me at least!) - the only way to do this I know of is to use the bruker built in 'polytools' function... (I don't have access to any other commerical MS software, only free/open source ones and the instrument itself). I have example data that I could share for use if anyone wants (as well as an example small molecule spectrum). I've been learning python and making a tool to analyze MS data is on my to-do list!

Also I found that mmass is a great open-source MS tool built using python, but has been out of development for a while now. Not sure if this would be a useful base for anything?

[lorbarlab]

Hi, great initiative. I would be interested in oligonucleotide MS data analysis.

[alessiodiianni]

Processing and anlayzing raw data from different vendors instrument would be great, as well as exploring Python packages e.g. pyOpenMS, OpenTIMSpy and MSstats package from R which allow analysis of quantitative proteomics analyses with robust statistical evaluation. Also how to export different MS file formats (mzML, mzID, mgf) I think would be a good common knowledge to share.

[BobChallen]

I'd agree with this - manipulating mzml data to extract certain values would be really useful as well!

[nfisher519]

I think a lot of what has been suggested so far would be great: read vendor files, knowing what kinds of packages exist in python already, how to work with mzml files(read and write). I would also be interested to learn how to work with publicly available databases to do searches and things like that (I’m mainly interested in proteomics).

[alexeybark]

Would love to see analysis of ion mobility data and its automation. Getting data in, fitting gaussians, creating summaries, visualisation etc

Many thanks for doing this!

[michaelmarty]

Awesome ideas, everyone! Keep posting, and I'll add them to the ideas list on the main page.

[akulmehta]

Maybe it is of value to split the club to beginners vs intermediate. For beginners, maybe cover more simple topics and introductions to the language and various existing packages one can use. For intermediate/advance, maybe cover topics on how you can contribute to or generate your own packages.

[michaelmarty]

Great idea. My thought was to start with a set of core tutorials for everyone to get the basics and then we could split into more specialized topics. But, I'm open to people posting anything relevant, including resources that already exist. Just need to organize them.

[ssybbc1004]

Thanks for asking people's input on this! I have been thinking about automating the spectrum searching process for proteomics, including data sorting and cleaning using data from available online databases, quality control, spectrum searching and peptide matching. I am also interested in metabolomics data analysis but basically had zero experience with it. I had extensive experience in proteomics but very limited proteomics data coding experience using python.

[srayGIT]

How to read a RAW file and construct TIC, XIC,BPC etc, How to find LC-MS features, How to align two simple LC-MS runs etc.
How to theoretically digest a fasta library using some enzyme specificity. How to create a theoretical spectra with b,y,a,neutral-loss etc. type of ions, how to combinatorically generate variable modification masses would be handy and useful
I came across some from Sam Payne's lab:
https://pubs.acs.org/doi/suppl/10.1021/jasms.4c00185/suppl_file/js4c00185_si_001.pdf