TIL about xidel for processing XML files, its template format is quite powerful and more intuitive than Xpath.

For example, It was quite easy to extract some scan metadata values from a mzML file without having to load a full blown parser in python/R/etc.

https://github.com/benibela/xidel

#bioinformatics #teammassspec

There are so many things I would like to improve in our proteomics / peptidomics pipeline analysis and data management. It is working but at what cost... 🙁 #bioinformatics #teammassspec

Happy to announce that we've just put up our preprint for the #OpenMS 3.0 release:

https://www.researchsquare.com/article/rs-3286368/v1

OpenMS is the by far the largest software project that I've ever worked on, and this is the first major release during my tenure here. Happy to answer any questions.

#TeamMassSpec #FOSS #OpenScience #OpenSource #Proteomics #massSpectrometry

Hum, in theory you can only find as many peptides as there are MS1 scans (except cases of chimeric spectra of course) right? 🤔

#teammassspec #bioinformatics #proteomics

What tool do you use to collect metadata for #massspectrometry experiments? I want to overhaul our current system to be more flexible and exhaustif. I started to record things in a spreadsheet using SDRF but it is a bit tedious and the format itself doesn't respect tabular data good practices. #teammassspec #bioinformatics

We have a free (already paid for) space available at this year's Ardgour Symposium! More details here - www.emsg-ardgour.site If you can get yourself to Aberdeen on the 20th August, then you could be enjoying a week of mass spec and related discussions, in the Highlands and with a free bar! #teammassspec #massspec #lipidomics #metabolomics #proteomics #ionization

#TeamMassSpec #Proteomics #MassSpectrometry: Have you used or hear of #OpenMS? Would you be interested in filling out a survey to guide our future development? Please go to: https://www.surveymonkey.de/r/9F6TMJL
You will get my gratitude, and, for a limited time, if you toot me that you filled it out a free random fact of my choosing. Come help support #OpenScience #FOSS #OpenSource

I’m the late 00’s I was enamored with AFFF-MALS (or DLS), and am always surprised I am not hearing about folks using it upstream of proteomics. Could definitely work (and did for me in 2008) for EVs and likely work for some organelles and even some cell types (I don’t actually know the upper limit on size range).

Is it something Wyatt did or…?

#proteomics #teamproteome #teammassspec

I know some vendors of mass spectrometers who could learn a lesson or 2 from ONT. Open source software running on all platforms, wow... #bioinformatics #teammassspec

Question for #teammassspec / #metabolomics / #proteomics / #lc-ms folks.

Is there some sort of content based hash of the instrument method stored (and accessible from, using non Thermo software) in Thermo’s .RAW format, or in .mzML conversions of .RAW?

I’m trying to determine which methods were used w/ hundreds of LC-MS samples run over months by a core with poor communication and some unexpected method changes “oh for some we ran the MS2 in the Orbitrap cause the linear trap was being weird”

@ProfSimonFisher
I do love doing Proteognomics.

#TeamMassSpec

Want to thank everyone here for some stellar discussion on SAAVs and searching.

Follow up: is there a SAAV-only open search option? So open-search but constrain fitting delta mass unknowns to AAs only (no funky ptms). I am off to poke around in #FragPipe but figured the crowd might know better.

#TeamMassSpec #teamProteome

https://fediscience.org/@neely/110666898318635047

#teammassspec @massspec you can probably guess what her father is working with?
(Thanks to the whole @warscheidlab for this great birth gift for our daughter!)
@academicchatter

I am back doing cool stuff with #ggplot2 and #ggtree. I spent way too much time polishing my plots though for such a simple analysis, but you know, if a tree is the best way to represent the experiment, I am going to make trees...

#bioinformatics #teammassspec

One thing I want to try is to store ms data in a database. It would be neat to have a schema/protocol based on MsBackendSql (https://rformassspectrometry.github.io/MsBackendSql/articles/MsBackendSql.htm) to use it from different programming languages.

#bioinformatics #teammassspec #rstats #rformassspectrometry

We are hiring a bioinformatician / analyst in the Proteomics and Analytical Sciences department (focus on peptidomics and mass spectrometry data) to assist research and product development activities.

https://www.linkedin.com/jobs/view/3632955467/

#bioinformatics #proteomics #peptidomics #teammassspec #Ireland

My wife has recently been reading a bunch of scientific literature for a new job. She's noticed that we are really bad about creating #backronyms. Would there be any interest in a hashtag or an account to collect the ones that we all come across*? #Science #TeamMassSpec #scientists

Her inaugural one is:
"SARGON ( SmArt eneRGy dOmain oNtology )"*

* to be clear I don't mean in a malicious manner. I work on " TOPP (The Openms PiPeline) for goodness sakes #OpenMS

What's the job market in the USA for proteomics / bioinformaticians people? Is there a huge supply of people trained analysing mass spec data and doing bioinformatics or do you have to train bioinformaticians into proteomics?

#teammassspec #bioinformatics

#ASMS2023 here we go! Looking forward to a week of science, (re)connecting with #TeamMassSpec folks and talking phospho-#proteomics. Hit me up if you're in Houston, Texas

I kind of laugh when I see figures with a simple straight line from organism to proteome (sad laugh, very sad laugh).

https://mstdn.science/users/pastelbio/statuses/110473272261800743

#bioinformatics #teammassspec