Discussion of AlphaPept preprint

[dschust-r]

AlphaPept, a modern and open framework for MS-based proteomics

Link to the paper: https://www.biorxiv.org/content/10.1101/2021.07.23.453379v1.full

Citation in manubot format: [@doi:10.1101/2021.07.23.453379]

1. What section does this paper fit into? (select at least one or add your own)

• Introduction
• protein extraction
• proteolysis
• Peptide and protein labeling
• enrichment of proteins or modifications
• peptide purification
• types of mass spectrometers used for proteomics
• Peptide ionization
• Data Acquisition (targeted and untargeted DDA and DIA)
• Basics of data analysis
• Biological Interpretation
• Experiment design and considerations not discussed elsewhere

2. Please provide a short summary of the work (1-2 sentences):

Preprint from the lab of Matthias Mann. They developed a python-based software with GUI for fast analysis of large data sets, easily implementable for workflow management and quality control.

4. Any additional details

I installed the software (GUI version) and tested it on a few QC runs. It is fast in analyzing the data, only needs a path to a folder with raw files and the FASTA file to use for the search. It can also be used with a FileWatcher option, that continuously checks for new files and analyzes them automatically the same way as the other files in the folder. The graphs are easy to compare. All around a good software for quality control, in my opinion.

Has anyone else tried AlphaPept so far? Any opinions?

[jessegmeyerlab]

Wow this software looks awesome. I haven't used it but we have some projects where this might help and I will definitely check it out. Also awesome that it can work for automated QC. Thanks for starting a discussion on this!