1. Metaproteomics Analysis from data output from liquid chromotography mass spectrometry run quantifying proteins involved with ZVS production in sulfate-reducing microorganisms using the ZVS pathway vs sulfate reduction pathway.
data Data aquired from PRoteomics IDEntifications Database from publication submission DOI: 10.1073/PNAS.2220725120
Understanding how dissimilatory sulfate reduction from diverse sulfate-reducing microorganisms can be generated with zero-valent sulfur(ZVS), as opposed to sulfate reduction to sulfide. Utilization of the ZVS pathways in processing sulfate can be induced at greater levels by increasing salinity of media for growing sulfate-reducing microorganisms. Furthermore, ZVS products produced by sulfate-reducing microorganisms can support the growth of other ZVS-metabolizing microorganisms, yielding its importance to the sulfur biogeochemical cycle.
(1) Raw data pre-processing: https://github.com/MannLabs/alphapept also: TidyMS in Python https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7602939/
(2) Peak picking and assignment: https://openms.de/
(3) Database search: UniProt
(4) Quantification: sprectral counting and peptide intensity
(5) Data Analysis: limma
(6) Visualization: MSnbase
non-targeted metabolic data analysis using data from synthetic bacteria communities on plant leaves
Using the NP3 MS workflow: https://github.com/danielatrivella/NP3_MS_Workflow