![]() ![]() Proteoforms with various PTMs and combinations thereof were identified using an unrestricted open modification search. Interestingly, these truncated proteoforms were considerably more abundant in the wildtype relative to the nifH- mutant, implicating protease activity as an important factor in nitrogen fixation. Leghemoglobin, the most abundant protein in the sample, existed in many truncated proteoforms. TDP captured 1648 proteoforms derived from 313 bacterial genes and 178 soybean genes. We performed TDP on soybean root nodules infected by the symbiotic Bradyrhizobium japonicum in both the wildtype bacterium and a nifH- mutant, which lacks the ability to fix nitrogen in the soybean root nodule. In contrast, top-down proteomics (TDP) directly characterizes intact proteins including all possible post-translational modifications (PTMs), thus offering unique insights into proteoform biology where combinations of individual PTMs may play important roles. Most well-established methods (known as bottom-up proteomics, BUP) employ an enzymatic digestion step to cleave intact proteins into smaller peptides for liquid chromatography (LC) mass spectrometry (MS) detection. Proteomic methods have been widely used to study proteins in complex biological samples to understand biological molecular mechanisms.
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