2 research outputs found
TrpB2 Enzymes are <i>O</i>‑Phospho‑l‑serine Dependent Tryptophan Synthases
The rapid increase of the number
of sequenced genomes asks for
the functional annotation of the encoded enzymes. We used a combined
computational–structural approach to determine the function
of the TrpB2 subgroup of the tryptophan synthase β chain/β
chain-like TrpB1–TrpB2 family (IPR023026). The results showed
that TrpB2 enzymes are <i>O</i>-phospho-l-serine
dependent tryptophan synthases, whereas TrpB1 enzymes catalyze the l-serine dependent synthesis of tryptophan. We found a single
residue being responsible for the different substrate specificities
of TrpB1 and TrpB2 and confirmed this finding by mutagenesis studies
and crystallographic analysis of a TrpB2 enzyme with bound <i>O</i>-phospho-l-serine
Protein-Centric Analysis of Personalized Antibody Repertoires Using LC-MS-Based Fab-Profiling on a timsTOF
Endogenous antibodies, or immunoglobulins (Igs), abundantly
present
in body fluids, represent some of the most challenging samples to
analyze, largely due to the immense variability in their sequences
and concentrations. It has been estimated that our body can produce
billions of different Ig proteins with different isotypes, making
their individual analysis seemingly impossible. However, recent advances
in protein-centric proteomics using LC-MS coupled to Orbitrap mass
analyzers to profile intact Fab fragments formed by selective cleavage
at the IgG-hinge revealed that IgG repertoires may be less diverse,
albeit unique for each donor. Serum repertoires seem to be dominated
by a few hundred clones that cumulatively make up 50–95% of
the total IgG content. Enabling such analyses required careful optimization
of the chromatography and mass analysis, as all Fab analytes are highly
alike in mass (46–51 kDa) and sequence. To extend the opportunities
of this mass-spectrometry-based profiling of antibody repertoires,
we here report the optimization and evaluation of an alternative MS
platform, namely, the timsTOF, for antibody repertoire profiling.
The timsTOF mass analyzer has gained traction in recent years for
peptide-centric proteomics and found wide applicability in plasma
proteomics, affinity proteomics, and HLA peptidomics, to name a few.
However, for protein-centric analysis, this platform has been less
explored. Here, we demonstrate that the timsTOF platform can be adapted
to perform protein-centric LC-MS-based profiling of antibody repertoires.
In a side-by-side comparison of the timsTOF and the Orbitrap we demonstrate
that the extracted serum antibody repertoires are alike qualitatively
and quantitatively, whereby in particular the sensitivity of the timsTOF
platform excels. Future incorporation of advanced top-down capabilities
on the timsTOF may make this platform a very valuable alternative
for protein-centric proteomics and top-down proteomics and thus also
for personalized antibody repertoire profiling