13 research outputs found
IMTBX and Grppr: Software for Top-Down Proteomics Utilizing Ion Mobility-Mass Spectrometry
Top-down
proteomics has emerged as a transformative method for
the analysis of protein sequence and post-translational modifications
(PTMs). Top-down experiments have historically been performed primarily
on ultrahigh resolution mass spectrometers due to the complexity of
spectra resulting from fragmentation of intact proteins, but recent
advances in coupling ion mobility separations to faster, lower resolution
mass analyzers now offer a viable alternative. However, software capable
of interpreting the highly complex two-dimensional spectra that result
from coupling ion mobility separation to top-down experiments is currently
lacking. In this manuscript we present a software suite consisting
of two programs, IMTBX (“IM Toolbox”) and Grppr (“Grouper”),
that enable fully automated processing of such data. We demonstrate
the capabilities of this software suite by examining a series of intact
proteins on a Waters Synapt G2 ion-mobility equipped mass spectrometer
and compare the results to the manual and semiautomated data analysis
procedures we have used previously
Identification of modified peptides using localization-aware open search
Mass spectrometry-based proteomics is the method of choice for the global mapping of post-translational modifications, but matching and scoring peaks with unknown masses remains challenging. Here, the authors present a refined open search strategy to score all peaks with higher sensitivity and accuracy
IMTBX and Grppr: Software for Top-Down Proteomics Utilizing Ion Mobility-Mass Spectrometry
Top-down
proteomics has emerged as a transformative method for
the analysis of protein sequence and post-translational modifications
(PTMs). Top-down experiments have historically been performed primarily
on ultrahigh resolution mass spectrometers due to the complexity of
spectra resulting from fragmentation of intact proteins, but recent
advances in coupling ion mobility separations to faster, lower resolution
mass analyzers now offer a viable alternative. However, software capable
of interpreting the highly complex two-dimensional spectra that result
from coupling ion mobility separation to top-down experiments is currently
lacking. In this manuscript we present a software suite consisting
of two programs, IMTBX (“IM Toolbox”) and Grppr (“Grouper”),
that enable fully automated processing of such data. We demonstrate
the capabilities of this software suite by examining a series of intact
proteins on a Waters Synapt G2 ion-mobility equipped mass spectrometer
and compare the results to the manual and semiautomated data analysis
procedures we have used previously
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Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genomic alterations, including oxidative phosphorylation-related metabolism, protein translation processes, and phospho-signaling modules. To assess the degree of immune infiltration in individual tumors, we identified microenvironment cell signatures that delineated four immune-based ccRCC subtypes characterized by distinct cellular pathways. This study reports a large-scale proteogenomic analysis of ccRCC to discern the functional impact of genomic alterations and provides evidence for rational treatment selection stemming from ccRCC pathobiology