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View article: Ancestry-Dependent Immunologic and Prognostic Effects Characterize the Prostate Cancer Urinary Proteome
Ancestry-Dependent Immunologic and Prognostic Effects Characterize the Prostate Cancer Urinary Proteome Open
Urine is an attractive biomarker analyte for non-invasive longitudinal monitoring of health and disease, particularly for diseases of the genitourinary tract, like prostate and bladder cancer. The composition of an individual’s urine refle…
View article: Identification of non-canonical peptides with moPepGen
Identification of non-canonical peptides with moPepGen Open
Proteogenomics is limited by the challenge of modeling the complexities of gene expression. We create moPepGen, a graph-based algorithm that comprehensively generates non-canonical peptides in linear time. moPepGen works with multiple tech…
View article: Protocol for generating high-fidelity proteomic profiles using DROPPS
Protocol for generating high-fidelity proteomic profiles using DROPPS Open
Deep mass spectrometry-based proteomic profiling of rare cell populations has been constrained by sample input requirements. Here, we present a protocol for droplet-based one-pot preparation for proteomic samples (DROPPS), an accessible lo…
View article: Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine
Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine Open
Biofluids contain molecules in circulation and from nearby organs that can be indicative of disease states. Characterizing the proteome of biofluids with DIA-MS is an emerging area of interest for biomarker discovery; yet, there is limited…
View article: Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage
Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage Open
Data independent acquisition (DIA) modes isolate and concurrently fragment populations of different precursors by cycling through segments of a predefined precursor m/z range. Although these selection windows collectively cover the entire …