Proteogenomics: integrating next-generation sequencing and mass spectrometry to characterize human proteomic variation
GM Sheynkman, MR Shortreed… - Annual review of …, 2016 - annualreviews.org
Mass spectrometry–based proteomics has emerged as the leading method for detection,
quantification, and characterization of proteins. Nearly all proteomic workflows rely on …
quantification, and characterization of proteins. Nearly all proteomic workflows rely on …
False discovery rate: the Achilles' heel of proteogenomics
Proteogenomics refers to the integrated analysis of the genome and proteome that
leverages mass-spectrometry (MS)-based proteomics data to improve genome annotations …
leverages mass-spectrometry (MS)-based proteomics data to improve genome annotations …
Bottom-up proteomics (2013–2015): keeping up in the era of systems biology
Over 17,000 papers related to proteomics have been published since our 2011− 2013
review. A subset are true gems reporting amazing applications of proteomics to better …
review. A subset are true gems reporting amazing applications of proteomics to better …
Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines
Background Onco-proteogenomics aims to understand how changes in a cancer's genome
influences its proteome. One challenge in integrating these molecular data is the …
influences its proteome. One challenge in integrating these molecular data is the …
Methods for proteogenomics data analysis, challenges, and scalability bottlenecks: a survey
Big Data Proteogenomics lies at the intersection of high-throughput Mass Spectrometry (MS)
based proteomics and Next Generation Sequencing based genomics. The combined and …
based proteomics and Next Generation Sequencing based genomics. The combined and …
Connecting proteomics to next‐generation sequencing: proteogenomics and its current applications in biology
Understanding the relationship between genotypes and phenotypes is essential to
disentangle biological mechanisms and to unravel the molecular basis of diseases. Genes …
disentangle biological mechanisms and to unravel the molecular basis of diseases. Genes …
Peptidomics and proteogenomics: background, challenges and future needs
R Vitorino, M Choudhury, S Guedes… - Expert Review of …, 2021 - Taylor & Francis
Introduction With available genomic data and related information, it is becoming possible to
better highlight mutations or genomic alterations associated with a particular disease or …
better highlight mutations or genomic alterations associated with a particular disease or …
Target-small decoy search strategy for false discovery rate estimation
Background One of the most important steps in peptide identification is to estimate the false
discovery rate (FDR). The most commonly used method for estimating FDR is the target …
discovery rate (FDR). The most commonly used method for estimating FDR is the target …
Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes
L Guillot, L Delage, A Viari, Y Vandenbrouck, E Com… - BMC genomics, 2019 - Springer
Background Accurate structural annotation of genomes is still a challenge, despite the
progress made over the past decade. The prediction of gene structure remains difficult …
progress made over the past decade. The prediction of gene structure remains difficult …
Proteogenomics 101: a primer on database search strategies
Proteogenomics refers to the integration of high-throughput genomics/transcriptomics with
proteomics data for genome annotation, novel gene discovery, and variant peptide detection …
proteomics data for genome annotation, novel gene discovery, and variant peptide detection …