POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability
Mass spectrometry-based proteomic technique has become indispensable in current
exploration of complex and dynamic biological processes. Instrument development has …
exploration of complex and dynamic biological processes. Instrument development has …
Systematic detection of functional proteoform groups from bottom-up proteomic datasets
To a large extent functional diversity in cells is achieved by the expansion of molecular
complexity beyond that of the coding genome. Various processes create multiple distinct but …
complexity beyond that of the coding genome. Various processes create multiple distinct but …
Addressing the challenge of defining valid proteomic biomarkers and classifiers
Background The purpose of this manuscript is to provide, based on an extensive analysis of
a proteomic data set, suggestions for proper statistical analysis for the discovery of sets of …
a proteomic data set, suggestions for proper statistical analysis for the discovery of sets of …
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 …
Toward an integrated pipeline for protein biomarker development
AP Drabovich, E Martínez-Morillo… - Biochimica et Biophysica …, 2015 - Elsevier
Protein biomarker development is a multidisciplinary task involving basic, translational and
clinical research. Integration of multidisciplinary efforts in a single pipeline is challenging …
clinical research. Integration of multidisciplinary efforts in a single pipeline is challenging …
Scoring proteomes with proteotypic peptide probes
Technologies for genome-wide analyses typically undergo a transition from a discovery
phase to a scoring phase. In the discovery phase, the genomic universe is explored and all …
phase to a scoring phase. In the discovery phase, the genomic universe is explored and all …
Statistical analysis of proteomics data: a review on feature selection
M Lualdi, M Fasano - Journal of proteomics, 2019 - Elsevier
The spread of “-omics” strategies has strongly changed the way of thinking about the
scientific method. Indeed, managing huge amounts of data imposes the replacement of the …
scientific method. Indeed, managing huge amounts of data imposes the replacement of the …
Identification and quantification of proteoforms by mass spectrometry
A proteoform is a defined form of a protein derived from a given gene with a specific amino
acid sequence and localized post‐translational modifications. In top‐down proteomic …
acid sequence and localized post‐translational modifications. In top‐down proteomic …
Proteogenomics: concepts, applications and computational strategies
AI Nesvizhskii - Nature methods, 2014 - nature.com
Proteogenomics is an area of research at the interface of proteomics and genomics. In this
approach, customized protein sequence databases generated using genomic and …
approach, customized protein sequence databases generated using genomic and …
The emergence of top-down proteomics in clinical research
JP Savaryn, AD Catherman, PM Thomas… - Genome medicine, 2013 - Springer
Proteomic technology has advanced steadily since the development of'soft-
ionization'techniques for mass-spectrometry-based molecular identification more than two …
ionization'techniques for mass-spectrometry-based molecular identification more than two …