Understudied proteins: opportunities and challenges for functional proteomics
Most research aiming at understanding the molecular foundations of life and disease has
focused on a limited set of increasingly well-known proteins while the biological functions of …
focused on a limited set of increasingly well-known proteins while the biological functions of …
Revisiting biomarker discovery by plasma proteomics
PE Geyer, LM Holdt, D Teupser… - Molecular systems biology, 2017 - embopress.org
Clinical analysis of blood is the most widespread diagnostic procedure in medicine, and
blood biomarkers are used to categorize patients and to support treatment decisions …
blood biomarkers are used to categorize patients and to support treatment decisions …
IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs
Missing values weaken the power of label-free quantitative proteomic experiments to
uncover true quantitative differences between biological samples or experimental …
uncover true quantitative differences between biological samples or experimental …
Bottom-up proteomics: advancements in sample preparation
Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a
powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom …
powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom …
Optimization of experimental parameters in data-independent mass spectrometry significantly increases depth and reproducibility of results
Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key
objectives of quantitative proteomics. Here, we present an implementation of data …
objectives of quantitative proteomics. Here, we present an implementation of data …
The Perseus computational platform for comprehensive analysis of (prote) omics data
A main bottleneck in proteomics is the downstream biological analysis of highly multivariate
quantitative protein abundance data generated using mass-spectrometry-based analysis …
quantitative protein abundance data generated using mass-spectrometry-based analysis …
StrucGP: de novo structural sequencing of site-specific N-glycan on glycoproteins using a modularization strategy
J Shen, L Jia, L Dang, Y Su, J Zhang, Y Xu, B Zhu… - Nature …, 2021 - nature.com
Precision mapping of glycans at structural and site-specific level is still one of the most
challenging tasks in the glycobiology field. Here, we describe a modularization strategy for …
challenging tasks in the glycobiology field. Here, we describe a modularization strategy for …
Andromeda: a peptide search engine integrated into the MaxQuant environment
J Cox, N Neuhauser, A Michalski… - Journal of proteome …, 2011 - ACS Publications
A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in
sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel …
sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel …
A scalable approach for protein false discovery rate estimation in large proteomic data sets [s]
Calculating the number of confidently identified proteins and estimating false discovery rate
(FDR) is a challenge when analyzing very large proteomic data sets such as entire human …
(FDR) is a challenge when analyzing very large proteomic data sets such as entire human …
Next-generation proteomics: towards an integrative view of proteome dynamics
Next-generation sequencing allows the analysis of genomes, including those representing
disease states. However, the causes of most disorders are multifactorial, and systems-level …
disease states. However, the causes of most disorders are multifactorial, and systems-level …