QuantUMS: uncertainty minimisation enables confident quantification in proteomics
F Kistner, JL Grossmann, LR Sinn, V Demichev - BioRxiv, 2023 - biorxiv.org
Mass spectrometry-based proteomics has been rapidly gaining traction as a powerful
analytical method both in basic research and translation. While the problem of error control …
analytical method both in basic research and translation. While the problem of error control …
Triqler for MaxQuant: Enhancing results from MaxQuant by Bayesian error propagation and integration
Error estimation for differential protein quantification by label-free shotgun proteomics is
challenging due to the multitude of error sources, each contributing uncertainty to the final …
challenging due to the multitude of error sources, each contributing uncertainty to the final …
Combining quantitative proteomics data processing workflows for greater sensitivity
We here describe a normalization method to combine quantitative proteomics data. By
merging the output of two popular quantification software packages, we obtained a 20 …
merging the output of two popular quantification software packages, we obtained a 20 …
apQuant: accurate label-free quantification by quality filtering
J Doblmann, F Dusberger, R Imre… - Journal of Proteome …, 2018 - ACS Publications
Label-free quantification of shotgun proteomics data is a frequently used strategy, offering
high dynamic range, sensitivity, and the ability to compare a high number of samples without …
high dynamic range, sensitivity, and the ability to compare a high number of samples without …
iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
TV Pham, AA Henneman, CR Jimenez - Bioinformatics, 2020 - academic.oup.com
We present an R package called iq to enable accurate protein quantification for label-free
data-independent acquisition (DIA) mass spectrometry-based proteomics, a recently …
data-independent acquisition (DIA) mass spectrometry-based proteomics, a recently …
[HTML][HTML] Artificial intelligence for proteomics and biomarker discovery
There is an avalanche of biomedical data generation and a parallel expansion in
computational capabilities to analyze and make sense of these data. Starting with genome …
computational capabilities to analyze and make sense of these data. Starting with genome …
Bioinformatics tools for mass spectrometry-based high-throughput quantitative proteomics platforms
AV Nefedov, MJ Gilski, RG Sadygov - Current proteomics, 2011 - ingentaconnect.com
Determining global proteome changes is important for advancing a systems biology view of
cellular processes and for discovering biomarkers. Liquid chromatography, coupled to mass …
cellular processes and for discovering biomarkers. Liquid chromatography, coupled to mass …
A statistical framework for protein quantitation in bottom-up MS-based proteomics
Y Karpievitch, J Stanley, T Taverner, J Huang… - …, 2009 - academic.oup.com
Motivation: Quantitative mass spectrometry-based proteomics requires protein-level
estimates and associated confidence measures. Challenges include the presence of low …
estimates and associated confidence measures. Challenges include the presence of low …
proteiNorm–A user-friendly tool for normalization and analysis of TMT and label-free protein quantification
The technological advances in mass spectrometry allow us to collect more comprehensive
data with higher quality and increasing speed. With the rapidly increasing amount of data …
data with higher quality and increasing speed. With the rapidly increasing amount of data …
MSImpute: Imputation of label-free mass spectrometry peptides by low-rank approximation
Recent developments in mass spectrometry (MS) instruments and data acquisition modes
have aided multiplexed, fast, reproducible and quantitative analysis of proteome profiles, yet …
have aided multiplexed, fast, reproducible and quantitative analysis of proteome profiles, yet …