PBLMM: Peptide‐based linear mixed models for differential expression analysis of shotgun proteomics data
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Cellular Biochemistry"
DOI: 10.1002/jcb.30225
Abstract: Here, we present a peptide‐based linear mixed models tool—PBLMM, a standalone desktop application for differential expression analysis of proteomics data. We also provide a Python package that allows streamlined data analysis workflows implementing the PBLMM… read more here.
Keywords: peptide based; proteomics data; based linear; differential expression ... See more keywords
A practical guide to interpreting and generating bottom‐up proteomics data visualizations
Sign Up to like & getrecommendations! Published in 2022 at "PROTEOMICS"
DOI: 10.1002/pmic.202100103
Abstract: Mass‐spectrometry based bottom‐up proteomics is the main method to analyze proteomes comprehensively and the rapid evolution of instrumentation and data analysis has made the technology widely available. Data visualization is an integral part of the… read more here.
Keywords: proteomics data; data visualizations; practical guide; bottom proteomics ... See more keywords
Dealing with missing values in proteomics data
Sign Up to like & getrecommendations! Published in 2022 at "PROTEOMICS"
DOI: 10.1002/pmic.202200092
Abstract: Proteomics data are often plagued with missingness issues. These missing values (MVs) threaten the integrity of subsequent statistical analyses by reduction of statistical power, introduction of bias, and failure to represent the true sample. Over… read more here.
Keywords: proteomics data; dealing missing; mvi; missing values ... See more keywords
Network Tools for the Analysis of Proteomic Data.
Sign Up to like & getrecommendations! Published in 2017 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-6740-7_14
Abstract: Recent advancements in high-throughput technologies such as mass spectrometry have led to an increase in the rate at which data is generated and accumulated. As a result, standard statistical methods no longer suffice as a… read more here.
Keywords: network; proteomics data; analysis; proteomic data ... See more keywords
Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis
Sign Up to like & getrecommendations! Published in 2019 at "Analytical Chemistry"
DOI: 10.1021/acs.analchem.9b00327
Abstract: Techniques that allow single cell analysis are gaining widespread attention, and most of these studies utilize genomics-based approaches. While nanofluidic technologies have enabled mass spectromet... read more here.
Keywords: cell proteomics; independent acquisition; proteomics data; data independent ... See more keywords
Eatomics: Shiny exploration of quantitative proteomics data.
Sign Up to like & getrecommendations! Published in 2020 at "Journal of proteome research"
DOI: 10.1021/acs.jproteome.0c00398
Abstract: Quantitative proteomics data is becoming increasingly more available and as a consequence is being analyzed and interpreted by a larger group of users. However, many of these users have less programming experience. Furthermore, experimental designs… read more here.
Keywords: shiny exploration; eatomics shiny; proteomics data; analysis ... See more keywords
multiFLEX-LF: A Computational Approach to Quantify the Modification Stoichiometries in Label-Free Proteomics Data Sets.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of proteome research"
DOI: 10.1021/acs.jproteome.1c00669
Abstract: In liquid-chromatography-tandem-mass-spectrometry-based proteomics, information about the presence and stoichiometry of protein modifications is not readily available. To overcome this problem, we developed multiFLEX-LF, a computational tool that builds upon FLEXIQuant, which detects modified peptide precursors… read more here.
Keywords: multiflex computational; modification; proteomics data; label free ... See more keywords
Validation of Top-Down Proteomics Data by Bottom-Up-Based N-Terminomics Reveals Pitfalls in Top-Down-Based Terminomics Workflows.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of proteome research"
DOI: 10.1021/acs.jproteome.2c00277
Abstract: Bottom-up proteomics (BUP)-based N-terminomics techniques have become standard to identify protein N-termini. While these methods rely on the identification of N-terminal peptides only, top-down proteomics (TDP) comes with the promise to provide additional information about… read more here.
Keywords: top proteomics; proteomics data; data bottom; based terminomics ... See more keywords
PACOM: A Versatile Tool for Integrating, Filtering, Visualizing, and Comparing Multiple Large Mass Spectrometry Proteomics Data Sets.
Sign Up to like & getrecommendations! Published in 2018 at "Journal of proteome research"
DOI: 10.1021/acs.jproteome.7b00858
Abstract: Mass-spectrometry-based proteomics has evolved into a high-throughput technology in which numerous large-scale data sets are generated from diverse analytical platforms. Furthermore, several scientific journals and funding agencies have emphasized the storage of proteomics data in… read more here.
Keywords: data sets; pacom; proteomics data; mass spectrometry ... See more keywords
PPIExp: A Web-Based Platform for Integration and Visualization of Protein-Protein Interaction Data and Spatiotemporal Proteomics Data.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of proteome research"
DOI: 10.1021/acs.jproteome.8b00713
Abstract: Integrating spatiotemporal proteomics data with protein-protein interaction (PPI) data can help researchers make an in-depth exploration of their proteins of interest in a dynamic manner. However, there is still a lack of proper tools for… read more here.
Keywords: protein interaction; network; proteomics data; ppi ... See more keywords
Philosopher: a versatile toolkit for shotgun proteomics data analysis
Sign Up to like & getrecommendations! Published in 2020 at "Nature Methods"
DOI: 10.1038/s41592-020-0912-y
Abstract: To the Editor — Here we introduce Philosopher (https://philosopher.nesvilab. org), a free, open-source, versatile and robust data analysis toolkit designed to bring easy access to a powerful and comprehensive set of computational tools for shotgun… read more here.
Keywords: philosopher; data analysis; proteomics data; analysis ... See more keywords