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   Articles with "proteomics data" as a keyword



PBLMM: Peptide‐based linear mixed models for differential expression analysis of shotgun proteomics data

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recommendations! 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

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recommendations! 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

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recommendations! 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

Data Processing and Analysis in Positional Proteomics

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recommendations! Published in 2025 at "Proteomics"

DOI: 10.1002/pmic.70069

Abstract: Proteolytic cleavage is an irreversible post‐translational modification (PTM), and dysregulation of protease activity is often a hallmark in disease. Aberrant proteolysis can alter protein abundance or function, disturbing cellular state and resulting in disease‐specific biomarkers… read more here.

Keywords: proteomics data; analysis; protein; positional proteomics ... See more keywords
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Network Tools for the Analysis of Proteomic Data.

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recommendations! 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

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recommendations! 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
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Eatomics: Shiny exploration of quantitative proteomics data.

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recommendations! 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.

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recommendations! 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.

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recommendations! 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

A Scalable, Web-Based Platform for Proteomics Data Processing, Result Storage and Analysis

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recommendations! Published in 2025 at "Journal of Proteome Research"

DOI: 10.1021/acs.jproteome.4c00871

Abstract: The exponential increase in proteomics data presents critical challenges for conventional processing workflows. These pipelines often consist of fragmented software packages, glued together using complex in-house scripts or error-prone manual workflows running on local hardware,… read more here.

Keywords: platform; analysis; proteomics data; result storage ... See more keywords

ProteoPlotter: An Executable Proteomics Visualization Tool Compatible with Perseus.

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recommendations! Published in 2025 at "Journal of proteome research"

DOI: 10.1021/acs.jproteome.4c00963

Abstract: Mass spectrometry-based proteomics experiments produce complex data sets requiring robust statistical testing and effective visualization tools to ensure meaningful conclusions are drawn. The publicly available proteomics data analysis platform, Perseus, is extensively used to perform… read more here.

Keywords: visualization; proteomics data; tool; perseus ... See more keywords