einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data

Soneson, Charlotte; Iešmantavičius, Vytautas; Heß, Daniel; Stadler, Michael

doi:10.1101/2023.07.27.550821

Cited by 4 publications

(4 citation statements)

References 36 publications

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“…The mouse subset of the UniProt version 2017_04 or 2021_05 combined with the contaminant DB from MaxQuant was searched and the protein and peptide FDR values were set to 0.05. Statistical analysis was done in Perseus version 1.5.2.6 62 or using limma within the einProt package (version 0.5.13) 63 . Results were filtered to remove reverse hits, contaminants and peptides found in only one sample.…”

Section: Methodsmentioning

confidence: 99%

ChAHP2 and ChAHP control diverse retrotransposons by complementary activities

Ahel,

Pandey,

Schwaiger

et al. 2024

Preprint

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Retrotransposon control in mammals is an intricate process that is effectuated by a broad network of chromatin regulatory pathways. We previously discovered ChAHP, a protein complex with repressive activity against SINE retrotransposons, composed of the transcription factor ADNP, chromatin remodeler CHD4, and HP1 proteins. Here we identify ChAHP2, a protein complex homologous to ChAHP, wherein ADNP is replaced by ADNP2. ChAHP2 is predominantly targeted to ERVs and LINEs, via HP1beta-mediated binding of H3K9 trimethylated histones. We further demonstrate that ChAHP also binds these elements in a mechanistically equivalent manner to ChAHP2, and distinct from DNA sequence-specific recruitment at SINEs. Genetic ablation of ADNP2 alleviates ERV and LINE1 repression, which is synthetically exacerbated by additional depletion of ADNP. Together, our results reveal that the ChAHP and ChAHP2 complexes function to control both non-autonomous and autonomous retrotransposons by complementary activities, further adding to the complexity of mammalian transposon control.

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Section: Methodsmentioning

confidence: 99%

ChAHP2 and ChAHP control diverse retrotransposons by complementary activities

Ahel,

Pandey,

Schwaiger

et al. 2024

Preprint

Self Cite

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“…Many tools already exist which cover some aspects of method optimization, like MS2 window placement 18,32,33 . Others focus on quality control 34,35 . DO-MS takes a different approach and offers a holistic view of the acquisition and data processing method specifically designed to diagnose analytical bottlenecks 31 .…”

Section: Introductionmentioning

confidence: 99%

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS

Wallmann

Leduc

Slavov

2023

Preprint

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Mass-spectrometry (MS) enables specific and accurate quantification of proteins with ever increasing throughput and sensitivity. Maximizing this potential of MS requires optimizing data acquisition parameters and performing efficient quality control for large datasets. To facilitate these objectives, we extended the DO-MS app (https://do-ms.slavovlab.net) to optimize and evaluate results from data independent acquisition (DIA) MS. The extension works with both label free and multiplexed DIA (plexDIA) and supports optimizations particularly relevant for single-cell proteomics. We demonstrate multiple use cases, including optimization of duty cycle methods, peptide separation, number of survey scans per duty cycle, and quality control of single-cell plexDIA data. DO-MS allows for interactive data display and generation of extensive reports, including publication quality figures, that can be easily shared. The source code is available at: https://github.com/SlavovLab/DO-MS.

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“…18,32,33 Others focus on quality control. 34,35 DO-MS takes a different approach and offers a holistic view of the acquisition and data processing method specifically designed to diagnose analytical bottlenecks. 31 With this release, DO-MS v2.0 can be used with both DDA data like MaxQuant and DIA data from tools like DIA-NN while having an open interface allowing for adoption to other search engines.…”

Section: ■ Introductionmentioning

confidence: 99%

“…These parameters must be simultaneously optimized for multiple objectives, including throughput, sensitivity, and coverage. Defining the optimal acquisition method therefore becomes a multi-objective, multi-parameter optimization. , Many tools already exist which cover some aspects of method optimization, like MS2 window placement. ,, Others focus on quality control. , DO-MS takes a different approach and offers a holistic view of the acquisition and data processing method specifically designed to diagnose analytical bottlenecks . With this release, DO-MS v2.0 can be used with both DDA data like MaxQuant and DIA data from tools like DIA-NN while having an open interface allowing for adoption to other search engines.…”

Section: Introductionmentioning

confidence: 99%

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS

Wallmann,

Leduc,

Slavov

2023

J. Proteome Res.

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Mass spectrometry (MS) enables specific and accurate quantification of proteins with ever-increasing throughput and sensitivity. Maximizing this potential of MS requires optimizing data acquisition parameters and performing efficient quality control for large datasets. To facilitate these objectives for dataindependent acquisition (DIA), we developed a second version of our framework for data-driven optimization of MS methods (DO-MS). The DO-MS app v2.0 (do-ms.slavovlab.net) allows one to optimize and evaluate results from both label-free and multiplexed DIA (plexDIA) and supports optimizations particularly relevant to single-cell proteomics. We demonstrate multiple use cases, including optimization of duty cycle methods, peptide separation, number of survey scans per duty cycle, and quality control of single-cell plexDIA data. DO-MS allows for interactive data display and generation of extensive reports, including publication of quality figures that can be easily shared. The source code is available at github.com/SlavovLab/DO-MS.

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einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data

Cited by 4 publications

References 36 publications

ChAHP2 and ChAHP control diverse retrotransposons by complementary activities

ChAHP2 and ChAHP control diverse retrotransposons by complementary activities

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS

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