Software:Article Title: Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data.
Article Snippet: .. Creation of a working imspy environment: step-by-step instructions for setting up an imspy Python environment; download of the results: guide to downloading data files from the Zenodo repository; downloading of RAW.d files and rerunning of the imspy_dda pipeline: instructions for downloading RAW data and executing the pipeline; HeLa samples: details on processing HeLa samples; HLA samples: details on processing HLA samples; recreating plots: scripts and Jupyter notebooks for plot reproduction; recreating trained machine learning models: scripts for training machine learning models used in the study; MGF creation with Compass DataAnalysis 6.1 (Bruker): instructions how to use the Compass DataAnalysis software to create MGF files from timsTOF DDA data; creation of a Docker image: instructions how to install the here presented collection of software packages and the full imspy_dda pipeline inside a Docker image; performance comparison of the imspy_dda pipeline with and without mokapot vs FragPipe + MSBooster on different gradient lengths of tryptic HeLa digest acquired with DDA-PASEF on the peptide level; distribution of hyperscores for target and decoy hits for all ranks; performance comparison of running Sage command line with Bruker vendor software extracted MGF files, Sage command line with TDF inputs, and imspy_dda; performance comparison of outputs from sagepy with TIMS2Rescore and imspy_dda with and without mokapot as postprocessor on the HeLa data sets; and comparison of outputs from PEAKS with MS2Rescore, sagepy with TIMS2Rescore, and imspy_dda on the HLA data sets (PDF) ■ AUTHOR INFORMATION Corresponding Authors David Teschner − Institute of Computer Science and Institute for Quantitative and Computer Biosciences (IQCB), Johannes-Gutenberg University, 55128 Mainz, Germany; orcid.org/0000-0002-1755-5382; Email: dateschn@uni- mainz.de Andreas Hildebrandt − Institute of Computer Science and Institute for Quantitative and Computer Biosciences (IQCB), Johannes-Gutenberg University, 55128 Mainz, Germany; Email: andreas.hildebrandt@uni-mainz.de ..
Article Title: Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data
Article Snippet: .. Creation of a working imspy environment: step-by-step instructions for setting up an imspy Python environment; download of the results: guide to downloading data files from the Zenodo repository; downloading of RAW.d files and rerunning of the imspy_dda pipeline: instructions for downloading RAW data and executing the pipeline; HeLa samples: details on processing HeLa samples; HLA samples: details on processing HLA samples; recreating plots: scripts and Jupyter notebooks for plot reproduction; recreating trained machine learning models: scripts for training machine learning models used in the study; MGF creation with Compass DataAnalysis 6.1 (Bruker): instructions how to use the Compass DataAnalysis software to create MGF files from timsTOF DDA data; creation of a Docker image: instructions how to install the here presented collection of software packages and the full imspy_dda pipeline inside a Docker image; performance comparison of the imspy_dda pipeline with and without mokapot vs FragPipe + MSBooster on different gradient lengths of tryptic HeLa digest acquired with DDA-PASEF on the peptide level; distribution of hyperscores for target and decoy hits for all ranks; performance comparison of running Sage command line with Bruker vendor software extracted MGF files, Sage command line with TDF inputs, and imspy_dda; performance comparison of outputs from sagepy with TIMS 2 Rescore and imspy_dda with and without mokapot as postprocessor on the HeLa data sets; and comparison of outputs from PEAKS with MS 2 Rescore, sagepy with TIMS 2 Rescore, and imspy_dda on the HLA data sets ( PDF ) ..
Data-dependent acquisition:Article Title: Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data.
Article Snippet: .. Creation of a working imspy environment: step-by-step instructions for setting up an imspy Python environment; download of the results: guide to downloading data files from the Zenodo repository; downloading of RAW.d files and rerunning of the imspy_dda pipeline: instructions for downloading RAW data and executing the pipeline; HeLa samples: details on processing HeLa samples; HLA samples: details on processing HLA samples; recreating plots: scripts and Jupyter notebooks for plot reproduction; recreating trained machine learning models: scripts for training machine learning models used in the study; MGF creation with Compass DataAnalysis 6.1 (Bruker): instructions how to use the Compass DataAnalysis software to create MGF files from timsTOF DDA data; creation of a Docker image: instructions how to install the here presented collection of software packages and the full imspy_dda pipeline inside a Docker image; performance comparison of the imspy_dda pipeline with and without mokapot vs FragPipe + MSBooster on different gradient lengths of tryptic HeLa digest acquired with DDA-PASEF on the peptide level; distribution of hyperscores for target and decoy hits for all ranks; performance comparison of running Sage command line with Bruker vendor software extracted MGF files, Sage command line with TDF inputs, and imspy_dda; performance comparison of outputs from sagepy with TIMS2Rescore and imspy_dda with and without mokapot as postprocessor on the HeLa data sets; and comparison of outputs from PEAKS with MS2Rescore, sagepy with TIMS2Rescore, and imspy_dda on the HLA data sets (PDF) ■ AUTHOR INFORMATION Corresponding Authors David Teschner − Institute of Computer Science and Institute for Quantitative and Computer Biosciences (IQCB), Johannes-Gutenberg University, 55128 Mainz, Germany; orcid.org/0000-0002-1755-5382; Email: dateschn@uni- mainz.de Andreas Hildebrandt − Institute of Computer Science and Institute for Quantitative and Computer Biosciences (IQCB), Johannes-Gutenberg University, 55128 Mainz, Germany; Email: andreas.hildebrandt@uni-mainz.de ..
Article Title: Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data
Article Snippet: .. Creation of a working imspy environment: step-by-step instructions for setting up an imspy Python environment; download of the results: guide to downloading data files from the Zenodo repository; downloading of RAW.d files and rerunning of the imspy_dda pipeline: instructions for downloading RAW data and executing the pipeline; HeLa samples: details on processing HeLa samples; HLA samples: details on processing HLA samples; recreating plots: scripts and Jupyter notebooks for plot reproduction; recreating trained machine learning models: scripts for training machine learning models used in the study; MGF creation with Compass DataAnalysis 6.1 (Bruker): instructions how to use the Compass DataAnalysis software to create MGF files from timsTOF DDA data; creation of a Docker image: instructions how to install the here presented collection of software packages and the full imspy_dda pipeline inside a Docker image; performance comparison of the imspy_dda pipeline with and without mokapot vs FragPipe + MSBooster on different gradient lengths of tryptic HeLa digest acquired with DDA-PASEF on the peptide level; distribution of hyperscores for target and decoy hits for all ranks; performance comparison of running Sage command line with Bruker vendor software extracted MGF files, Sage command line with TDF inputs, and imspy_dda; performance comparison of outputs from sagepy with TIMS 2 Rescore and imspy_dda with and without mokapot as postprocessor on the HeLa data sets; and comparison of outputs from PEAKS with MS 2 Rescore, sagepy with TIMS 2 Rescore, and imspy_dda on the HLA data sets ( PDF ) ..
Comparison:Article Title: Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data.
Article Snippet: .. Creation of a working imspy environment: step-by-step instructions for setting up an imspy Python environment; download of the results: guide to downloading data files from the Zenodo repository; downloading of RAW.d files and rerunning of the imspy_dda pipeline: instructions for downloading RAW data and executing the pipeline; HeLa samples: details on processing HeLa samples; HLA samples: details on processing HLA samples; recreating plots: scripts and Jupyter notebooks for plot reproduction; recreating trained machine learning models: scripts for training machine learning models used in the study; MGF creation with Compass DataAnalysis 6.1 (Bruker): instructions how to use the Compass DataAnalysis software to create MGF files from timsTOF DDA data; creation of a Docker image: instructions how to install the here presented collection of software packages and the full imspy_dda pipeline inside a Docker image; performance comparison of the imspy_dda pipeline with and without mokapot vs FragPipe + MSBooster on different gradient lengths of tryptic HeLa digest acquired with DDA-PASEF on the peptide level; distribution of hyperscores for target and decoy hits for all ranks; performance comparison of running Sage command line with Bruker vendor software extracted MGF files, Sage command line with TDF inputs, and imspy_dda; performance comparison of outputs from sagepy with TIMS2Rescore and imspy_dda with and without mokapot as postprocessor on the HeLa data sets; and comparison of outputs from PEAKS with MS2Rescore, sagepy with TIMS2Rescore, and imspy_dda on the HLA data sets (PDF) ■ AUTHOR INFORMATION Corresponding Authors David Teschner − Institute of Computer Science and Institute for Quantitative and Computer Biosciences (IQCB), Johannes-Gutenberg University, 55128 Mainz, Germany; orcid.org/0000-0002-1755-5382; Email: dateschn@uni- mainz.de Andreas Hildebrandt − Institute of Computer Science and Institute for Quantitative and Computer Biosciences (IQCB), Johannes-Gutenberg University, 55128 Mainz, Germany; Email: andreas.hildebrandt@uni-mainz.de ..
Article Title: Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data
Article Snippet: .. Creation of a working imspy environment: step-by-step instructions for setting up an imspy Python environment; download of the results: guide to downloading data files from the Zenodo repository; downloading of RAW.d files and rerunning of the imspy_dda pipeline: instructions for downloading RAW data and executing the pipeline; HeLa samples: details on processing HeLa samples; HLA samples: details on processing HLA samples; recreating plots: scripts and Jupyter notebooks for plot reproduction; recreating trained machine learning models: scripts for training machine learning models used in the study; MGF creation with Compass DataAnalysis 6.1 (Bruker): instructions how to use the Compass DataAnalysis software to create MGF files from timsTOF DDA data; creation of a Docker image: instructions how to install the here presented collection of software packages and the full imspy_dda pipeline inside a Docker image; performance comparison of the imspy_dda pipeline with and without mokapot vs FragPipe + MSBooster on different gradient lengths of tryptic HeLa digest acquired with DDA-PASEF on the peptide level; distribution of hyperscores for target and decoy hits for all ranks; performance comparison of running Sage command line with Bruker vendor software extracted MGF files, Sage command line with TDF inputs, and imspy_dda; performance comparison of outputs from sagepy with TIMS 2 Rescore and imspy_dda with and without mokapot as postprocessor on the HeLa data sets; and comparison of outputs from PEAKS with MS 2 Rescore, sagepy with TIMS 2 Rescore, and imspy_dda on the HLA data sets ( PDF ) ..
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