DIA proteomics data from a UPS1-spiked E.coli protein mixture processed with six software tools
In this article, we provide a proteomic reference dataset that has been initially generated for a benchmarking of software tools for Data-Independent Acquisition (DIA) analysis. This large dataset includes 96 DIA .raw files acquired from a complex proteomic standard composed of an E.coli protein bac...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-04-01
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| Series: | Data in Brief |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340922000415 |
| _version_ | 1818773649133404160 |
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| author | Clarisse Gotti Florence Roux-Dalvai Charles Joly-Beauparlant Loïc Mangnier Mickaël Leclercq Arnaud Droit |
| author_facet | Clarisse Gotti Florence Roux-Dalvai Charles Joly-Beauparlant Loïc Mangnier Mickaël Leclercq Arnaud Droit |
| author_sort | Clarisse Gotti |
| collection | DOAJ |
| description | In this article, we provide a proteomic reference dataset that has been initially generated for a benchmarking of software tools for Data-Independent Acquisition (DIA) analysis. This large dataset includes 96 DIA .raw files acquired from a complex proteomic standard composed of an E.coli protein background spiked-in with 8 different concentrations of 48 human proteins (UPS1 Sigma). These 8 samples were analyzed in triplicates on an Orbitrap mass spectrometer with 4 different DIA window schemes. We also provide the spectral libraries and FASTA file used for their analysis and the software outputs of the six tools used in this study: DIA-NN, Spectronaut, ScaffoldDIA, DIA-Umpire, Skyline and OpenSWATH. This dataset also contains post-processed quantification tables where the peptides and proteins have been validated, their intensities normalized and the missing values imputed with a noise value. All the files are available on ProteomeXchange. Altogether, these files represent the most comprehensive DIA reference dataset acquired on an Orbitrap instrument ever published. It will be a very useful resource to the proteomic scientists in order to assess the performance of DIA software tools or to test their processing pipelines, to the software developers to improve their tools or develop new ones and to the students for their training on proteomics data analysis. |
| first_indexed | 2024-12-18T10:28:36Z |
| format | Article |
| id | doaj.art-a9325bf542b34b708e4d16a4e0f34353 |
| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-12-18T10:28:36Z |
| publishDate | 2022-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj.art-a9325bf542b34b708e4d16a4e0f343532022-12-21T21:10:55ZengElsevierData in Brief2352-34092022-04-0141107829DIA proteomics data from a UPS1-spiked E.coli protein mixture processed with six software toolsClarisse Gotti0Florence Roux-Dalvai1Charles Joly-Beauparlant2Loïc Mangnier3Mickaël Leclercq4Arnaud Droit5Proteomics Platform, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada; Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, CanadaProteomics Platform, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada; Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, CanadaComputational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, CanadaComputational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, CanadaComputational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, CanadaProteomics Platform, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada; Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada; Corresponding author.In this article, we provide a proteomic reference dataset that has been initially generated for a benchmarking of software tools for Data-Independent Acquisition (DIA) analysis. This large dataset includes 96 DIA .raw files acquired from a complex proteomic standard composed of an E.coli protein background spiked-in with 8 different concentrations of 48 human proteins (UPS1 Sigma). These 8 samples were analyzed in triplicates on an Orbitrap mass spectrometer with 4 different DIA window schemes. We also provide the spectral libraries and FASTA file used for their analysis and the software outputs of the six tools used in this study: DIA-NN, Spectronaut, ScaffoldDIA, DIA-Umpire, Skyline and OpenSWATH. This dataset also contains post-processed quantification tables where the peptides and proteins have been validated, their intensities normalized and the missing values imputed with a noise value. All the files are available on ProteomeXchange. Altogether, these files represent the most comprehensive DIA reference dataset acquired on an Orbitrap instrument ever published. It will be a very useful resource to the proteomic scientists in order to assess the performance of DIA software tools or to test their processing pipelines, to the software developers to improve their tools or develop new ones and to the students for their training on proteomics data analysis.http://www.sciencedirect.com/science/article/pii/S2352340922000415Data Independent AcquisitionComplex proteomic standardSoftware tools benchmarkSpiked UPS1 human proteins |
| spellingShingle | Clarisse Gotti Florence Roux-Dalvai Charles Joly-Beauparlant Loïc Mangnier Mickaël Leclercq Arnaud Droit DIA proteomics data from a UPS1-spiked E.coli protein mixture processed with six software tools Data in Brief Data Independent Acquisition Complex proteomic standard Software tools benchmark Spiked UPS1 human proteins |
| title | DIA proteomics data from a UPS1-spiked E.coli protein mixture processed with six software tools |
| title_full | DIA proteomics data from a UPS1-spiked E.coli protein mixture processed with six software tools |
| title_fullStr | DIA proteomics data from a UPS1-spiked E.coli protein mixture processed with six software tools |
| title_full_unstemmed | DIA proteomics data from a UPS1-spiked E.coli protein mixture processed with six software tools |
| title_short | DIA proteomics data from a UPS1-spiked E.coli protein mixture processed with six software tools |
| title_sort | dia proteomics data from a ups1 spiked e coli protein mixture processed with six software tools |
| topic | Data Independent Acquisition Complex proteomic standard Software tools benchmark Spiked UPS1 human proteins |
| url | http://www.sciencedirect.com/science/article/pii/S2352340922000415 |
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