Software

R code for amino acids substitution analysis

Commonwealth Scientific and Industrial Research Organisation

Escobar Correas, Sophia

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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.25919/fwts-a152&rft.title=R code for amino acids substitution analysis&rft.identifier=https://doi.org/10.25919/fwts-a152&rft.publisher=Commonwealth Scientific and Industrial Research Organisation&rft.description=Set of R codes allowing to do amino acid substitution analysis on proteomic data. \nThe data this code was built was generated with TripleTOF® 6600 mass spectrometer (SCIEX) and then search with ProteinPilot software specifying a search including amino acid substitution. The FDR reports generated from this search were then analysed with the set of codes. The codes include filtering peptides with amino acid substitution from the FDR report, filtering per number of substitutions, and validating those peptides.\nLineage: This R code was generated using RStudio version 4.0.5. Packages used were Tidyverse and Biostrings&rft.creator=Escobar Correas, Sophia &rft.date=2021&rft.edition=v1&rft_rights=GPLv3 Licence with CSIRO Disclaimer https://research.csiro.au/dap/licences/gplv3-licence-with-csiro-disclaimer/&rft_rights=Data is accessible online and may be reused in accordance with licence conditions&rft_rights=All Rights (including copyright) CSIRO 2021.&rft_subject=proteins&rft_subject=amino acid substitution&rft_subject=discovery&rft_subject=R code&rft_subject=Protein Pilot&rft_subject=Proteomics and metabolomics&rft_subject=Bioinformatics and computational biology&rft_subject=BIOLOGICAL SCIENCES&rft_subject=Bioinformatics and computational biology not elsewhere classified&rft.type=Computer Program&rft.language=English Access the software

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Gpl

GPLv3 Licence with CSIRO Disclaimer
https://research.csiro.au/dap/licences/gplv3-licence-with-csiro-disclaimer/

Data is accessible online and may be reused in accordance with licence conditions

All Rights (including copyright) CSIRO 2021.

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Brief description

Set of R codes allowing to do amino acid substitution analysis on proteomic data.
The data this code was built was generated with TripleTOF® 6600 mass spectrometer (SCIEX) and then search with ProteinPilot software specifying a search including amino acid substitution. The FDR reports generated from this search were then analysed with the set of codes. The codes include filtering peptides with amino acid substitution from the FDR report, filtering per number of substitutions, and validating those peptides.
Lineage: This R code was generated using RStudio version 4.0.5. Packages used were Tidyverse and Biostrings

Available: 2021-08-10

Data time period: 2020-08-03 to 2021-03-31

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Subjects

Biological Sciences | Bioinformatics and Computational Biology | Bioinformatics and Computational Biology Not Elsewhere Classified | Protein Pilot | Proteomics and Metabolomics | R code | amino acid substitution | discovery | proteins |

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Identifiers

DOI : 10.25919/FWTS-A152
Handle : 102.100.100/422731
URL : data.csiro.au/collection/csiro:52098

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