Software

R code to filter FDR reports from discovery proteomics generated in ProteinPilot Software

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/e2aw-vd18&rft.title=R code to filter FDR reports from discovery proteomics generated in ProteinPilot Software&rft.identifier=https://doi.org/10.25919/e2aw-vd18&rft.publisher=Commonwealth Scientific and Industrial Research Organisation&rft.description=R code filters proteins with a 1% or 5% false discovery rate (FDR) generating a final protein file, it removes reverse proteins and proteins coming from cRAP database. The code also analyses peptides with 1% or 5% FDR, it removes peptides from cRAP proteins and from reverse proteins. The code is also able to filter peptides according to the user's needs, tryptic, semitryptic peptides, or both, up to two missed cleavages and filtering allowing modifications as Carbamidomethyl (C), Gln->pyro-Glu, Oxidation (M). It generates a final peptide file. \nLineage: This R code was generated using RStudio version 4.0.5. Packages used were Tidyverse and Readxl.&rft.creator=Escobar Correas, Sophia &rft.date=2021&rft.edition=v2&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=false discovery rate&rft_subject=proteins&rft_subject=peptides&rft_subject=proteomics&rft_subject=discovery&rft_subject=Protein Pilot&rft_subject=R code&rft_subject=Bioinformatics and computational biology not elsewhere classified&rft_subject=Bioinformatics and computational biology&rft_subject=BIOLOGICAL SCIENCES&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

R code filters proteins with a 1% or 5% false discovery rate (FDR) generating a final protein file, it removes reverse proteins and proteins coming from cRAP database. The code also analyses peptides with 1% or 5% FDR, it removes peptides from cRAP proteins and from reverse proteins. The code is also able to filter peptides according to the user's needs, tryptic, semitryptic peptides, or both, up to two missed cleavages and filtering allowing modifications as Carbamidomethyl (C), Gln->pyro-Glu, Oxidation (M). It generates a final peptide file.
Lineage: This R code was generated using RStudio version 4.0.5. Packages used were Tidyverse and Readxl.

Available: 2021-05-27

Data time period: 2020-03-26 to 2021-05-26

This dataset is part of a larger collection

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Subjects

Biological Sciences | Bioinformatics and Computational Biology | Bioinformatics and Computational Biology Not Elsewhere Classified | Protein Pilot | R code | discovery | false discovery rate | peptides | proteins | proteomics |

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Identifiers

DOI : 10.25919/E2AW-VD18
Handle : 102.100.100/394334
URL : data.csiro.au/collection/csiro:50687

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