https://github.com/lgatto/pbase
Manipluating and exploring protein and proteomics data
https://github.com/lgatto/pbase
Last synced: 23 days ago
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Manipluating and exploring protein and proteomics data
- Host: GitHub
- URL: https://github.com/lgatto/pbase
- Owner: lgatto
- Created: 2014-04-29T21:08:19.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2019-08-08T13:35:03.000Z (over 5 years ago)
- Last Synced: 2025-03-24T04:23:47.743Z (about 1 month ago)
- Language: R
- Size: 24.2 MB
- Stars: 8
- Watchers: 6
- Forks: 3
- Open Issues: 17
-
Metadata Files:
- Readme: README.md
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README
Pbase
=====
Manipulating and exploring protein and proteomics data.
## Installation
From github using `devtools::install_github`:
library("devtools")
install_github("ComputationalProteomicsUnit/Pbase")
### Dependencies
See the `DESCRIPTION` file for a complete list.
## Getting started
Currently, the best way to get started is `?Proteins` and the
[`Pbase-data`](http://bioconductor.org/packages/devel/bioc/vignettes/Pbase/inst/doc/Pbase-data.html)
vignette. More documentation is on its way.
## Development
`Pbase` is under heavy development and is likely to considerably
change in the near future. Suggestion and bug reports are welcome and
can be filed as
[github issues](https://github.com/ComputationalProteomicsUnit/pbase/issues).
If you would like to contribute, please directly send pull requests
for minor contributions and typos. For major contributions, we suggest
to first get in touch with the package maintainers.
## Ideas
### Assessing the redundancy of a protein fasta database
Given a protein fasta file, what is the maximal sensitivity that can
be expected from a mass spectrometry experiment with 0, 1,
... miscleavages. This should probably also include a filtering step
for peptide *flyability*.
#### Flyability/Detectability
Some literature about estimating detectability:
- LogR: [Liu, Hui, et al. "The Prediction of Peptide Detectability in MS Data Analysis Using Logistic Regression." Bioinformatics and Biomedical Engineering,(iCBBE) 2011 5th International Conference on. IEEE, 2011.](http://dx.doi.org/10.1109/icbbe.2011.5780167)
- SVM: [Webb-Robertson, Bobbie-Jo M., et al. "A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics." Bioinformatics 24.13 (2008): 1503-1509.](http://dx.doi.org/10.1093/bioinformatics/btn218)
- NN: [Sanders, William S., et al. "Prediction of peptides observable by mass spectrometry applied at the experimental set level." BMC bioinformatics 8.Suppl 7 (2007): S23.](http://dx.doi.org/10.1186/1471-2105-8-S7-S23)
- Gausian Mixed Discrimination [Mallick, Parag, et al. "Computational prediction of proteotypic peptides for quantitative proteomics." Nature biotechnology 25.1 (2007): 125-131.](http://dx.doi.org/10.1038/nbt1275)
##### Liu et al. 2011:
Requirements for in-silico created peptides: `missedCleavages = 0:2`, `length(peptides) >= 6`, `mass(peptides) < 6000` (Da)
Logistic Regression based on Hydrophobicity, Isoelectric point, length,
molecular weight, average hydrophobicity, average isoelectric point
##### Webb-Robertson et al. 2007:
Requirements for in-silico created peptides: `missedCleavages = 0:2`, `length(peptides) >= 6`, `mass(peptides) < 6000` (Da)
35 features: length, weidght, # of (non-)polar, # of (un)charged, # of pos./neg. charged residues, hydrophobicity (different models), polarity (different models), bulkiness, AA singlet counts
##### Sanders et al. 2007
Requirements for in-silico created peptides: `length(peptides) >= 6`
Features: Length, Charge, Isoelectric Point, Molecular Weight, Hydropathicity, Counts of each AA (20 Features), Percent composition of each AA (20 Features), Percent of polar, psoitive, negative, hydrophobic AA
take-home-message: a model of one species/dataset could not be transfered to another dataset (without dramatically decreasing the performance)
##### Mallick et al. 2007
~1000 Features.
Some of the most discriminating properties:
Total/Average net/positive charge, hydrophobic moment, isoelectric point, Histidine composition
take-home-message: The model of one species is comparable to another if the evolutionary
distance is small (e.g. yeast and human) but you can't compare different devices/datasets (e.g. MALDI vs ESI)
###### Simple Rules
Mass: `500:4500`
http://www.nature.com/nbt/journal/v25/n1/extref/nbt1275-S5.pdf
http://ieeexplore.ieee.org/ielx5/5779756/5779971/5780167/html/img/5780167-fig-1-large.gif
Length: `5:40`
http://www.nature.com/nbt/journal/v25/n1/extref/nbt1275-S6.pdf
http://ieeexplore.ieee.org/ielx5/5779756/5779971/5780167/html/img/5780167-fig-1-large.gif
95% of all peptides are of length `5:30`:
http://www.nature.com/nbt/journal/v25/n1/extref/nbt1275-S24.pdf
Average Isoelectric point: `seq(0, 1.4)`
http://ieeexplore.ieee.org/ielx5/5779756/5779971/5780167/html/img/5780167-fig-1-large.gif
### Hydropathy/Hydrophobicity
http://web.expasy.org/tools/protparam/protparam-doc.html
http://web.expasy.org/compute_pi/pi_tool-doc.html
[Kyte, Jack, and Russell F. Doolittle. "A simple method for displaying the hydropathic character of a protein." Journal of molecular biology 157.1 (1982): 105-132.](http://dx.doi.org/10.1016/0022-2836(82)90515-0)
### Selection of optimal heavy peptides for absolute quantitation
See Pavel's [idea](https://github.com/sgibb/cleaver/issues/5).
### Protein domains
Available through the integration with the `EnsmbleDb` package. See the `Pbase-with-ensembldb` vignette.
### Mapping a Protein Sequence to a Genome Sequence
See the [`mapping`](http://bioconductor.org/packages/devel/bioc/vignettes/Pbase/inst/doc/mapping.html) vignette.
See also
[this document](https://github.com/ComputationalProteomicsUnit/Intro-Integ-Omics-Prot/blob/master/mapping.md)
for additional examples and integration with RNA-seq data.
## Interoperability
The package allows to easily interact with `AAString` and
`AAStringSet` instances, protein databases such as UniProt (and
possibly biomaRt in the future) using protein identifiers, protein
identification results (`mzID` or (devel) `mzR` packages) and possibly
also `MSnExp` and `MSnSet` instances.