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bittremieux committed Apr 25, 2019
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# ANN-SoLo notebooks

These notebooks allow you to easily recreate all figures and tables in the ANN-SoLo manuscript ([doi:10.1021/acs.jproteome.8b00359](https://doi.org/10.1021/acs.jproteome.8b00359)).
These notebooks allow you to easily recreate all figures and tables in the ANN-SoLo manuscripts ([doi:10.1021/acs.jproteome.8b00359](https://doi.org/10.1021/acs.jproteome.8b00359) and [doi:TODO](https://to.do/)).

## Notebook overview

* `ann_index.ipynb`: Illustration of the ANN indexing procedure.
* `hek293_stats.ipynb`: Comparison between ANN-SoLo, SpectraST, and MSFragger on the HEK293 data set.
* `iprg2012_ann_hyperparameters.ipynb`: Effect of the ANN hyperparameters on index construction and querying for the iPRG2012 data set.
* `iprg2012_cascade.ipynb`: Comparison between a cascade open search and a direct open search for the iPRG2012 data set.
* `iprg2012_consensus.ipynb`: Comparison of the ANN-SoLo identifications to the iPRG2012 consensus results.
* `iprg2012_fdr.ipynb`: Number of identifications for various types of searches for the iPRG2012 data set.
* `iprg2012_profiling.ipynb`: Code profiling of brute-force versus ANN searches for the iPRG2012 data set.
* `iprg2012_spectrum_representation.ipynb`: Evaluation of spectrum representation options for the iPRG2012 data set.
* `ann_index.ipynb`: Illustration of the ANN indexing procedure (v0.1).
* `hek293_stats.ipynb`: Comparison between ANN-SoLo, SpectraST, and MSFragger on the HEK293 data set (v0.1).
* `iprg2012_ann_hyperparameters.ipynb`: Effect of the ANN hyperparameters on index construction and querying for the iPRG2012 data set (v0.2).
* `iprg2012_cascade.ipynb`: Comparison between a cascade open search and a direct open search for the iPRG2012 data set (v0.2).
* `iprg2012_consensus.ipynb`: Comparison of the ANN-SoLo identifications to the iPRG2012 consensus results (v0.2).
* `iprg2012_fdr.ipynb`: Number of identifications for various types of searches for the iPRG2012 data set (v0.2).
* `iprg2012_num_candidates.ipynb`: Evaluation of potentially missed identifications versus the number of candidates retrieved from the ANN index for the iPRG2012 data set (v0.2).
* `iprg2012_profiling.ipynb`: Code profiling of brute-force versus ANN searches for the iPRG2012 data set (v0.2).
* `iprg2012_spectrum_hashing.ipynb`: Evaluation of vectorization bin width and hash length for the iPRG2012 data set (v0.2).
* `iprg2012_spectrum_representation.ipynb`: Evaluation of spectrum representation options for the iPRG2012 data set (v0.2).
* `kim2014_stats.ipynb`: Analysis of the Kim draft human proteome identification results (v0.2).
* `spec_lib_size.ipynb`: Historical evolution of spectral library sizes.

## Data

The necessary data to execute the notebooks is available on the PRIDE repository at identifier [PXD009861](https://www.ebi.ac.uk/pride/archive/projects/PXD009861).
The necessary data to execute the notebooks is available on the PRIDE repository at identifier [PXD009861](https://www.ebi.ac.uk/pride/archive/projects/PXD009861) (v0.1) and [PDX00TODO](https://to.do/).

The directory structure is based on the [Cookiecutter Data Science](https://drivendata.github.io/cookiecutter-data-science/) project. A `data` directory is expected at the same level of the `notebooks` directory. Additionally, the ANN-SoLo source code should be present in the `src` directory. The full directory and file structure is as follows:
The directory structure is based on the [Cookiecutter Data Science](https://drivendata.github.io/cookiecutter-data-science/) project. A `data` directory is expected at the same level of the `notebooks` directory. Additionally, ANN-SoLo should be installed as a Python package or the ANN-SoLo source code should be present in the `src` directory. The full directory and file structure is as follows:

```
├── data
│ ├── external
│ │ │ ├── iPRG2012.mgf <--- The iPRG2012 query file downloaded from MassIVE.
│ │ │ ├── iprg2012ConsensusSpectrumIDcomparison.tsv <--- The iPRG2012 consensus spectrum identifications downloaded from MassIVE.
│ │ │ ├── b19xx_293T_proteinID_01A_QE3_122212.raw <--- The HEK293 raw files downloaded from PRIDE.
│ │ ├── hek293
│ │ │ └── b19xx_293T_proteinID_01A_QE3_122212.raw <--- The HEK293 raw files downloaded from PRIDE.
│ │ ├── iprg2012
│ │ | ├── iPRG2012.mgf <--- The iPRG2012 query file downloaded from MassIVE.
│ │ | └── iprg2012ConsensusSpectrumIDcomparison.tsv <--- The iPRG2012 consensus spectrum identifications downloaded from MassIVE.
│ │ └── kim2014 <--- The Kim2014 raw files downloaded from PRIDE.
│ ├── interim
│ │ │ ├── b19xx_293T_proteinID_01A_QE3_122212.mgf <--- The HEK293 mgf files converted from raw.
│ │ ├── hek293 <--- The HEK293 mgf files converted from raw.
│ │ └── kim2014 <--- The Kim2014 mgf files converted from raw.
│ ├── processed
│ │ ├── hek293
│ │ │ ├── massive_human_hcd_unique_targetdecoy.splib <--- The compiled spectral library for the HEK293 data set.
│ │ │ ├── ann-solo <--- The ANN-SoLo mztab identification results and logs.
│ │ │ ├── ann-solo <--- The ANN-SoLo mzTab identification results and logs.
│ │ │ │ ├── std
│ │ │ │ └── oms
│ │ │ └── msfragger <--- The MSFragger tab-separated identification results and logs.
Expand All @@ -40,14 +47,17 @@ The directory structure is based on the [Cookiecutter Data Science](https://driv
│ │ │ └── spectrast <--- The SpectraST tab-separated (xls extension converted to txt) identification results and logs.
│ │ │ ├── std
│ │ │ └── oms
│ │ └── iprg2012
│ │ ├── human_yeast_targetdecoy.splib <--- The compiled spectral library for the iPRG2012 data set.
│ │ ├── iprg2012
│ │ │ ├── human_yeast_targetdecoy.splib <--- The compiled spectral library for the iPRG2012 data set.
│ │ │ ├── human_yeast_targetdecoy.pepidx <--- The compiled spectral library for the iPRG2012 data set.
│ │ ├── ann_hyperparameters <--- The ANN-SoLo mztab identification results and logs for various hyperparameter settings.
│ │ ├── brute_force <--- The brute-force mztab identification results and logs.
│ │ ├── build_trees <--- The logs to build the ANN indexes.
│ │ ├── profiling <--- The ANN-SoLo profiling results.
│ │ └── spectrum_representation <--- The ANN-SoLo mztab identification results to evaluate spectrum representation options.
│ │ │ ├── ann_hyperparameters <--- The ANN-SoLo mzTab identification results and logs for various hyperparameter settings.
│ │ │ ├── brute_force <--- The brute-force mzTab identification results and logs.
│ │ │ ├── build_trees <--- The logs to build the ANN indexes.
│ │ │ ├── profiling <--- The ANN-SoLo profiling results.
│ │ │ └── spectrum_representation <--- The ANN-SoLo mzTab identification results to evaluate spectrum representation options.
│ │ └── kim2014
│ │ ├── massivekb_targetdecoy.splib <--- The compiled spectral library for the Kim2014 data set.
│ │ └── gpu <--- The Kim2014 mzTab identification results.
│ └── raw
├── notebooks
└── src
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