diff --git a/notebooks/README.md b/notebooks/README.md
index 8be65cd..bf2f5fe 100644
--- a/notebooks/README.md
+++ b/notebooks/README.md
@@ -1,37 +1,44 @@
 # 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.
@@ -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