MSLibrarian

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MSLibrarian is an R-package to optimize predicted spectral libraries for DIA proteomics

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# MSLibrarian

MSLibrarian is an R-package to optimize predicted spectral libraries from Prosit (https://www.proteomicsdb.org/prosit/) for usage in targeted analysis of a given set of DIA-MS data.\ 
Available optimization steps build on 
* (i) Spectrum-centric conversion and database search of the DIA data via DIA-Umpire and MSFragger
* (ii) Comparison of identified spectra vs. spectra predicted using variable Collision Energy (CE) settings in Prosit
* (iii) Retention time prediction by DeepLC, with calibration on observed retention times on this LC setup
* (iv) Subsetting to most relevant protein set (at relaxed FDR to avoid exclusion of false negatives)
* (v) Reduction of library to top N most-intense fragment ions to improve filezise and downstream processing speeds
Refined libraries are written out in openswath or spectronaut format, ready for use in downstream peptide-centric analysis tools such as DIA-NN 1.8.

## Requirements and recommendations

### Hardware

In its current form, MSLibrarian **must** be installed on a computer with **Windows** as the operating system. This requirement is mainly a consequence of the current third party softwares that the package uses for its operation. A future aim is to make MSLibrarian into a cross-platform application, and also provide it as a docker image.

A recommendation is to use a computer with at least 32 GB RAM to avoid issues during some of the more memory-requiring tasks that MSLibrarian performs.

### Software

To run all features of MSLibrarian, the following softwares/pipelines **must** be installed on the **C:/**-drive

* [**R version 4.0.0**](https://cran.r-project.org/) or later. 
 * [**Proteowizard suite version 3.0.20365**](http://proteowizard.sourceforge.net/download.html) or later 
 * [**Trans-proteomic pipeline version 5.2.0**](https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/) or later
 * [**MSFragger version 3.2**](http://msfragger-upgrader.nesvilab.org/upgrader/) or later 
 * [**OpenMS version 2.5.0**](https://github.com/OpenMS/OpenMS/releases/tag/Release2.6.0) or later
 * [**DeepLC GUI version 0.1.29**](https://github.com/compomics/DeepLC/releases) or later._Follow the installation guide to setup the miniconda environment._ 
  As an alternative, the **DeepLC CLI (.exe)** can be installed instead. 
 * [**DIA-NN version 1.8**](https://github.com/vdemichev/DiaNN/releases/tag/1.8). Currently the most recent version, but older versions should also work.

## MS Data

The input MS data must conform to the following:

* **Format:** Thermo raw (other file formats should be available in the future) 
* **Acquisition mode:** DIA (must contain both MS1 and MS2 scans)
 
## Getting started

### Download and install MSLibrarian from Github

To both download and install _MSLibrarian_ from Github, use the [**devtools**](https://cran.r-project.org/web/packages/devtools/index.html) package.

```
library(devtools)
install_github("MarcIsak/MSLibrarian")

```
### Prosit Spectral Warehouse Databases

MSLibrarian relies on Spectral Warehouse SQLite databases to make predicted spectral libraries. SQLite databases can be downloaded from [**Zenodo**](https://doi.org/10.5281/zenodo.5749924) for the following common species:
* Homo sapiens (Human)
* Mus musculus (Mouse)
* Saccharomyces cerevisiae (Baker´s yeast)
* Caenorhabditis elegans (Roundworm) 
* Drosophila melanogaster (Fruit fly)
* Escherichia coli K12 (Bacterium)

Alternatively, these databases can be downloaded from within MSLibrarian by the use of the function **get.spectral.db()**.

To manually create a  Spectral Warehouse SQLite Database, go to the **Wiki** of this repository for full details.

### Parameter files

Some of the third-party tools that MSLibrarian uses, such as Comet (or MSFragger), DIA-Umpire or Spectrast require parameters files. Example parameter files can be found in the folder **params** in this repository. Make sure to add the folder to the C:/-drive and that the path to the files **do not** contain any spaces.

These parameter files can be edited, but it is **not recommended** to do so.

### Run MSLibrarian

Go to the **Wiki** of this repository to learn how to create a predicted spectral library in MSLibrarian.

MSLibrarian

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