Getting Started

Convert your files to mzML

Sage aims for full compatibility with the mzML specification, and has been extensively tested on files from the following two conversion tools:

1. msConvert (opens in a new tab)

• Enable peak-picking/centroiding for MS1 spectra
• Do not use numpress

2. ThermoRawFileParser (opens in a new tab)

• Sage can be used to calculate TMT S/N measurements if ThermoRawFileParser is configured to write noise values into the mzML

Sage can directly read gzipped-mzMLs, as well as mzMLs with internal zlib compression of m/z and intensity values. I generally recommend writing 32-bit, compressed values to mzMLs.

Download or install the latest version of Sage

There are several easy ways to download Sage - you don't need to install any additional software, packages, or runtimes to use it:

1. Download the latest binary release (recommended)
2. Compile from source code
3. Install via bioconda
4. Run via Docker

Download the latest binary release

This is the easiest way to run Sage - Sage uses a continuous integration/deployment system to automatically compile binaries and publically distribute them as Github Releases (opens in a new tab).

Visit this link and download the file corresponding to your operating system and CPU architecture.

Most users will probably want one of the following:

Additional binary builds are supplied for other, less-common configurations

Compile from source code

• Install the Rust programming language compiler (opens in a new tab) toolchain

Once you have Rust installed, you can copy and paste the following lines of code into your terminal (assuming you have git installed!)

git clone https://github.com/lazear/sage.git
cd sage
cargo run --release tests/config.json

Install via bioconda

Sage can be installed from bioconda (opens in a new tab):

conda install -c bioconda -c conda-forge sage-proteomics
sage --help

Run via Docker

docker pull ghcr.io/lazear/sage:latest
docker run -it --rm -v ${PWD}:/data ghcr.io/lazear/sage:latest /app/sage -o /data /data/config.json

-v ${PWD}:/data will mount your current directory as /data in the docker image. Make sure all the paths in your command and configuration use the location in the image and not your local directory

Run Sage

Please see the configuration section for details. Understanding how Sage works might also be useful!

Once you're ready to go, run Sage via the command line:

# Everything can be configured from a single file
sage experiment_242.json
 
# Or you can set some arguments from the command line!
sage base_config.json -f human.fasta --write-pin *.mzML

Interpret results

Please see the results section for details!