diff --git a/Linux/64bit/Sage/README.md b/Linux/64bit/Sage/README.md index 3825efd..a617233 100644 --- a/Linux/64bit/Sage/README.md +++ b/Linux/64bit/Sage/README.md @@ -25,6 +25,13 @@ Additionally, Sage was designed with cloud computing in mind - massively paralle Sage is **simple to configure**, **powerful** and **flexible**. It also happens to be well-tested, **mind-boggingly fast**, open-source (MIT-licensed) and free. +## Citation + +If you use Sage in a scientific publication, please cite the following paper: + +[Sage: An Open-Source Tool for Fast Proteomics Searching and Quantification at Scale](https://doi.org/10.1021/acs.jproteome.3c00486) + + ## Features - Incredible performance out of the box @@ -44,6 +51,5 @@ It also happens to be well-tested, **mind-boggingly fast**, open-source (MIT-lic - Support for reading/writing directly from [AWS S3](https://sage-docs.vercel.app/docs/configuration/aws) - Check out the [blog post introducing Sage](https://lazear.github.io/sage/) for more information and full benchmarks! \ No newline at end of file diff --git a/Linux/64bit/Sage/sage b/Linux/64bit/Sage/sage index a0b3b54..6531190 100755 Binary files a/Linux/64bit/Sage/sage and b/Linux/64bit/Sage/sage differ diff --git a/MacOS/64bit/Sage/README.md b/MacOS/64bit/Sage/README.md index 3825efd..a617233 100644 --- a/MacOS/64bit/Sage/README.md +++ b/MacOS/64bit/Sage/README.md @@ -25,6 +25,13 @@ Additionally, Sage was designed with cloud computing in mind - massively paralle Sage is **simple to configure**, **powerful** and **flexible**. It also happens to be well-tested, **mind-boggingly fast**, open-source (MIT-licensed) and free. +## Citation + +If you use Sage in a scientific publication, please cite the following paper: + +[Sage: An Open-Source Tool for Fast Proteomics Searching and Quantification at Scale](https://doi.org/10.1021/acs.jproteome.3c00486) + + ## Features - Incredible performance out of the box @@ -44,6 +51,5 @@ It also happens to be well-tested, **mind-boggingly fast**, open-source (MIT-lic - Support for reading/writing directly from [AWS S3](https://sage-docs.vercel.app/docs/configuration/aws) - Check out the [blog post introducing Sage](https://lazear.github.io/sage/) for more information and full benchmarks! \ No newline at end of file diff --git a/MacOS/64bit/Sage/sage b/MacOS/64bit/Sage/sage index 895cb3d..8e8fd5b 100755 Binary files a/MacOS/64bit/Sage/sage and b/MacOS/64bit/Sage/sage differ diff --git a/Windows/64bit/Sage/DOCS.md b/Windows/64bit/Sage/DOCS.md index 6788ac2..6283147 100644 --- a/Windows/64bit/Sage/DOCS.md +++ b/Windows/64bit/Sage/DOCS.md @@ -198,7 +198,10 @@ For additional information about configuration options and output file formats, "peak_scoring": "Hybrid", // See DOCS.md for details - recommend that you do not change this setting "integration": "Sum", // Optional["Sum" | "Apex"], use sum of MS1 traces in peak, or MS1 intensity at peak apex "spectral_angle": 0.7, // Optional[float] {default = 0.7}, normalized spectral angle cutoff for calling an MS1 peak - "ppm_tolerance": 5.0 // Optional[float] {default = 5.0}, tolerance (in p.p.m.) for DICE window around calculated precursor mass + "ppm_tolerance": 5.0, // Optional[float] {default = 5.0}, tolerance (in p.p.m.) for DICE window around calculated precursor mass + // Optional[bool] {default = true}. Combine all charge states for quantification. Setting this to false + // quantifies each peptide-charge precursor in `precursor_charge` range (see below) separately + "combine_charge_states": true } }, "precursor_tol": { // Tolerance can be either "ppm" or "da" diff --git a/Windows/64bit/Sage/README.md b/Windows/64bit/Sage/README.md index 1e6b465..1247f01 100644 --- a/Windows/64bit/Sage/README.md +++ b/Windows/64bit/Sage/README.md @@ -25,6 +25,13 @@ Additionally, Sage was designed with cloud computing in mind - massively paralle Sage is **simple to configure**, **powerful** and **flexible**. It also happens to be well-tested, **mind-boggingly fast**, open-source (MIT-licensed) and free. +## Citation + +If you use Sage in a scientific publication, please cite the following paper: + +[Sage: An Open-Source Tool for Fast Proteomics Searching and Quantification at Scale](https://doi.org/10.1021/acs.jproteome.3c00486) + + ## Features - Incredible performance out of the box @@ -44,6 +51,5 @@ It also happens to be well-tested, **mind-boggingly fast**, open-source (MIT-lic - Support for reading/writing directly from [AWS S3](https://sage-docs.vercel.app/docs/configuration/aws) - Check out the [blog post introducing Sage](https://lazear.github.io/sage/) for more information and full benchmarks! \ No newline at end of file diff --git a/Windows/64bit/Sage/sage.exe b/Windows/64bit/Sage/sage.exe index ab530f2..569bf43 100644 Binary files a/Windows/64bit/Sage/sage.exe and b/Windows/64bit/Sage/sage.exe differ