chore: release v0.14.6

- add ion mobility to parquet outputs
- update changelog
- cargo fmt

CHANGELOG.md

@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.14.6]
+### Added
+- Support for MGF files
+- Support for writing ion mobility measurements to output files: `ion_mobility`, `predicted_mobility`, `delta_mobility` added to primary tsv and parquet reports. Ion mobility is predicted in a similar manner to RT, using a linear model trained on the data from the search.
+
 ## [v0.14.5]
 ### Added
 - Support for semi-enzymatic digests (`database.enzyme.semi_enzymatic` parameter)

crates/sage-cli/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "sage-cli"
-version = "0.14.5"
+version = "0.14.6"
 authors = ["Michael Lazear <michaellazear92@gmail.com"]
 edition = "2021"
 rust-version = "1.62"

crates/sage-cli/src/main.rs

@@ -275,8 +275,7 @@ impl Runner {
                 self.parameters.mzml_paths.len(),
             );
             let _ = sage_core::ml::retention_model::predict(&self.database, &mut outputs.features);
-            let _ =
-                sage_core::ml::mobility_model::predict(&self.database, &mut outputs.features);
+            let _ = sage_core::ml::mobility_model::predict(&self.database, &mut outputs.features);
             Some(alignments)
         } else {
             None

crates/sage-cloudpath/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "sage-cloudpath"
-version = "0.14.5"
+version = "0.14.6"
 authors = ["Michael Lazear <michaellazear92@gmail.com"]
 edition = "2021"
 rust-version = "1.62"

crates/sage-cloudpath/src/parquet.rs

@@ -52,6 +52,9 @@ pub fn build_schema() -> Result<Type, parquet::errors::ParquetError> {
             required float aligned_rt;
             required float predicted_rt;
             required float delta_rt_model;
+            required float ion_mobility;
+            required float predicted_mobility;
+            required float delta_mobility;
             required int32 matched_peaks;
             required int32 longest_b;
             required int32 longest_y;
@@ -204,6 +207,9 @@ pub fn serialize_features(
         write_col!(aligned_rt, FloatType);
         write_col!(predicted_rt, FloatType);
         write_col!(delta_rt_model, FloatType);
+        write_col!(ims, FloatType);
+        write_col!(predicted_ims, FloatType);
+        write_col!(delta_ims_model, FloatType);
         write_col!(matched_peaks, Int32Type);
         write_col!(longest_b, Int32Type);
         write_col!(longest_y, Int32Type);

crates/sage/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "sage-core"
-version = "0.14.5"
+version = "0.14.6"
 authors = ["Michael Lazear <michaellazear92@gmail.com"]
 edition = "2021"
 rust-version = "1.62"

crates/sage/src/ml/mobility_model.rs

@@ -106,7 +106,7 @@ impl MobilityModel {
             // Embed N- and C-terminal AA's
             // 2 on each end
             match aa_idx {
-                0 | 1=> embedding[N_TERMINAL + idx] += 1.0,
+                0 | 1 => embedding[N_TERMINAL + idx] += 1.0,
                 x if x > cterm => embedding[C_TERMINAL + idx] += 1.0,
                 _ => {}
             }