feat: add spectronaut tsv support

Cargo.toml

@@ -12,7 +12,7 @@ members = [
 ]
 
 [workspace.package]
-version = "0.25.0"
+version = "0.26.0"
 edition = "2024"
 authors = ["Sebastian Paez"]
 license = "Apache-2.0"

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "timsseek-workspace"
-version = "0.25.0"
+version = "0.26.0"
 requires-python = ">=3.11,<3.13"
 dependencies = [
     "jupyter[python]>=1.1.1",
@@ -55,7 +55,7 @@ packages = [
 ]
 
 [tool.bumpver]
-current_version = "0.25.0"
+current_version = "0.26.0"
 version_pattern = "MAJOR.MINOR.PATCH[-PYTAGNUM]"
 tag_message = "v{new_version}"
 commit_message = "chore: bump version to {new_version}"

python/speclib_builder/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "speclib_builder"
-version = "0.25.0"
+version = "0.26.0"
 requires-python = ">=3.11,<3.13"
 dependencies = [
   "rich",

python/timsseek_rescore/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "timsseek_rescore"
-version = "0.25.0"
+version = "0.26.0"
 requires-python = ">=3.11,<3.13"
 dependencies = [
   "polars",

python/timsseek_rts_receiver/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "timsseek_rts_receiver"
-version = "0.25.0"
+version = "0.26.0"
 requires-python = ">=3.11,<3.13"
 description = "Add your description here"
 dependencies = [

rust/timsquery/src/models/aggregators/spectrum_agg.rs

@@ -167,3 +167,4 @@ impl Add for MzMobilityStatsCollector {
         }
     }
 }
+

rust/timsquery/src/models/indexed_data.rs

@@ -65,6 +65,7 @@
 
 use crate::models::aggregators::{
     ChromatogramCollector,
+    MzMobilityStatsCollector,
     PointIntensityAggregator,
     SpectralCollector,
 };
@@ -453,3 +454,54 @@ impl<FH: KeyLike> QueriableData<ChromatogramCollector<FH, f32>> for IndexedPeaks
         }
     }
 }
+
+impl<FH: KeyLike> QueriableData<SpectralCollector<FH, MzMobilityStatsCollector>> for IndexedPeaksHandle {
+    fn add_query(
+        &self,
+        aggregator: &mut SpectralCollector<FH, MzMobilityStatsCollector>,
+        tolerance: &Tolerance,
+    ) {
+        match self {
+            IndexedPeaksHandle::Eager(eager) => eager.add_query(aggregator, tolerance),
+            IndexedPeaksHandle::Lazy(lazy) => {
+                let ranges = QueryRanges::from_elution_group(aggregator, tolerance, |rt| {
+                    lazy.rt_ms_to_cycle_index(rt)
+                });
+
+                let cycle_range_u32 = match ranges.ms1_cycle_range {
+                    Restricted(x) => Restricted(
+                        TupleRange::try_new(x.start().as_u32(), x.end().as_u32()).unwrap(),
+                    ),
+                    Unrestricted => Unrestricted,
+                };
+
+                aggregator
+                    .iter_mut_precursors()
+                    .for_each(|((_idx, mz), ion)| {
+                        let mz_range = tolerance.mz_range_f32(mz as f32);
+                        lazy.query_peaks_ms1(mz_range, cycle_range_u32, ranges.im_range)
+                            .for_each(|peak| {
+                                *ion += peak;
+                            });
+                    });
+
+                aggregator
+                    .iter_mut_fragments()
+                    .for_each(|((_idx, mz), ion)| {
+                        let mz_range = tolerance.mz_range_f32(*mz as f32);
+                        let results = lazy.query_peaks_ms2(
+                            ranges.quad_range,
+                            mz_range,
+                            cycle_range_u32,
+                            ranges.im_range,
+                        );
+                        for (_isolation_scheme, peaks) in results {
+                            for peak in peaks {
+                                *ion += peak;
+                            }
+                        }
+                    });
+            }
+        }
+    }
+}

rust/timsquery/src/models/tolerance.rs

@@ -406,4 +406,21 @@ impl Tolerance {
             ..self
         }
     }
+
+    /// Scale the mobility tolerance by `factor` (e.g. 2.0 to double the window).
+    pub fn with_wider_mobility(self, factor: f32) -> Self {
+        let wider = match self.mobility {
+            MobilityTolerance::Absolute((low, high)) => {
+                MobilityTolerance::Absolute((low * factor, high * factor))
+            }
+            MobilityTolerance::Pct((low, high)) => {
+                MobilityTolerance::Pct((low * factor, high * factor))
+            }
+            MobilityTolerance::Unrestricted => MobilityTolerance::Unrestricted,
+        };
+        Self {
+            mobility: wider,
+            ..self
+        }
+    }
 }

rust/timsquery/src/serde/library_file.rs

@@ -9,6 +9,11 @@ use super::elution_group_inputs::{
     ElutionGroupInput,
     ElutionGroupInputError,
 };
+pub use super::spectronaut_io::SpectronautPrecursorExtras;
+use super::spectronaut_io::{
+    read_library_file as read_spectronaut_tsv,
+    sniff_spectronaut_library_file,
+};
 use crate::TimsElutionGroup;
 use crate::ion::IonAnnot;
 use std::path::Path;
@@ -40,6 +45,7 @@ impl From<ElutionGroupInputError> for LibraryReadingError {
 #[derive(Debug)]
 pub enum FileReadingExtras {
     Diann(Vec<DiannPrecursorExtras>),
+    Spectronaut(Vec<SpectronautPrecursorExtras>),
 }
 
 #[derive(Debug)]
@@ -187,14 +193,48 @@ impl ElutionGroupCollection {
 
         Err(LibraryReadingError::UnableToParseElutionGroups)
     }
+
+    fn try_read_spectronaut(path: &Path) -> Result<Self, LibraryReadingError> {
+        match sniff_spectronaut_library_file(path) {
+            Ok(()) => {
+                info!("Detected Spectronaut TSV library file");
+                let egs = match read_spectronaut_tsv(path) {
+                    Ok(egs) => egs,
+                    Err(e) => {
+                        warn!("Failed to read Spectronaut TSV library file: {:?}", e);
+                        return Err(LibraryReadingError::UnableToParseElutionGroups);
+                    }
+                };
+                let (egs, extras): (Vec<_>, Vec<_>) = egs.into_iter().unzip();
+                info!("Successfully read Spectronaut TSV library file");
+                Ok(ElutionGroupCollection::MzpafLabels(
+                    egs,
+                    Some(FileReadingExtras::Spectronaut(extras)),
+                ))
+            }
+            Err(e) => {
+                debug!("File is not Spectronaut format: {:?}", e);
+                Err(LibraryReadingError::UnableToParseElutionGroups)
+            }
+        }
+    }
 }
 
 pub fn read_library_file<T: AsRef<Path>>(
     path: T,
 ) -> Result<ElutionGroupCollection, LibraryReadingError> {
+    // Try DIA-NN first
     let diann_attempt = ElutionGroupCollection::try_read_diann(path.as_ref());
     if let Ok(egs) = diann_attempt {
         return Ok(egs);
     }
+
+    // Try Spectronaut next
+    let spectronaut_attempt = ElutionGroupCollection::try_read_spectronaut(path.as_ref());
+    if let Ok(egs) = spectronaut_attempt {
+        return Ok(egs);
+    }
+
+    // Fall back to JSON
     ElutionGroupCollection::try_read_json(path.as_ref())
 }

rust/timsquery/src/serde/mod.rs

@@ -3,6 +3,7 @@ mod diann_io;
 mod elution_group_inputs;
 pub mod index_serde;
 mod library_file;
+mod spectronaut_io;
 
 pub use chromatogram_output::*;
 pub use index_serde::*;
@@ -11,5 +12,7 @@ pub use library_file::{
     ElutionGroupCollection,
     FileReadingExtras,
     LibraryReadingError,
+    SpectronautPrecursorExtras,
     read_library_file,
 };
+pub use spectronaut_io::LibrarySniffError;