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Targets

Target lists are collections of peak definitions used to extract MS intensities for specific metabolites. The Targets tab allows you to manage, review, and refine these definitions before processing. To import a target list, click the LOAD TARGETS button. This opens a file browser where you can navigate your filesystem and select a CSV file containing your peak definitions.

Targets

Tip: Click the help icon (small "i" symbol) next to the "Targets" title to take a guided tour of this section.

The Targets Table

The target list can be provided as a CSV file with the following columns. A MINT-compatible template can be downloaded in the Targets tab (DOWNLOAD TEMPLATE button on the top right corner).

Targets table columns and descriptions
Column Name Description
peak_label Unique metabolite/feature name
peak_selection True if selected for analysis
bookmark True if bookmarked
mz_mean Mean m/z (centroid)
mz_width m/z window or tolerance
mz Precursor m/z (MS2)
rt Retention time (default: in seconds)
rt_min Lower RT bound (default: in seconds)
rt_max Upper RT bound (default: in seconds)
rt_unit RT unit (e.g. s or min; default: in seconds)
intensity_threshold Intensity cutoff (anything lower than this value is considered zero)
polarity Polarity (Positive or Negative)
filterLine Filter ID for MS2 scans
ms_type ms1 or ms2
category Category
formula Chemical formula (used to derive m/z when mz_mean is missing)
maven_id Maven ID or Group ID (optional identifier)
adduct_name Adduct name (e.g. [M+H]+); optional and can be auto-populated
score Optional legacy score field
notes Free-form notes
source Data source or file

Targets

Once loaded, your targets are displayed in an interactive table with the following key columns:

  • Peak Label: The unique identifier for the metabolite or feature.
  • Selection & Bookmark: Selection is meant for selection of targets for processing. Bookmarking is meant for bookmarking specific targets for later use.
  • MZ Data: mz_mean and mz_width define the mass-to-charge ratio window for extraction.
  • Retention Time: rt_min and rt_max define the expected time window for the peak. The rt column typically represents the expected retention time of the peak.
  • Filtering: Each column header includes a filter icon, allowing you to search for specific compounds or filter by values.

Selection and Bookmark Semantics

MINT uses peak_selection and bookmark with a few workflow rules that affect Optimization and Processing:

  • Selection drives default target scope: selected targets are included first.
  • If no targets are selected, MINT falls back to treating this as all targets selected (instead of processing zero targets).
  • Bookmark implies selection: when a target is bookmarked, MINT also marks it selected so bookmarked subsets remain processable.
  • Bookmarked-only mode (Processing): enabling Bookmarked Targets Only intersects the processing scope with bookmarked targets.

Importing from External Software

MINT supports importing target lists directly from other software formats, such as EL-MAVEN (peak lists and group exports).

Key features of this import functionality include:

  • Format Support: Reads CSV, TSV, Excel, and JSON (EL-MAVEN group exports) files.
  • Automatic Column Mapping: MINT automatically detects and renames columns from common formats to the MINT standard.
    • compound, compoundName, name -> peak_label
    • meanMz, medMz, parent, row m/z -> mz_mean
    • meanRt, medRt, expectedRt, row retention time -> rt
    • formula, parentformula -> formula
  • Unit Conversion: Retention times in EL-MAVEN files (typically in minutes) are automatically converted to seconds.
  • Priority Handling: If a file contains multiple potential columns for the same value (e.g., both meanMz and medMz), MINT automatically selects the most appropriate one based on a predefined priority list.

Untargeted analysis (via Asari)

If you don't have a pre-defined target list, MINT can automatically detect features in your processed files using Asari.

  1. Click the Untargeted analysis button to open the configuration modal.
  2. Adjust the parameters to suit your data (ionization mode, mass tolerance, signal-to-noise ratio, etc.).
  3. Click Run Analysis. MINT will process the files in the background and populate the table with detected features.

Asari Modal

Key Parameters:

  • CPU: Number of cores to use for parallel processing.
  • Mode: Ionization mode (Positive or Negative).
  • MZ Width (ppm): Mass tolerance for grouping peaks.
  • Signal/Noise Ratio: Minimum signal-to-noise ratio for peak detection.
  • Min Peak Height: Minimum intensity required for a peak to be considered.
  • Min Timepoints: Minimum number of scans required to define a peak shape.

Import Validation and Auto-Fill

MINT only strictly requires peak_label plus enough RT information to define a window. For each target row, MINT accepts valid RT input patterns and auto-fills missing values. Below, we explain in detail some of the rules MINT uses to fill missing elements in the targets table. Click the banner to expand.

RT Auto-Derivation and Validation

RT Auto-Derivation and Validation

  • rt_min + rt_max only: MINT derives rt as the midpoint.
  • rt only: MINT initializes rt_min and rt_max using a temporary symmetric bootstrap window (rt ± 5.0 s) so targets can be processed immediately. The ±5.0 s rule is an initial import fallback, not the final recommended span. After chromatograms are computed, refine RT bounds in the Optimization tab using the observed peak shape and apex.
  • rt + rt_min: MINT derives rt_max symmetrically around rt.
  • rt + rt_max: MINT derives rt_min symmetrically around rt.
  • All three (rt, rt_min, rt_max): MINT keeps them, then validates consistency.

Invalid RT inputs:

  • Only rt_min (without rt or rt_max)
  • Only rt_max (without rt or rt_min)
  • Missing all RT fields (rt, rt_min, and rt_max)

Additional RT validation done during import:

  • rt_min must be less than rt_max
  • rt_min/rt_max/rt cannot be negative
  • If rt is outside [rt_min, rt_max], MINT resets rt to the span midpoint
  • rt_unit values in minutes are converted to seconds, and stored as seconds
Defaults and Overrides

Defaults and Overrides

During import, MINT applies a few defaults and override rules so target rows are immediately usable:

  • mz_width default: If mz_width is missing, MINT sets it to 10.0 (ppm).
  • peak_selection default: If missing/blank, targets default to True (selected).
  • bookmark default: If missing/blank, targets default to False.
  • ms_type source of truth: MINT derives ms_type from filterLine:
    • filterLine present -> ms2
    • filterLine absent -> ms1
  • ms_type conflict handling: If your file provides ms_type that contradicts filterLine, MINT keeps the derived value and logs a warning.
  • rt_unit normalization: Units in minutes are converted to seconds, and stored with rt_unit = s.
Duplicate Label Handling

Duplicate Label Handling

When imported targets contain repeated peak_label values, MINT resolves them automatically:

  • Duplicate labels are renamed to peak_label@RT (for example, Succinate@315.20) when RT is available.
  • Exact duplicate rows after renaming (same final label) are collapsed to one entry.
  • A summary of duplicate-label handling is reported in processing notifications/logs.
Smart Enrichment After Import

Smart Enrichment After Import

After parsing and validation, MINT applies additional enrichment to improve incomplete target tables:

  • Polarity inference from loaded MS files: If loaded samples have one consistent polarity, missing target polarities are auto-filled from that value.
  • Polarity mismatch warning: If a target explicitly specifies a different polarity than the loaded MS files, MINT keeps the row but emits a warning.
  • Adduct auto-fill: If adduct_name is missing, MINT derives defaults from polarity ([M+H]+ for positive, [M-H]- for negative).
  • Formula-based mz_mean fill: If mz_mean is missing and formula is present, MINT attempts to calculate mz_mean from formula + polarity.
  • MS1 precursor cleanup: For ms1 targets, mz (precursor field) is cleared to avoid redundant/confusing values.
Backup Snapshot

Backup Snapshot

Whenever targets are imported (file upload) or generated via Asari, MINT writes a workspace-local backup snapshot:

  • Path: <workspace>/data/targets_backup.csv
  • Purpose: Fast recovery/export of the current target table and safer downstream workflows.
  • Update behavior: The file is refreshed after each successful target load/generation.

Options Menu

The Options dropdown (top right) provides bulk actions for list management:

  • Delete selected: Remove currently checked rows from the workspace.
  • Clear table: Remove all targets.