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MS-Files

The MS-Files tab is the entry point for your analysis. Here you organize the raw mass spectrometry data that constitutes your workspace. MINT currently supports .mzXML and .mzML file formats for MS data. To import MS files, click the LOAD MS-FILES button. This opens a file browser where you can navigate your filesystem and select the MS files.

MS-files

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

The MS-FILES Table

Once loaded, your MS files are displayed in an interactive table. For sample metadata, use LOAD METADATA and import a tabular file (CSV, TSV, TXT, XLS, XLSX). You can also download the template via DOWNLOAD TEMPLATE on the top right corner.

Metadata columns and descriptions
Column Name Description
ms_file_label Unique file name; must match the MS file label on disk
label Friendly label to display in plots and reports
color Hex color for visualizations
use_for_optimization True to include in optimization steps (COMPUTE CHROMATOGRAMS)
use_for_processing True to include in processing (RUN MINT)
use_for_analysis True to include in analysis outputs
sample_type Sample category (e.g.; Sample; QC; Blank; Standard)
group_1 User-defined grouping field 1 for analysis/grouping (free text)
group_2 User-defined grouping field 2 for analysis/grouping (free text)
group_3 User-defined grouping field 3 for analysis/grouping (free text)
group_4 User-defined grouping field 4 for analysis/grouping (free text)
group_5 User-defined grouping field 5 for analysis/grouping (free text)
polarity Polarity (Positive or Negative)
ms_type Acquisition type (ms1 or ms2)

MS-files

  • Checkbox: Select multiple files for batch actions (delete/export).
  • Color: Used in plots and previews. You can edit manually or regenerate via Options.
  • For Optimization / Processing / Analysis: Toggle inclusion per workflow stage.
  • Metadata Columns: Label, Sample Type, and Group columns help organize downstream analysis.
  • Acquisition Metadata: MINT stores metadata such as polarity, MS level/type, file format, and acquisition datetime (when available from file headers) and user-defined metadata (e.g., Group 1, 2, etc.).

Import Validation and Auto-Fill

MINT applies several automatic behaviors during MS file and metadata import.

Filename-based sample typing and color defaults

Automatic Sample-Type and Color Inference

When metadata is not provided yet, MINT initializes sample_type and color from MS-file labels:

  • Blank-like names (for example blank, blk, solvent) -> Blank
  • Standard-like names (for example std, standard, cal) -> Standard
  • QC-like names (for example qc, control, pool) -> QC
  • If no pattern matches -> sample_type = Sample
  • Default fallback color for unmatched samples -> #BBBBBB
Metadata merge behavior

Metadata Merge Defaults

During metadata import, MINT merges values into existing rows instead of blindly replacing everything.

  • Required column: ms_file_label
  • On ingestion, blank use_for_optimization and use_for_processing are treated as TRUE
  • On DB update, non-null metadata values overwrite current values; null/blank values keep existing values
  • Colors can be regenerated after merge to keep palettes consistent across sample groups
Workflow flag dependencies

Workflow Dependency Rules

To keep stage flags consistent, MINT enforces:

  • If use_for_analysis is set to TRUE, use_for_processing is auto-set to TRUE
  • If use_for_processing is set to FALSE, use_for_analysis is auto-set to FALSE
Duplicate import behavior

Duplicate File Handling

When importing MS files, MINT uses ms_file_label (filename stem) as the identity key.

  • Already imported labels are skipped (not duplicated)
  • Import summary/notifications report skipped duplicates

Options Menu

The Options dropdown (top right) provides quick actions:

  • Generate colors: Recompute colors for table entries.
  • Delete selected files: Remove checked rows from the workspace.
  • Clear table: Remove all MS files from the workspace.