Output Files

The formats of the INTEGRATOR result files written to the project folder

INTEGRATOR writes its results to the project folder as plain CSV tables, a binary results folder, and — optionally — chromatogram PDFs. The CSV files are the interface to downstream tools.

File Written by Contents
long.csv Step 3 Long-format peak table, one row per sample × feature.
quant_raw.csv Step 3 Wide-format peak-area matrix (samples × features).
RT_matrix.csv Step 2 Per-sample integration borders; editable for manual per-peak adjustment.
misc/ Step 3 Binary results, read by MRMhub-viz and step 4.
PDF folders Step 4 Chromatogram PDFs (optional).

All CSV tables are plain comma-separated files. See the Processing Workflow for the steps that produce them.

long.csv

Long format: one row per sample × feature, for every integrated peak. Only feature_name and raw_data_filename (plus at least one intensity column) are essential; the remaining columns are metadata and measurements carried through for downstream processing. Columns, in file order:

Column Meaning
feature_name Feature (analyte) identifier — the feature name from the feature list, or the compound name where no feature name is given.
internal_standard Assigned ISTD feature, from the feature list.
raw_data_filename Source mzML file name; becomes the analysis identifier.
time_stamp Acquisition timestamp, read from the mzML.
batch Batch identifier, from run_order.csv.
sample_type Sample / QC type, from run_order.csv.
precursor_mz Precursor-ion m/z.
product_mz Product-ion m/z.
collision_energy Collision energy.
polarity Ionisation polarity (+ / −).
rt_apex Retention time at the peak apex (min).
area Integrated peak area.
height Peak height.
FWHM Full width at half maximum (min).
rt_int_start Left integration border (min).
rt_int_end Right integration border (min).

Where no peak was found for a sample × feature, the measurement fields (rt_apex…rt_int_end) are left empty.

quant_raw.csv

A wide matrix of peak areas: one column per feature, one row per sample, preceded by header rows. It carries areas only. The first column holds the row labels:

feature 1 feature 2 …
name LPC 20:4 PC 34:1 …
precursor 544.3 760.6 …
product 184.1 184.1 …
RT 4.21 6.05 …
sample01.mzML 15234.0 88213.0 …
sample02.mzML … … …

The RT row is the expected retention time from the feature list (not the peak apex); each sample row holds that sample’s integrated peak area per feature.

RT_matrix.csv

Produced in step 2: a wide matrix of the per-sample integration borders. It can be edited to adjust individual peaks by hand; re-running step 3 only re-integrates with the edited bounds (see Processing Workflow — step 2).

Layout: each sample is a row, and each feature occupies two adjacent columns — its left and right integration border, as an absolute retention time in that sample (min). Two header rows identify the columns, and a blank spacer column separates the transition groups:

  • Header row 1 — the transition (compound / transition), repeated over each feature’s border pair.
  • Header row 2 — compound name, then each feature’s name over its border pair.
  • One row per mzML file — the file name, then the left and right border for each feature.
ImportantStep 2 overwrites RT_matrix.csv

Make a backup of RT_matrix.csv before re-running Step 2 in case you manually edited RT_matrix.csv, as step 2 overwrites all manual edits!

Folder ‘misc/’

A folder of binary result files written during step 3. It is consumed by the MRMhub-viz visualiser and by step-4 PDF generation, and is not intended for direct reading. If the folder is removed, MRMhub-viz and step 4 cannot run until step 3 is repeated.

Chromatogram PDFs

Optional, written by step 4 into three folders:

Folder Contents
by_transition/ One PDF per transition, over all samples with a peak above the minimum-intensity threshold.
by_transition_low/ Transitions with no peak above the threshold (low_intensity_threshold in MRMhub_plot.r).
by_sample/ One PDF per reference sample, with all its transitions.

See also