Run this workflow and export what it produces. It stays as its author left it: nothing you change here is saved. To change it, copy it into your own projects.
Input Parameters
Loading the workflow's inputs…
This workflow has no inputs. Add a File or Text node to the pipeline to give it data.
View only — you can run this workflow but not change it.
Needs attention
This workflow is empty
To add a node, right-click anywhere on the canvas or press Ctrl + Space.
- File
- Plot
- Comparison
- Text
- Parse
- Export
- Simulation
- Mass Spec
- Digest
- Debug
Select a node to see what it does.
Node Inspector
No nodes selected
Workflow Settings
Where nodes come to rest when placed, dragged, or loaded — every grid cell, or only the major lines. Snapping only affects how a node is drawn: each one keeps the position it was actually released at, so switching this off puts everything back exactly where you left it. Mirrors the toolbar button.
Automatically zoom to fit all nodes when they are moved or modified.
Time for the zoom animation. Set to 0 for instant zoom.
Automatically save changes to the workflow.
The one lattice: grid line spacing, where nodes snap to, and the step node dimensions round up to (a node is always a whole number of cells across and down).
Display minor grid lines between major lines.
Results
Run the workflow to see its results here: every file its Export nodes write.
No file selected
or drag and drop a file or folder here
Files the parser uses from this folder
Override the automatic file type detection
Output Destinations
Where to dump the input data. The node always passes data through unchanged.
⚠ Full output may be very large and slow to render.
Run the workflow to capture its output.
Columns
No columns match.
No render yet — run the workflow, or open the editor.
Text
Emitted downstream as TextData.
Cleavage Agent
Sequence Input
A single FASTA record only. Ambiguity codes (B, Z, X) are rejected — they have no exact mass.
Peptide Filters
Modifications
Each variable modification multiplies the peptide count. The digest refuses to run past 20,000 forms.
Last Digest
No digest yet — run the workflow.
Ionization
Chromatography
Peptides are ordered by their mean coefficient on the selected scale, then mapped onto this digest's own range. The order is indicative; absolute times are not a chromatographic prediction. To compare against a real run, enable Ignore retention time on the Comparison node.
Acquisition
b and y for CID/HCD; c and z for ETD. Fragment intensities are uniform — no fragmentation-propensity model is applied.
Isotopes
Exact convolves the real IUPAC abundances of each peptide's own formula, so sulfur-containing peptides show their true M+2 shoulder. Averagine is offered for like-for-like comparison against deconvolution tools that assume it.
Last Run
No run yet — execute the workflow.
Peak intensities carry no abundance information. Every peptide is given the same amplitude; only the elution profile varies.
Method
Method is dispatched at run time from the upstream input kinds:
MsData+MsData→ RT-aware 2D spectral-angle similarityColumnData+ColumnData→ name-matched cell agreementTextData+TextData→ Myers line-diff similarity
Leave empty to use algorithm defaults.
No mode-specific options for the current inferred input kind.
Last Result
No score yet — run the workflow.
Run the workflow to enable this button.
Filename
Columns to include
Unchecked columns are dropped from the exported file.
Plots to export
Run the workflow to list the plots coming in.
Unchecked plots are left out from the next run. A plot that first appears on a later run is exported.
Last Export
No artifact yet — run the workflow.
Explorer
Opens the interactive Mass Spec Explorer for the upstream MsData
(TIC + per-scan spectrum view). Everything this node emits is configured
there: its detection settings and whether each detected peak becomes a
spectrum view for the nodes downstream.
No type information available.
Notes
Ports
Actions
MS Explorer
Total Ion Chromatogram
Mass Spectrum
Extracted Ion Chromatogram
Fragments
Comparison Explorer
Ignored: none
Plot
Plot editorThis view keeps the shape of the in the Mass Spec explorer. Drag that plot's lower edge there to change it.
The size of the exported image and the thumbnail.
Canvas controls
- Drag
- Select a region
- Right-drag
- Pan the view
- Double-click
- Reset the view
- Scroll
- Zoom. Over an axis, zooms that axis only
- Ctrl-drag
- Move the title, a label or the legend
- Click
- Select a label or a legend row
- Click again
- Edit a selected label's text in place
- Drag + Data label / + Note
- Drop it on the canvas to place it
- Plots
- The name in the header opens the node's plots: its own, and every Mass Spec view. + adds a plot; the pin keeps the list open beside the plot
- MSn views
- Open a range in the list and choose one; it is drawn when chosen
- Esc
- Deselect, then close the editor
Axis zoom and Ctrl-drag are switches in Interaction.
Showing the first of matches; type more to narrow them. No plot or view matches.
↑ ↓ move · → ← open, close · Enter show · Esc close