Gnomesh Product Roadmap

Highlights

• Faster peptide identification. The Mass Spec node identifies peptides faster and uses less memory on large runs.
• Progress you can trust. The progress bars on the Mass Spec and Comparison nodes cover the whole run, so a full bar means the node is done.
• Faster comparisons. The Comparison node computes the agreement score when the Comparison Explorer opens, not on every run. To compute it on every run, tick Compute the agreement score on every run in the inspector.
• Report an issue. Send us a bug, a problem or an idea with Report issue on the project page or from your profile menu.

Mass spec

• Estimate false matches. In the MS Explorer's Peptides panel, Estimate false matches (decoys) also searches two sets of shifted peptides. It reports how many matches chance alone would make. It is off by default and makes the search about three times longer.
• Search at. Choose whether a peptide is looked for at the apex of any peptide's ion trace or only at its own. Searching only at its own apex finds fewer matches, and fewer of them are by chance.

Fixes

• A File node shortens a long file name to fit the node and keeps the extension visible.
• Security and reliability improvements throughout.

Highlights

• Peptide identifications. The Mass Spec node searches for each peptide across the whole run, scores every match on its isotope series, and keeps only matches above a confidence threshold (0.95 by default). Every charge state that passes is kept and labeled, for example PEPTIDEK (+2), and the mass tolerance follows the instrument type.
• Sequence coverage. With a digest connected, the Mass Spec node reports observed sequence coverage as an output. Coverage views tell identified peptides apart from those seen below the confidence threshold and from those not seen at all.
• A rebuilt comparison explorer. Results A and B are shown side by side as one synchronized tree, field by field, with Differences only to hide what agrees. One-dimensional fields get mirror and error plots, and two-dimensional fields a heatmap. Differences from rounding are set aside, and an error threshold on a log scale ignores relative errors below it.
• The plot chooser. The plot editor lists a node's plots, the upstream mass spec views and per-input copies in one searchable tree, pinned beside the canvas or opened as a flyout. A plot can keep its aspect ratio (1:1, 4:3, 3:2, 16:9) or fill the space.

Mass spec and plots

• Peptides panel. The MS Explorer has a Peptides panel listing every peptide the node looked for. A found peptide's row takes you to its range, and identified peptides are marked with a symbol on the spectrum and chromatogram, each with its own switch.
• Peak sensitivity. Peak detection is set with a 0–100 slider. Lower settings merge neighboring humps into one peak, and higher ones split them more readily.
• Panels and exports. The explorer's panels can be resized by height, and a plot taken from a Mass Spec view keeps those proportions, so an export looks like what you saw.
• Open the explorer at any time. The MS Explorer opens before a node has run, or while it runs, so you can change settings and run from there. Looking around without changing anything does not make the node run again.
• Plot types. Heatmaps have a color bar, box and violin plots can sit side by side, and violins can be smoothed.
• Modifications. Carboxymethyl (C) is available as a modification.

Workflow

• Comparison scores. The Comparison node scores Thermo RAW runs, and a score is shown the same way on the node, in the inspector and in the explorer, with enough digits to tell a near match from a perfect one. Fields that only describe a run are shown in yellow and never count against a score; you can choose them in Settings.
• Export node. Choose which incoming plots to export under Plots to export. Plots added later are included by default, and only Export nodes put plots in Results.
• Data chooser. Use for this node adds a file from your computer and assigns it in one step, and files already in the project are marked. There is a file-type filter, and double-clicking a File node opens the chooser.
• Debug node. Any node's output can be connected to it.

Projects and accounts

• Copy an example. Copy to my projects on a public example copies its workflow and the files it reads into your account.
• My Projects. A new header with status tabs and counts, one toolbar for search (Ctrl+K), filters and sort, and a Cards/Table switch. The Share button's icon shows who can open a project.
• Your account. Settings has Download My Data, which gives you a zip of your account and your projects' files, and Delete Account.

Fixes

• A run with a single scan shows its point on the chromatogram.
• Comparing a run with itself scores exactly 1, and comparing a long run with a much shorter one completes.
• Dragging a connection onto empty canvas opens the node menu in any direction.
• Scrolling over a list in the inspector scrolls the list.
• Annotation labels are created only once you type, and opening an existing label keeps its text.
• Security and reliability improvements throughout.

Highlights

• Bruker directory handling. Improved handling of bruker directories, including the ability to add a whole acquisition at once, and to open a project with a missing acquisition and have it restored from the original directory.
• The data chooser. Files and folder-based acquisitions are now added the same way, from one dialog with two panes: In this project, which lists what the project already holds, and On this computer, a folder you choose to browse. An acquisition is listed as one item with its files. Dropping a single file or acquisition adds it at once, and dropping several opens the chooser with all of them selected. A copy in progress can be canceled.
• A redesigned project page. Input Parameters and Results can be shown as a list, a grid or cards. Inputs, the pipeline and results can be stacked or placed side by side, and the pipeline folds down to a small map of its nodes that shows which ones need attention. A compact header shows the project's status, when it was last edited, its files and sharing.
• Results by plot. Results are grouped by Plot node, with thumbnails, and you can download a group's plots all at once or only the ones you select.
• Saving you can see. The Save button shows whether your changes are saved, waiting or failed. Changes are saved when you leave the page, and one-click settings are saved immediately.

Workflow

• Input Parameters. Every input in the workflow is listed, in the order it appears on the canvas, and you can drag the rows into the order you prefer.
• Problems are visible on the canvas. A connection between incompatible nodes is drawn in red, and its inspector says what the receiving node expects. A File node whose file is no longer in the project is marked and names the missing file.
• Inspector beside the node. Besides docking and popping out, the inspector can open next to the selected node.
• Opening a project. The canvas shows what it is loading, and projects with mass spec files open faster. Run After Opening is now a button on the toolbar.
• Stepping through. Each node is marked complete as you step through a workflow, and confirmations appear in the app instead of as browser pop-ups.

Mass spec and plots

• Extracted ion chromatograms. The MS Explorer shows when an XIC is loading, clears the previous trace as soon as you pick a new m/z, and remembers whether you had the XIC panel open.
• m/z readout. The spectrum's tooltip appears whenever the cursor settles on a point, not only on an exact hover.
• Ranges. Revert ranges returns the chromatogram's ranges to the detected ones, and a range's tip says when its peak could not be fitted.
• Finding a view. The plot editor lists a Mass Spec node's views as a searchable tree.

Accounts and sharing

• Username or email. You can sign in with either, and share a project by either, with the people you already work with suggested.
• View-only access. A collaborator who can only view a project sees it read-only, with no controls for changes they cannot save.
• Documentation. Resources now has a getting-started guide and a user manual, and the Roadmap has its own button in the navigation bar.

Highlights

• Bruker acquisitions. Add a Bruker .d folder and its timsTOF (TDF) or BAF data opens in the workflow, with the calibration files that come with it so masses are reported as the instrument was calibrated. Large BAF runs are read on demand rather than held in memory. Adding a single file from inside a .d folder now tells you to add the whole folder.
• Fragmentation-rich runs, much faster. Runs with tens of thousands of MS/MS spectra no longer build every fragmentation view up front: the Mass Spec node now finishes in a fraction of the time and memory, and the plot editor opens a fragmentation spectrum's tab only when you ask for it.
• More Thermo files open. Thermo files whose MS/MS scans were recorded in profile mode now open with every scan and its retention time, and profile spectra are in strict m/z order. A file that contains no readable spectra now fails with an explanation rather than appearing empty.

Accounts and sharing

• Email confirmation. New accounts confirm their email address by link, and projects can only be shared with or transferred to a confirmed address.
• Sharing takes effect at once. A collaborator you add can open the project straight away and is listed on it. Collaborator email addresses are shown only to the project's owner.
• Deactivated means signed out. Deactivating an account ends its open sessions immediately.
• Required password changes are enforced. An account that must change its password can do nothing else until it has.

Mass spec and plots

• Draw ranges freely. A range you draw on the chromatogram goes exactly where you put it: an edge dragged past the other edge turns the range round, and one range may start inside another.
• Peak fitting stays responsive. Very crowded regions are no longer fitted indefinitely, and a fitted shoulder peak no longer lands on top of a neighboring peak.
• Plot colors carried forward. Saved plots and presets are brought up to date with the new plotting engine on first open, and keep their colors.
• Saved workflows are named for their project. Saving or exporting a workflow names it after the project and keeps its original creation date.

Fixes

• Files. Two files whose names differ only in case can no longer overwrite each other, files whose names begin with a dot download again, a batch upload that fails partway still shows the files that arrived, and a failed save can no longer lose the previous workflow.
• Errors reach you. Problems in background processing and failed server lookups are reported on screen instead of showing as empty results.
• Explorer and editor. Extracted ion chromatograms no longer mix up results when you click quickly, and data labels are renumbered when a series is removed.
• Smaller fixes. The broken Import links are gone from the projects page and project menu, and the admin page no longer errors for users who are not administrators.

Highlights

• Every peak on the chromatogram is a range. The MS Explorer finds the peaks on the chromatogram and shades each one as a range. Hover a range for its apex, height and area; click it to see the combined spectrum of just that range; step through them with ◀ ▶ or the arrow keys. Ranges are shaded by where they came from, so a range you have changed is easy to tell from one the detector found.
• Adjust ranges by hand. Drag either edge of a range to where the peak really starts or ends, add a range the detector missed, or remove one it should not have found. Your changes are saved on the Mass Spec node and survive re-runs. Ranges may overlap, for peaks that elute together.
• Overlapping peaks, fitted apart. Turn on Fit peaks and co-eluting peaks are modeled together (Gaussian or exponentially modified Gaussian) so each gets its own area rather than a share of its neighbor's. The fitted curve is drawn over the chromatogram, and a peak that sits on the shoulder of another, with no dip between them, is now found and reported as a peak of its own.
• Extracted ion chromatograms. Turn on XIC and click a peak in the spectrum: a panel beside it shows how that m/z window elutes across the run, with its own ranges and its own threshold and sensitivity. A cursor marks the peak a click will take before you click.
• Check a digest against the run. Connect a Digest node to a Mass Spec node, and every peptide is looked for across the chromatogram's ranges — by mass at each charge, with its isotope pattern — with a report of where each one was found and why the others were not.
• The ranges become plots. The Mass Spec node now outputs the chromatogram plus one spectrum per range, and fragmentation spectra beneath the peaks they came from. A Plot node draws each as its own tab, and an Export node writes them all, as one zip.

Mass spec

• Choose how peaks are found. Each panel of the explorer has a detection method setting. Besides local maxima, the chromatogram panel offers a derivative method that reads a peak's edges from its slopes.
• Auto threshold says what it picked. Auto sets the threshold at the boundary between noise and signal, or at the conventional limit when there is no clear boundary, and tells you which.
• Apexes between samples. A peak's apex is placed where the curve peaks, not only on the nearest sample.
• Label peaks on the spectrum. Click a peak to label it. Labels are keyed by m/z, so a label you place follows that peak to every other scan and range, and they are saved on the node.
• Color peaks by charge. Spectra can color each peak by the charge the instrument assigned it, with a legend naming each one.
• Fragmentation spectra under the selection. When a range was fragmented, its MS2 (and MS3) spectra open in panels beneath it, and the explorer scrolls to hold them.
• Summed and averaged spectra are drawn truly. On a wide selection, a summed or averaged spectrum is combined first and reduced for display afterwards, so each peak is drawn at its real height and its label sits on top of it.
• Bruker bundles no longer collide. Two .d folders that each contain files of the same name can live in one project; previously one overwrote the other.

Plots and the canvas

• Several plots per node. A Plot node can hold more than one plot, each on its own tab in the editor, with its own columns and style. Export writes one image per plot.
• Translucent colors everywhere. Every color control in the plot editor opens a picker with transparency.
• Labels on a secondary axis stay put. A data label dropped on a point plotted against the right-hand axis now stays on that point.
• Rearrange the plot editor. Its sidebars resize, and the panels in them can be dragged from one side to the other. Clicking a label in the sidebar selects it on the plot.
• Switch a node off. Any node or connection can be suppressed, so it is skipped without being deleted.
• Notes on nodes. Every node has a notes field for whatever you want to remember about it.
• Drop a connection to add a node. Letting go of a connection on empty canvas opens the node list and connects the node you pick. Dragging one of several selected nodes moves them all.
• Several inputs into one node. A Digest node given more than one text input digests each in turn, one plot per input, and every node now says how it treats more than one input.
• Run on open. A workflow can be set to run as soon as it is opened.
• Docked panels stay out of the way. Docking the inspector or pinning notifications only moves the page when the panel would otherwise cover it.

Fixes

• Problems are shown, not hidden. Failures that used to appear only in the browser console now appear on screen, and a project whose file index cannot be read now says so instead of looking empty.
• Files are safe across tabs. Adding or removing files in two tabs at once, or adding two files in quick succession, can no longer lose one of them.
• Results always match their settings. A change made while a workflow is running now leaves that node marked for re-running, rather than showing results from the old settings as current. The explorer no longer detects peaks on a previous run's data after a re-run, and a result that arrives after you have moved to another node is no longer applied to it.
• Plot fixes. Download PNG matches the preview, a plot with an unfinished series row still exports, and dragging a Note onto the plot works.
• Mass spec fixes. A charge envelope's isotopes are no longer merged into one peak, a peak spread over several scans is labeled once rather than once per scan, and a fitted curve never dips below zero.
• Workflow fixes. The Digest node uses the value you just cleared or changed on the very next run, a second input into a node is no longer silently ignored, and swapping the file under a Parse node no longer leaves the plot editor with no columns to choose.
• Smaller fixes. Notifications can be closed while the MS Explorer is open, the Export node reports the format and size you chose, coverage-plot popups stay on screen, and resetting a password updates its last-changed date.

Highlights

• A real plot editor. Double-click a Plot node — or use Open plot editor… — and the plot opens full-screen with room to work. A searchable list of sections down the left, that section's controls top right, and whatever you clicked on the plot below them. Both side rails collapse when you want the figure to have the screen. The node itself is now a clean summary with a thumbnail of the current plot.
• Everything redraws as you type. Titles, colors, point sizes, axis ranges, padding — the plot follows the keystroke instead of waiting for you to click away. Choosing a different column re-runs the node for you when its data is already loaded, and there is a Run button in the editor header for when it isn't, so you never have to close the editor to see a change.
• Several series on one plot. + Series plots another column against the same X axis, each series with its own name and color, and the legend and title keep up as you add them.
• Figure presets. Start from Screen, Paper — single column (85 mm at 300 dpi, 8 pt type), Paper — double column (174 mm at 300 dpi) or Presentation (1920 × 1080, large type for a projected slide). Save your current settings as a preset of your own, star one as your default so every new plot begins there, and export or import presets as JSON. A preset only changes what it names, so a paper style applies to any kind of plot without replacing the plot type. Presets are stored with your account, so they follow you to any browser you sign in from.

Working on the plot itself

• Drag your labels. Ctrl-drag any label — the title, an axis label, an annotation — to exactly where you want it, and it stays there through re-runs and reloads. A reset control puts it back.
• Drag a label to where it belongs. + Data label and + Note are drag sources: drag one onto the plot and a marker follows the pointer, with a data label snapping to the nearest point and naming its values, so you can see what it will attach to before you let go. Clicking the button still drops one in the middle as before.
• A key to the canvas gestures. The editor header carries a help icon listing every gesture the plot understands — pan, zoom, move, select, edit in place — so none of them has to be discovered by accident.
• Click to edit what you clicked. Selecting an element on the canvas opens its own controls — text, font size, color, position, angle, leader line — in the panel beneath the section controls.
• Zoom one axis at a time. Scrolling over the plot zooms both axes; scrolling over an axis gutter scales just that axis.
• Legend inside or outside. Place the legend over the plot or beside it, where the plot area makes room for it, and click an entry to hide or show that series.
• Hover for values. Pointing at a point reads out its values, including any extra fields the data carries.
• Axis labels write themselves. Titles and axis labels default from the columns you bound — Intensity vs Retention Time — and a label you have written yourself is never overwritten by a later change.
• Export at the size you meant. PNG, JPEG and SVG, with the export dimensions set in the editor and honored on the way out.

Fixes

• Cosmetic edits no longer discard your plot. Changing a title or a color after a run re-renders in place; only changing which columns are plotted asks for the data again.
• Plot settings stay saved. Values you had entered are no longer replaced with defaults when the panel refreshes, and a second edit lands on the same plot as the first.
• Adding a node no longer breaks the next run. Adding or rewiring a node and pressing Execute used to fail with a "node not found" error until the page was refreshed. Rewiring an already-run node also gave a result computed from the old connections — quietly, with no error. Both are fixed.
• Moving a label to a corner keeps it on screen. Setting a label’s position to a corner used to hang most of the text off the edge of the plot. A corner now means the label’s matching corner, so it lands where you asked.
• Dragged labels render cleanly. A label moved to certain positions could come out with broken strokes and a stem stepping sideways part-way down, most visibly on displays at 125% scaling. Text now lands on the pixel grid wherever it is placed — which also sharpens the rotated y-axis title in every plot, moved or not.

Highlights

• Categorical bar charts. A text column — sample names, conditions, genes — can now be the X axis of a bar chart, with the bars labeled by your actual category names. Columns that can't be plotted numerically are called out clearly, down to the exact cell.
• Run Node handles everything. The inspector's run button executes any not-yet-run upstream nodes automatically and works from a fresh workflow — no need to run anything else first. The button reads Run Node or Re-run Node to match whether the node has produced output.
• Pop-out inspector. The inspector can detach into its own window (Chrome/Edge) and keeps following your node selection live — handy on a second monitor while you work the canvas.

Workflow Editor

• A better-behaved inspector. The floating panel sizes itself to its content, its header controls are always reachable, and every section reads correctly in light and dark themes.
• Tooltips everywhere they belong. Tooltips are never cut off by a panel edge and reposition themselves when space is tight.
• Missing values are handled per row. A gap in your data skips just that row of the plot, and the warning states exactly how many rows were left out of which column.

Files and Notifications

• Smarter duplicate handling. Re-adding a file the project already holds just tells you it's there — the overwrite question only appears when the content actually differs.
• Notifications wait for you. Hovering a notification holds it open until you move away, and every notification can be dismissed.

Accounts and Admin

• Live password feedback. Registration shows the password requirements as a live checklist with a strength meter, updated as you type.
• Clearer server-error visibility for admins. Each entry in the error log expands to show when it happened, to whom, and whether the alert notification went out — plus a test control to verify the alert pipeline end to end. Alert delivery itself is more dependable.

Highlights

• Much less waiting on load. Everything the site sends is now compressed — the main application binary arrives in under half the bytes it used to — files you already have are re-used between page views instead of downloaded again, and the footer no longer pulls in the entire analysis runtime just to print a version number.
• The workflow canvas tells you how to start. An empty canvas now says what to do, and the insert menu explains what each node is for and when you would reach for it — with arrow-key navigation and a keyboard shortcut (Ctrl+Space) to open it.
• Protein coverage maps. A Digest node can now be plotted directly. Connect Text → Digest → Plot and you get a coverage map of the peptides across the protein sequence, grouped by missed-cleavage count.

Workflow Editor

• Empty-canvas hint. Shown only while the canvas is genuinely empty, and it waits for a saved workflow to finish loading rather than flashing on the way in.
• Node help in the insert menu. Every node carries a short "when would I reach for this" description alongside its inputs and outputs. The panel remembers whether you left it open.
• The advanced view is now the default. New accounts land on the full workflow canvas instead of the simplified view.
• Faster plot framing. Reset view, auto-size and range framing no longer re-scan the data in the browser — the plot answers from what it already knows, which is most noticeable on large selections.

Accounts and Admin

• Fixed the defaults a brand-new account starts on — theme and page size could come up empty or zero before the first save.

Fixes

• When a part of the application fails to load, you now get a message saying so instead of a page that silently does nothing.

Highlights

• Large vendor files just open now. Thermo RAW acquisitions that used to stall or run out of memory — including multi-gigabyte runs with tens of thousands of scans — load and plot. Spectra are read as you look at them instead of all at once, so opening a file is quick and stays responsive as you scroll.
• Faster, smoother plots. Plotting is GPU-accelerated end to end. Zoom, pan, cursor readout and click-drag range selection all happen on the plot itself, so large chromatograms and spectra stay fluid.
• In-silico digestion and LC-MS/MS simulation. Two new workflow nodes: Digest takes a protein sequence (raw residues or FASTA), applies the cleavage agent and modifications you choose, and produces peptides. Simulation turns those peptides into a synthetic MS run — charge states, fragment ions, isotope envelopes, gradient elution, an MS1 scan grid and DDA MS2 scans. Useful for testing a workflow before you have instrument data, or for sanity-checking what you expect to see.

Mass Spec Explorer

• Peak labeling with a sensitivity slider. Label peaks on the TIC and on the spectrum, and dial detection up or down without leaving the plot.
• Auto threshold. One button picks a sensible signal-to-noise cutoff for the current data and re-frames the view around what it found.
• Reset view and auto-size buttons for getting back to the full range, or framing the detected peaks.
• Fast display toggle. Wide selections are approximated for speed by default; turn it off in the info bar when you need exact points, and the choice sticks.
• Performance improvements. Scan tables, spectrum extraction and export were reworked, and are considerably faster on large files.

Workflow Editor

• New nodes: Digest, Simulation, Comparison, Text and Export, alongside the existing File, Parse, Mass Spec, Plot and Debug nodes.
• Comparison got smarter. Text comparisons now use a proper line diff rather than a rough character-overlap score, with an ignore whitespace option. Mass spec comparisons gained a 2D retention-time × m/z heatmap view, with retention-time bin width and drift tolerance you can tune.
• Run timer. Workflows show elapsed time while they run.
• Full-output download. The Debug node's file export now writes the complete output — every column, every scan, every line — with progress shown on the button, instead of a truncated preview.

Accounts, Projects and Site

• Terms of Service, Privacy Policy and Refund Policy are now published on the site, and downloadable as PDFs.
• Friendlier 404, 429 and 500 pages.
• Notification preferences, the project header and the settings page were reworked; login, registration and password-reset flows are more consistent and give better errors.
• The app version is shown in the footer.

Fixes

• Fixed workers becoming unresponsive after an internal error — this is now detected and recovered automatically, instead of leaving a workflow stuck.
• Fixed the m/z plot coming up blank for some RAW files.
• Fixed spectrum failures being silent; they now surface as a visible notification, and the session keeps working.
• Fixed scans with an unspecified MS level being excluded from MS1 queries.
• Fixed the Data Explorer freezing on deeply nested data.
• Changing your password no longer logs out your active session.
• Fixed notification preferences reverting immediately after being changed, and notifications showing regardless of those preferences.
• Numerous stability and memory fixes around parsing, plotting and file handling.

Notes

• The older Datasets view has been retired. The workflow canvas is the place to load and inspect data; everything the Datasets view did is available there.
• workflow.json is reserved — project uploads using that filename are rejected.

• Node-based workflows. Build an analysis by wiring nodes together on a canvas, and run it without leaving the page.
• Mass spec analysis. Load instrument files, browse scans, and inspect chromatograms and spectra.
• Custom plot generation from any workflow output.
• Projects and accounts. Keep files and workflows organized per project, with registration, login and password recovery.