DIA peak inspection

SpectraLens

Targeted DIA peak inspection for the precursor you care about.

SpectraLens is built for the moment when you do not want to run a full DIA pipeline. Load raw files, enter the precursor you care about, and quickly inspect the MS1/MS2 peak evidence.

Download Latest Read Docs
SpectraLens desktop application showing precursor selection and XIC peak plots
Targeted Precursor-first
Views MS1 and MS2 XIC
Context iRT, RT, spectra
Output CSV export

Why it exists

Fast answers before a full analysis run

SpectraLens is for targeted visual confirmation: a few precursors, selected raw files, and immediate chromatographic evidence without waiting for a full DIA analysis workflow.

Precursor-centered inspection

Add the peptide sequence and charge state you want to verify, then inspect only the targeted signal instead of processing the full experiment.

Interactive XIC views

Review precursor-level MS1 XICs and fragment-level MS2 XICs with linear or log scale, legends, and optional TIC or base peak overlays.

iRT and charge prediction

Use model-based iRT and charge predictions to seed a focused search window when library information is incomplete.

Spectrum context

Compare experimental and predicted spectra so a peak can be checked with chromatographic and fragment evidence together.

Raw file workspace

Create a local workspace, add raw files, and reuse converted files during repeated precursor checks.

Exportable review

Export analysis results as CSV for review notes, sharing, or downstream manual curation.

Workflow

From raw file to peak evidence

  1. 1

    Create a workspace

    Choose a local workspace for raw files, converted files, peptide lists, and analysis settings.

  2. 2

    Add raw files

    Select DIA raw files. SpectraLens prepares local analysis-ready files and keeps their status visible.

  3. 3

    Enter precursors

    Paste peptide sequences, optional charge suffixes, UniMod modifications, or supported glycan notation.

  4. 4

    Inspect peaks

    Run targeted extraction. Setup collapses into the icon rail so the results take the full window, then switch between iRT-RT, spectra, MS1 XIC, and MS2 XIC tabs.

Docs

Install and use SpectraLens

This page keeps the working notes and user docs together because SpectraLens has a focused surface area.

Download

SpectraLens is distributed as a desktop application for macOS and Windows. Download the binary for your platform, launch it locally, and create a workspace to inspect DIA precursor peaks.

macOS Desktop app Windows Desktop app

Troubleshooting

macOS: app cannot be opened because the developer cannot be verified

Due to macOS Gatekeeper security settings, you may need to manually approve SpectraLens because the current macOS build may not have an Apple Developer code signature.

  1. Open System Settings or System Preferences.
  2. Go to Privacy & Security.
  3. Scroll down to the Security section.
  4. Find the message about SpectraLens being blocked because it is not from an identified developer, then click Open Anyway.

After approving the app, open SpectraLens again from Finder or Launchpad.

Quick start

Start by creating or opening a local workspace. SpectraLens keeps selected raw files, target precursors, settings, and exported results inside that workspace.

Step 1

Add raw files

Open the Raw Files panel, click Add files, and choose the raw files you want to inspect. After the files are listed, tick the checkbox for the file or files that should be included in the targeted analysis.

SpectraLens Raw Files panel with two raw files listed and selected
Add raw files, then select the files to use for analysis.
Step 2

Open the precursor input dialog

Click Add precursors below the precursor list to open the sequence input dialog.

SpectraLens Add Precursors dialog opened over the precursor list
Use Add precursors to open the sequence input dialog.
Step 3

Enter target sequences

Add the sequence or precursor you want to check, then click Add. Use UniMod notation for modifications, such as C(UniMod:4). Separate multiple sequences with line breaks or commas. Add a charge state after a period, such as PEPTIDESEQ.2.

SpectraLens Add Precursors dialog with three target sequences entered
Enter one or more target sequences, then add them to the precursor list.
Step 4

Select precursors and run

Select the sequence rows you want to analyze. Anchor precursors are used for RT-iRT mapping. SpectraLens automatically fills many settings from the raw file metadata, but you can adjust tolerances, instrument, NCE, RT window, and fragment limits in Experiment Settings when needed. Click Analyze to extract and inspect the target peaks. Setup collapses into the icon rail once the run succeeds, so the results get the full window.

SpectraLens setup with every raw file and precursor selected, ready to analyze
Select target sequences, review settings, and run Analyze.

Precursor input

Paste one sequence per line or separate multiple entries with commas. Add a charge suffix with .2 or .3 when you want a specific charge state. If the charge is omitted, SpectraLens predicts likely charge states and iRT values. 

PEPTIDESEQ.2
PEPC(UniMod:4)TIDESEQ.3
AA[Hex(1)HexNAc(2)]DD
PEPTIDES(UniMod:21)EQ,PEPTIDEM(UniMod:35)SEQ

Settings reference

MS1 tolerance
Precursor m/z extraction window in ppm.
MS2 tolerance
Fragment ion extraction window in ppm.
RT window
Seconds around the predicted or entered retention time used for targeted XIC extraction.
Instrument
Mass spectrometer model used for prediction and display context.
NCE
Normalized collision energy used for predicted fragment spectra.
Max fragments
Optional cap on the number of fragment ions extracted.
Intensity aggregation
How intensities inside each tolerance window are combined: sum, mean, or maximum.

Outputs

SpectraLens keeps precursor rows, local file status, analysis settings, and extracted result tables inside the selected workspace. Use Export CSV from the visualization panel to save a reviewable result table for downstream notes or manual curation.

Support & community

SpectraLens uses GitHub Discussions and Issues for community support, bug reports, and feature ideas.

  • Questions and usage help: ask in GitHub Discussions.
  • Bug reports: open a GitHub Issue with your operating system, SpectraLens version, input file type, and a short description of what happened.
  • Feature ideas: share suggestions in Discussions so they can be discussed before becoming issues.