Compare
Overlay spectra. Highlight every difference.
Stack spectra at native resolution—mirrored or overlaid—then reveal diverging peaks and intensity changes with one click.
A single workflow, compared
See one feature move at web speed.
The same spectra. The same scientific question. A much shorter path from raw data to a measured answer.
ONE FEATURE, NOT THE WHOLE PLATFORM. This short demo compares shift measurement in Spectrum Studio with the traditional Xcalibur workflow.
Both sides play at 2× so the demo finishes soonerAfter Spectrum Studio finishes, the remaining Xcalibur source footage is shown at 10×
Spectrum Studio00:51
Open, overlay, measure, and convert.
Traditional workflow08:58
Export, format, align, and calculate.
Time returned08:07
On this feature alone.
The core workspace · every application
From spectrum to decision, without breaking context.
Compare, identify, measure and quantify directly on the spectrum. These tools work the same whether you are looking at an oligonucleotide, a peptide or a PEG conjugate.
Identify
Click a peak. See its charge state.
Select Charge, click an isotope peak, and its charge appears instantly—for example, z = 5−—with the neutral mass below.
CClick peak
Measure
Find the shift. Get Daltons automatically.
Pick two peaks across overlaid spectra. Spectrum Studio reports Δ m/z, converts it to neutral Δmass using the charge state, and suggests what the difference could be.
DClick × 2
Inspect
Bring quiet peaks into view smoothly.
Increase or decrease intensity without leaving the spectrum. The keyboard and on-screen scale stay in sync.
↑↓
Quantify
Integrate by drawing or typing a range.
Drag directly across peaks or enter exact start and end values. Signal sums and percentages update beside the spectrum, and the same windows can be copied to every sample of a series.
IDrag
01 · Oligonucleotide analysis
From peak areas to binding constants.
For native MS of DNA and RNA targets and their ligands: define the free host and complex windows once, correct for how differently they ionise, and read Ka across a whole titration.
Binding constants
Ka for 1:1 and 1:2, live.
Areas of the free host and each complex at every charge state become concentrations and log Ka. Ammonium-adduct windows are summed into their species, and the windows are copied across the series in one step.
Response factors
Correct for how each species ionises.
The internal-standard method published in Anal. Chem. (2009) gives each complex its own electrospray response factor R, so Ka no longer assumes every species flies equally well. A built-in check reproduces the paper's worked example.
Exact mass
Sequence in. Charge series out.
Type a DNA or RNA sequence, set the number of strands, and get the formula, monoisotopic and average mass, and every charge state to look for—before you open the spectrum.
Charge states
Every charge state, kept apart or combined.
Results are reported per charge state so disagreements stay visible, or grouped when a species is too weak to stand alone—never averaged away silently.
Report
Turn every selected spectrum into a table, plot, or bar chart.
Pull calculated and supplied parameters into one table, add spreadsheet-style formulas like =log10(C), then plot with a linear fit, R² and equation—without manual copy-and-paste.
02 · Peptide analysis
Know what is in the crude before you purify it.
For solid-phase peptide synthesis: open the LC-MS run, find the target at every charge state, and have every other major peak explained—deletions, protecting groups left on, side reactions, reagent by-products.
LC-MS · choose the moment
Open the run. Choose the moment.
Agilent ChemStation .D folders open directly—or drop them on the window—ESI+ and ESI− as two spectra, with TIC, UV and extracted-ion traces.
Automatically: Spectrum Studio proposes the averaging window itself—the main elution region of the TIC—and explains why: the baseline, the apex and the threshold it used.
Or by hand: drag across any peak, type the start and end times, jump to the single scan at one time, and zoom into the chromatogram with the buttons or the mouse wheel.
AutoDrag windowFrom – toAt [min]🔍 Zoom
Compound detection
One compound, one colour—across its charge states.
Diff Compound Detection reads the charge state of each peak and links the peaks that are the same molecule at different charges, by mass agreement and co-elution. Each compound gets its own colour on the spectrum, with one mass and its uncertainty.
◉ Diff Compound Detection
Peptide builder
Type it, build it, or open the drawing.
Natural and non-natural amino acids, D-residues, protecting groups kept or removed by your reagents, disulfide bridges and modifications. Or open a ChemDraw .cdx / SMILES and the residues and bridges are read for you.
Side products
Predict the side products. Match them to the peaks.
From the target and everything that was in the flask, Spectrum Studio lists what a synthesis can produce—deletions and truncations, protecting groups left on, aspartimide, oxidation, cation adducts, reagent by-products—then explains each major peak, ranked from likely to unexplained. Unit-resolution clusters are compared on the right isotope, not just the monoisotopic mass.
Instant Target Detection
Your peptide, at every charge state.
One click searches the whole spectrum for every ion of the target—each charge state and Na⁺, K⁺ and NH₄⁺ adduct—and checks that they co-elute on the chromatogram, so a peak that only happens to have the right mass is not counted.
🎯 Instant Target Detection
03 · PEG & lipid conjugates
Read a polymer distribution, not just its tallest peak.
For PEGylated peptides and PEG–lipid conjugates: build the conjugate from its blocks, and let each ladder of peaks 44 Da apart be fitted, centred and assigned—with the chain length and the cations carrying the charge.
PEG builder
Build the conjugate, block by block.
Just like the peptide builder: pick the lipid, the link, the PEG chain with its range of n, the end group and the peptide it is joined to, choose the conjugation reaction, and tick everything that was in the sample. The formula follows every choice, and a ChemDraw or SMILES drawing can be read in and checked against it.
Lipid(PEG)ₙEnd groupPeptide
Retention window
The widest window that does not shift the answer.
PEG chains separate on the column, so a wide averaging window smears the chain length. The window finder tries widths around a chosen time and recommends the widest one before the centred peaks start to move.
Centred peak
Fit the ladder. Read the centre, n and the charge.
Peaks 44.03/z apart are chained into ladders, a Gaussian is fitted to each, and its centred peak gives the mean chain length and the ion form—even where the 3+ and 4+ ladders interleave. Build the conjugate as peptide + (PEG)n + lipid, so every reading is checked against a real formula.
Adducts
Every carrier, every alternative.
Each distribution is explained by species × cation sets—H⁺, NH₄⁺, Na⁺, K⁺ and base adducts, salt or free acid. Readings that the instrument cannot tell apart, such as two Na⁺ for two H⁺ against one more ethylene-oxide unit, are shown side by side instead of guessed.
Built for real laboratory data
Your machine. Your files. Your analysis.
Spectrum Studio is a Windows desktop program that also runs in the browser. It reads Thermo .RAW files and Agilent ChemStation .D runs directly, and ChemDraw structures as they are. There is no upload step and no cloud account between you and your data.
That keeps unpublished spectra private—and keeps analysis available on instrument PCs behind locked-down networks.
Data locationStays on your machine
Network requiredNone
Instrument inputThermo .RAW · Agilent .D, direct
StructuresChemDraw .cdx/.cdxml · SMILES
Analysis resolutionFull profile data
OutputTables, CSV, plots & PNG
The analysis belongs with the spectrum
Stay in the science, not the software.
See how Spectrum Studio can turn your oligonucleotide, peptide or PEG workflow into one clear, connected workspace.
Or write to spectrumstudio.admin@gmail.com