Data acquisition and analysis simplified

Data acquisition and analysis simplified

Simplify your mass spectrometry data acquisition and analysis with our unique software platforms for peptides, glycans, lipids and novel compounds. Our software enables you to go all the way from initial compound discovery and quantitation to in-depth HR/AM and MS/MS analysis.

Popular LC-MS software
Featured LC-MS software categories
Compound and drug discovery
Drug discovery

Identify and quantitate small molecules, interpret complex spectral data, perform targeted screening, and assess the pharmacokinetic properties of novel drug candidates with our many compound and drug discovery software platforms.

Environmental applications
Environmental applications

Quantify persistent organic pollutants (POPs) using data derived from different LC-MS systems on a single software platform. Thermo Scientific™ TargetQuan 3 software includes POPs workflows and processes MS, MS/MS and high-resolution MS data, while our High-Resolution Accurate-Mass Libraries provide spectra for over 2,600 compounds.

General screening applications
General screening applications

Manage, evaluate and interpret LC mass spectral data, and manage trace analysis workflows in testing laboratories with our general screening platforms.

High throughput and MS/MS proteomics
High throughput and MS/MS proteomics

Isolate proteins from complex biological matrices and when using different dissociation and fragmentation techniques. Simplify your proteomics workflows, including ion ratio calculation, PTM analysis and isobaric mass tagging.

Clinical research and forensic toxicology analysis
Clinical research and forensic toxicology analysis

Simplify screening and targeted screening, routine quantitation, and qualitative review of GC, GC-MS, LC, LC-MS and LC-MS/MS data with software workflows specifically designed for the clinical research and forensic toxicology laboratory.

Lipidomics analysis

Discover lipid species confidently using our LipidSearch Software, which interprets MS/MS-generated spectra through predictive fragmentation and comparison to fragment and adduct databases.

Regulatory and MS/MS assays
Regulatory and compliance

Acquire and manage quantitative LC-MS data in a 21 CFR Part 11-compliant environment, and generate deconvoluted data of intact proteins, peptides, oligonucleotides, and other biomolecules assayed in ion trap and quadrupole systems.

Protein analysis
Protein analysis

Transition from initial proteomic discovery to small molecule structural analysis and verification of biomarkers with predictive SRM algorithms, quantitation of disulfide bonds and PTMs, and identification of meta-proteins via de novo and assisted manual sequencing.

Glycan analysis
Glycan analysis

Characterize complex glycan isomeric spectra produced by MS/MS analysis using SimGlycan™ software from PREMIER Biosoft. This software compares generated spectra against its comprehensive databases and generates a scored list of candidate structures.


As protein-based drugs become more important in treating major diseases, producers face the critical challenge of deeply characterizing these highly complex molecules for efficacy and safety, as well as to meet quality requirements. A new software tool, Thermo Scientific PepFinder, is designed to increase the speed, quality and accuracy in comprehensive biotherapeutic protein characterization during drug development and production quality control.

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Planet Orbitrap

Tips, applications, product information, community, technical papers and other resources for Orbitrap-based mass spectrometers.

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