List of mass spectrometry software

Mass spectrometry software is used for data acquisition, analysis, or representation in mass spectrometry.

Proteomics software

In protein mass spectrometry, tandem mass spectrometry experiments are used for protein/peptide identification. Peptide identification algorithms fall into two broad classes: database search and de novo search. The former search takes place against a database containing all amino acid sequences assumed to be present in the analyzed sample. In contrast, the latter infers peptide sequences without knowledge of genomic data.

Database search algorithms

De novo sequencing algorithms

De novo peptide sequencing algorithms are, in general, based on the approach proposed in Bartels et al..

Name	Type	Description
Casanovo	Open source	Casanovo is a machine learning model that uses a transformer neural network architecture to translate the sequence of peaks in a tandem mass spectrum into the sequence of amino acids that comprise the generating peptide, enabling de novo peptide sequencing without prior information.
CycloBranch	Open source	CycloBranch is a stand-alone, cross-platform and open-source de novo engine for identification of nonribosomal peptides from accurate product ion spectra.
DeNoS		Sequencing of peptides uses all information from CAD and ECD spectra; it is part of the software tool Proteinmatching Analysis Software which in turn is part of the software package Medicwave Bioinformatics Suite.
DeNovoX	Proprietary	De novo sequencing on CID spectra acquired with ion trap mass spectrometers delivers complete and/or partial peptide sequences.
InstaNovo	Open source	InstaNovo is a transformer neural network that can translate fragment ion peaks into the sequence of amino acids that make up the studied peptide, enabling de novo peptide sequencing without prior information. Trained on 28 million labeled spectra, it outperforms current state-of-the-art methods on benchmark datasets. InstaNovo+, a multinomial diffusion model built upon human intuition, further improves performance through iterative refinement of predicted sequences.
Lutefisk	Open source	This is software for the de novo interpretation of peptide CID spectra.
Novor	Proprietary, free for academic research	This real-time de novo peptide sequencing engine is claimed to be fast, accurate and easily integrated into research pipelines.
PEAKS	Proprietary	PEAKS provides de novo sequencing for each peptide, confidence scores on individual amino acid assignments with manually assisted mode and automated de novo sequencing on an entire LC run, with data processed faster than 1 spectrum per second.
Supernovo	Proprietary	This software automates de novo sequencing of monoclonal antibodies.

Homology searching algorithms

MS/MS peptide quantification

Name	Type	Description
BACIQ	Open source	BACIQ is a mathematically rigorous approach that integrates peptide intensities and peptide-measurement agreement into confidence intervals for protein ratios.
Byos	Proprietary	Byos commercial software allows XIC of peptide level mass spec data from any MS vendor and relative quantity of PTM vs unmodified. It is specialized for biopharmaceutical applications.
DIA-NN	Freeware	This automated quantitative Data-independent acquisition-proteomics software, developed by the Demichev and Ralser labs at the Charité in Berlin, Germany, implements a machine-learning algorithm based on an ensemble of deep neural networks, to boost proteomic depth and reliability of peptide and protein identification. DIA-NN is optimized for processing of large-scale experiments. It supports DIA-based profiling of PTMs, such as phosphorylation and ubiquitination, new technologies such as Scanning SWATH and dia-PASEF, and can perform library-free analyses.
FlashLFQ	Open source	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. FlashLFQ is also bundled into MetaMorpheus search software, which is described above.
MarkerView Software	Proprietary	This commercial software is for statistical analysis of quantitative mass spec data sets from metabolomics and proteomic profiling applications.
Mascot Distiller	Proprietary	This software for peak picking and raw data preprocessing has an optional toolbox for label-free quantification, as well as isobaric labeling and isotopic labeling. It supports raw file formats from all major instrument vendors.
Mascot Server	Proprietary	The search engine supports quantification based on isobaric labeling as long as all the required information is part of the MS/MS spectrum.
MassChroQ	Open source	Peptide quantification analysis of label-free or various isotopic labeling methods works with high and low resolution spectrometer systems and supports complex data treatments, such as peptide or protein fractionation, prior to LC-MS analysis.
	Freeware	Quantitative proteomics software developed by Jürgen Cox and others at the Max Planck Institute of Biochemistry in Martinsried, Germany was written in C#, which allows the analysis of label free and SILAC-based proteomics experiments. MaxQuant uses the andromeda search engine for the interpretation of the MS/MS spectra.
MultiQuant Software	Proprietary	This software can process quantitative data sets from TripleTOF or QTRAP systems, including MRM and SWATH Acquisition.
OpenMS / TOPP	Open source	The software C++ library for LC-MS/MS data management and analysis offers an infrastructure for the development of mass spectrometry-related software. It allows peptide and metabolite quantification and supports label-free and isotopic-label-based quantification as well as targeted SWATH-MS quantification.
OpenPIP	Website, open access	OpenPIP is a tool developed by InterVenn Biosciences to integrate peaks acquired in multiple reaction monitoring experiments. The software is powered by recurrent neural networks and guided by a large collection of manually-annotated chromatographic peaks.
ProtMax	Freeware	ProtMAX is a software tool for analyzing shotgun proteomics mass spectrometry data sets, developed by Volker Egelhofer at the University of Vienna.
Skyline	Open source	Skyline is open source Windows client software developed in the MacCoss lab at University of Washington. It supports building Selected Reaction Monitoring / Multiple Reaction Monitoring, Parallel Reaction Monitoring, Data Independent Acquisition and targeted DDA with MS1 quantitative methods and analysis of the resulting mass spectrometer data.
Spectronaut	Proprietary	Biognosys AG developed this commercial software for quantitative proteomics based on the mProphet algorithm that allows the targeted analysis of data independent acquisition data sets for label-free peptide quantitation, also called SWATH acquisition.
SWATH Software 2.0	Proprietary	This commercial software processing tool within PeakView allows targeted data processing of SWATH acquisition data. Using a protein/peptide ion library, fragment ion extracted ion chromatograms are generated, scored and quantified for peptides from the library. After false discovery rate analysis, results are filtered and quantitative peptide/protein data can be exported for statistical analysis.