Curated links for the mass spectrometry research community — data references, open-source software, simulation tools, and key literature resources.
Chemistry Reference
The definitive reference for exact masses, isotope patterns, molecular formulas, and thermochemical data. Essential for mass calibration and peak identification.
webbook.nist.gov/chemistry
Proteomics
Web-based tools for protein and peptide mass calculations, fragment ion prediction, and database searching. Widely used for bottom-up proteomics workflows.
prospector.ucsf.edu
Ion Mobility / CCS
Community database of experimental collision cross section (CCS) values for small molecules and peptides across multiple instrument platforms and buffer gases.
collisiondb.ca
Lipids
Comprehensive lipid structure database with exact masses, MS/MS fragmentation data, and pathway tools. The reference standard for lipidomics research.
lipidmaps.org
Literature Search
Free full-text archive and search engine for biomedical and life sciences literature maintained by the NIH National Library of Medicine. The primary resource for finding mass spectrometry methods papers, instrumentation articles, and application studies.
pubmed.ncbi.nlm.nih.gov
Data Processing
Free, open-source mass spectrum interpreter for Windows and macOS. Excellent for manual spectrum annotation, isotope pattern matching, and sequence analysis.
mmass.org
Ion Mobility / CCS
Open-source software for collision-induced unfolding (CIU) data analysis. Fingerprinting, classification, and comparison of protein CIU datasets from IM-MS instruments.
github.com/bhattlab/CIUSuite2
CCS Calculation
Computational tools for calculating theoretical CCS values from molecular structures using trajectory (TM), projection approximation (PA), and EHSS methods.
github.com — IMoS2 / MOBCAL
Instrument Control
Open-source firmware, Arduino libraries, and control software for MIPS and associated GAA Custom Electronics hardware. Actively maintained with community contributions welcome.
github.com/GordonAnderson
Multi-Tool Suite
A suite of open-source tools developed at Pacific Northwest National Laboratory covering proteomics, metabolomics, data processing, and instrument control. Includes MASIC, DeconTools, Protein Digestion Simulator, and many others widely used in the mass spec community.
pnnl-comp-mass-spec.github.io
Targeted Proteomics
Freely available, open-source Windows application for building and analyzing targeted mass spectrometry experiments. Widely used for SRM/MRM method development, spectral library building, and quantitative proteomics workflows. Developed and maintained by the MacCoss Lab at the University of Washington.
skyline.ms
Data Conversion
Open-source libraries and tools for mass spectrometry data conversion and analysis. The msConvert tool supports conversion between virtually all vendor formats (Thermo RAW, Waters MassLynx, Agilent, Bruker, etc.) to open formats such as mzML and mzXML. An essential utility in any mass spec lab.
proteowizard.sourceforge.io
Data Analysis Framework
Open-source C++ library and Python bindings for LC-MS data processing, feature detection, quantification, and identification. Provides a large toolkit of algorithms for proteomics and metabolomics workflows, and integrates with KNIME and Galaxy for pipeline-based analysis.
github.com/openms/openms
Ion Optics Simulation
The industry-standard ion trajectory simulation software. Models electrostatic and magnetic fields, ion optics, and mass analyzer geometries. Used by instrument designers worldwide.
simion.com
RF Ion Trap Simulation
Simulation environment specifically designed for ion trap mass spectrometers. Models ion motion in RF fields, space charge effects, and resonance ejection.
ionsimulation.com
Molecular Dynamics
High-performance molecular dynamics package widely used for native MS and ion mobility structure prediction. Free and open source with excellent GPU support.
gromacs.org
Electronics Simulation
Free SPICE-based circuit simulator from Analog Devices. Invaluable for designing RF driver circuits, FET switch networks, and power supply topologies for mass spec electronics.
analog.com — LTspice
Primary Journal
The leading mass spectrometry journal covering instrumentation, methodology, and applications. Published by the American Society for Mass Spectrometry.
pubs.acs.org/journal/jasms
Broad Analytical
High-impact journal covering the full range of analytical methods including mass spectrometry, ion mobility, and related detector technologies. Biweekly publication.
pubs.acs.org/journal/ancham
Rapid Communication
Fast-track publication for new MS techniques, instrumentation innovations, and novel applications. Good source for emerging ion mobility and native MS developments.
Wiley — Rapid Commun. Mass Spectrom.
Community
Professional society hosting the annual ASMS conference — the largest gathering of mass spectrometrists worldwide. Resources include short courses, job postings, and the MS education portal.
asms.org