"Skyline is a freely-available and open source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM - Targeted MS/MS), Data Independent Acquisition (DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data."
Resources
Software
"SIMION Version 8.1 is a software package primarily used to calculate electric fields and the trajectories of charged particles in those fields when given a configuration of electrodes with voltages and particle initial conditions, including optional RF (quasistatic), magnetic field, and collisional effects."
"OpenMS is an open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS and Linux."
"Tools are available to process your data such as re-calibration, smoothing, baseline correction, auto peak picking, deconvolution etc."
Online Tools
Given a chemical formula, it will output the expected isotope pattern, either in low or high resolution.
Interactive tool for displaying isotope patterns, with variable resolution
Tool that calculates possible molecular formulas from exact mass measurements