Software: Mass Spectrometry

Handy pieces of software and web servers for mass spectrometry

1. ESIprot: "ESIprot 1.0 enables the charge state determination and molecular weight calculation for low resolution electrospray ionization (ESI) mass spectrometry (MS) data of proteins." http://bit.ly/14vt9tw

2. iso2L: (java)  "software to calculate the isotopic distribution of a chemical formula or a amino acid chain" http://sourceforge.net/projects/iso2l/ 

3. IPC (Isotope Pattern Calculator): (java) "The Isotope Pattern Calculator calculates and displays the isotopic distribution and exact masses for peptides and other molecules." http://omics.pnl.gov/software/isotope-pattern-calculator

Note that both iso2L and IPC can predict mass spectra (not just peak lists but output simulated spectra) from a fasta sequence.

4. ExPASy Peptide Mass: "cleaves a protein sequence...with a chosen enzyme, and computes the masses of the generated peptides... also returns theoretical isoelectric point and mass values for the protein of interest... If desired, PeptideMass can return the mass of peptides known to carry post-translational modifications..." http://web.expasy.org/peptide_mass/