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NIST Mass and Fragment Calculator Software


The NIST Mass and Fragment Calculator is a program written in Visual Basic which calculates the mass of an input peptide or protein sequence along with m/z ions corresponding to 1+, 2+, and 3+ charge states when selecting average mass results.  The option exists to select monoisotopic results which will also generate y, b, c, and z product ions. Two forms of the z product ions are displayed. z-CID is the structure from Johnson et al. (Anal. Chem. 59(21) 2621-2625 (1987)) which is relevant to higher-energy fragmentation associated with CID. z-ETD is the fragmentation associated with ETD or ECD as shown in Syka et al. (PNAS 26 9528-9533 (2004).)

Sequence Masses are calculated based on the accumulated occurrences of all the elements within each residue contained in the input sequence according to the residue formula displayed in the Residue Formula menu option. The sequence mass is the sum of the product of the accumulated totals (plus water) by the elemental masses obtained from:  

The Residue Codes menu option lists the valid single-letter codes for the residues including some modified residues. A useful feature is the ability to add a desired mass to a specific residue enabling the identification of fragment peak profiles which match experimental data.


 mass fragment calc


Version: 1.2

Last Updated: March 24, 2012

Type of software: Visual Basic Executable for PC


Eric L. Kilpatrick


Windows XP, Vista, or Windows 7

Download information:

Download NIST Mass and Fragment Calculator v1.2

V1.2 includes mass calculation of specific carbohydrate moieties associated with protein glycosylation at specified residues for N- or O-linked forms.


This software was developed at the National Institute of Standards and Technology by employees of the Federal Government in the course of their official duties. Pursuant to title 17 Section 105 of the United States Code this software is not subject to copyright protection and is in the public domain. Each of these packages is an experimental system. NIST assumes no responsibility whatsoever for its use by other parties, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic. We would appreciate acknowledgement if the software is used; please cite Kilpatrick et al., Protein Purification and Expression 85 (2012) 94-99. This software can be redistributed and/or modified freely provided that any derivative works bear some notice that they are derived from it, and any modified versions bear some notice that they have been modified.