A programmable fragmentation analysis of proteins by in-source decay in MALDI-TOF mass spectrometry

Analytical Chemistry
Jialing GaoLin Xu

Abstract

Here we describe an algorithm for identifying peptides/ proteins of known sequence and unknown peptides from partial spectra generated by an in-source decay (ISD) technique coupled with matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. The identification of protein fragments is processed with a software program called CMATCH, which generates candidate subsequences for both known peptides/proteins and unknown peptides for the major product ions in the spectral range m/z 400-5000 and then matches these to known protein sequences contained in a reference database for the known peptides/proteins. CMATCH, which is compiled for MSDOS or WINDOWS95/NT, has two main advantages: first, the candidate subsequences are generated automatically without the need for supplementary information concerning the distribution of either N-terminal or C-terminal ions in the spectra for both known peptides/proteins and unknown peptides; second, the highest coordinated homologous sequences are picked up automatically from the reference database as the best matches with known peptides/proteins. Examples from the ISD spectra of several test proteins demonstrate the efficacy of this protein identification software.

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Citations

Jul 20, 2010·Annual Review of Analytical Chemistry·Mélanie AbonnencHubert H Girault
Sep 1, 2009·Bioanalysis·Marcus Macht
Jul 26, 2003·Analytical Sciences : the International Journal of the Japan Society for Analytical Chemistry·Maria Balcerzak
May 11, 2016·Mass Spectrometry·Mitsuo Takayama
Jun 22, 2005·Expert Review of Proteomics·Simone Cristoni, Luigi Rossi Bernardi
Jul 19, 2002·Journal of Mass Spectrometry : JMS
Oct 27, 2006·Rapid Communications in Mass Spectrometry : RCM·Simone CristoniCristina Banfi
Jun 23, 2011·Analytical Chemistry·Tyler A ZimmermanEdwin De Pauw

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