TY - GEN
T1 - Understanding the impact of fractionation and dynamic exclusion on proteomics
AU - Zavala, Cynthia
AU - Nixon, Scott
AU - Southey, Bruce R.
AU - Wu, Cong
AU - Romanova, Elena Vikentievna
AU - Sweedler, Jonathan V
AU - Rodriguez-Zas, Sandra Luisa
PY - 2014
Y1 - 2014
N2 - The subject of this study was to evaluate the impact of dynamic exclusion and protein size on the capability of database search programs to identify protein in tandem mass spectrometry (MS/MS) experiments. Through the two stages of mass fragmentation, MS/MS spectrometry allows for an identification of peptides. Furthermore, the identification of proteins is heightened with the use of dynamic exclusion and fractionation. This bioinformatics study was applied to mass spectra from the brain macrophages of healthy wild type mice and mice exposed to an infection. The database search software PEAKS was used to identify peptides and proteins across protein sizes (fractionations) and exclusion options. Parameter specifications to optimize the identification of proteins and peptides were: parent mass error tolerance (15.0 Da) and fragment mass error tolerance (0.1 Da) specifications. After analysis, proteins such as Beta-globin (A8DUK40) and Actin cytoplasmic 1 (ACTB) were identified.
AB - The subject of this study was to evaluate the impact of dynamic exclusion and protein size on the capability of database search programs to identify protein in tandem mass spectrometry (MS/MS) experiments. Through the two stages of mass fragmentation, MS/MS spectrometry allows for an identification of peptides. Furthermore, the identification of proteins is heightened with the use of dynamic exclusion and fractionation. This bioinformatics study was applied to mass spectra from the brain macrophages of healthy wild type mice and mice exposed to an infection. The database search software PEAKS was used to identify peptides and proteins across protein sizes (fractionations) and exclusion options. Parameter specifications to optimize the identification of proteins and peptides were: parent mass error tolerance (15.0 Da) and fragment mass error tolerance (0.1 Da) specifications. After analysis, proteins such as Beta-globin (A8DUK40) and Actin cytoplasmic 1 (ACTB) were identified.
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M3 - Conference contribution
AN - SCOPUS:84905821280
SN - 9781632665140
T3 - Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
SP - 93
EP - 96
BT - Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
PB - International Society for Computers and Their Applications
T2 - 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
Y2 - 24 March 2014 through 26 March 2014
ER -