Proteome informatics by Conrad Bessant, Simon J Gaskell, Bin Ma, Surendra Dasari,
By Conrad Bessant, Simon J Gaskell, Bin Ma, Surendra Dasari, Jyoti Choudhary, Andrew Jones, Rune Matthieson, Andrew Dowsey, Marc Vaudel, Birgit Schilling, Pedro Navarro, Juan Antonio Vizcaíno, Lars Nilse, Timothy J Griffin, Laurent Gatto
The sphere of proteomics has built speedily during the last decade nurturing the necessity for a close advent to some of the informatics issues that underpin the most liquid chromatography tandem mass spectrometry (LC-MS/MS) protocols used for protein id and quantitation. Proteins are a key component to any organic procedure, and tracking proteins utilizing LC-MS/MS proteomics is turning into general in a variety of organic learn parts. besides the fact that, many researchers deal with proteomics software program instruments as a black field, drawing conclusions from the output of such instruments with no contemplating the nuances and barriers of the algorithms on which such software program is predicated. This publication seeks to handle this case through bringing jointly global specialists to supply transparent motives of the most important algorithms, workflows and research frameworks, in order that clients of proteomics information may be convinced that they're utilizing applicable instruments in appropriate methods
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Additional resources for Proteome informatics
During the dynamic programming, the fragment ions at the two mass values are examined for possible overlap. A peak that is matched by more than one fragment ion is only counted once. The Sandwich algorithm solved the double-count problem. However, the complexity of that algorithm is significantly higher than with the algorithm MassArray described previously. For computing efficiency, the algorithm used in later versions of the PEAKS software is based on the MassArray algorithm with many unpublished improvements.
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Vanduijn, T. M. Luider, N. Tolic, Q. Kou, M. Dvorkin, S. Alexandrova, K. Vyatkina and L. Pas, De Novo Protein Sequencing by Combining Top-Down and Bottom- Up Tandem Mass Spectra, J. , 2014, 13, 3241–3248. X. Han, L. He, L. Xin, B. Shan and B. Ma, PeaksPTM: Mass spectrometry-based identification of peptides with unspecified modifications, J. , 2011, 10, 2930–2936. A. Chacon, D. S. Masterson, H. Yin, D. C. Liebler and N. A. Porter, N-Terminal amino acid side-chain cleavage of chemically modified peptides in the gas phase: A mass spectrometry technique for N-terminus identification, Bioorg.