The classification of samples on a molecular level has manifold applications, from patient classification regarding cancer treatment to phylogenetics for identifying evolutionary relationships between species. Modern methods employ the alignment of DNA or amino acid sequences, mostly not genome-wide but only on selected parts of the genome. Recently proteomics-based approaches have become popular. An established method for the identification of peptides and proteins is liquid chromatography-tandem mass spectrometry (LC-MS/MS). First, protein sequences from MS/MS spectra are identified by means of database searches, given samples with known genome-wide sequence information, then sequence based methods are applied. Alternatively, de novo peptide sequencing algorithms annotate MS/MS spectra and deduce peptide/protein information without a database. A newer approach independent of additional information is to directly compare unidentified tandem mass spectra. The challenge then is to compute the distance between pairwise MS/MS runs consisting of thousands of spectra.
Rieder V., Blank-Landeshammer B., Stuhr M., Schell T., Biß K., Kollipara L., Meyer A., Pfenninger M., Westphal H., Sickmann A. and Rahnenführer J. (2017) DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs. BMC Bioinformatics 18(1). 10.1186/s12859-017-1514-2
@article{Rieder2017,
Title = {DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs},
Author = {Rieder, Vera and Blank-Landeshammer, Bernhard and Stuhr, Marleen and Schell, Tilman and Biß, Karsten and Kollipara, Laxmikanth and Meyer, Achim and Pfenninger, Markus and Westphal, Hildegard and Sickmann, Albert and Rahnenführer, Jörg},
Editor = {},
Journal = {BMC Bioinformatics},
Year = {2017},
Volume = {18},
Doi = {10.1186/s12859-017-1514-2},
Abstract = {The classification of samples on a molecular level has manifold applications, from patient classification regarding cancer treatment to phylogenetics for identifying evolutionary relationships between species. Modern methods employ the alignment of DNA or amino acid sequences, mostly not genome-wide but only on selected parts of the genome. Recently proteomics-based approaches have become popular. An established method for the identification of peptides and proteins is liquid chromatography-tandem mass spectrometry (LC-MS/MS). First, protein sequences from MS/MS spectra are identified by means of database searches, given samples with known genome-wide sequence information, then sequence based methods are applied. Alternatively, de novo peptide sequencing algorithms annotate MS/MS spectra and deduce peptide/protein information without a database. A newer approach independent of additional information is to directly compare unidentified tandem mass spectra. The challenge then is to compute the distance between pairwise MS/MS runs consisting of thousands of spectra.},
}
TY - JOUR
AU - Rieder, Vera
AU - Blank-Landeshammer, Bernhard
AU - Stuhr, Marleen
AU - Schell, Tilman
AU - Biß, Karsten
AU - Kollipara, Laxmikanth
AU - Meyer, Achim
AU - Pfenninger, Markus
AU - Westphal, Hildegard
AU - Sickmann, Albert
AU - Rahnenführer, Jörg
TI - DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs
T2 - BMC Bioinformatics
PY - 2017
VL - 18
DO - 10.1186/s12859-017-1514-2
AB - The classification of samples on a molecular level has manifold applications, from patient classification regarding cancer treatment to phylogenetics for identifying evolutionary relationships between species. Modern methods employ the alignment of DNA or amino acid sequences, mostly not genome-wide but only on selected parts of the genome. Recently proteomics-based approaches have become popular. An established method for the identification of peptides and proteins is liquid chromatography-tandem mass spectrometry (LC-MS/MS). First, protein sequences from MS/MS spectra are identified by means of database searches, given samples with known genome-wide sequence information, then sequence based methods are applied. Alternatively, de novo peptide sequencing algorithms annotate MS/MS spectra and deduce peptide/protein information without a database. A newer approach independent of additional information is to directly compare unidentified tandem mass spectra. The challenge then is to compute the distance between pairwise MS/MS runs consisting of thousands of spectra.
ER -
