Software

MASS SPECTROMETRY


 * == CStat: Computational methods for biomarker discovery in proteomics and glycomics link] ==


 * == LipidAT: Automated analysis of lipidomic mass spectrometry data link] ==

> **GlyPID 2.0**, a software tool for accurate characterization of protein glycosylation through a combination of the following techniques. > > == == > > == == > == == >> ====[1]Mayampurath et. al., DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics. 2008 Apr 1;24(7):1021-3==== >> ====[2]Horn, et. al. Automated Reduction and Interpretation of High Resolution Electrospray Mass Spectra of Large Molecules. J. Am. Soc. Mass Spectrom. 2000, 11, 320-332.==== >> ====[3]Wu et. al. A Comp. Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry, Lecture Notes in Comp Sci, 2007, 4532:96-107.==== > > == ==
 * == GlyPID: N-glycosylation peptide identification tool link] ==
 * Accurate precursor ion mass calculated using THRASH–based deisotoping methods
 * A CID score calculated from Collision-Induced Dissociation (CID) spectra, similar to previous version of GlypID [1]. The model is based on spacing between fragment peaks indicative of glycan fragmentation.
 * A new HCD score calculated from High-energy C-trap Dissociation (HCD) spectra scoring technique based on the presence of characterestic glycan peaks. HCD is available on the LTQ Orbitrap XL.


 * == MultiGlycan: Glycan profiling tool (MALDI/LC-ESI) link] ==


 * MultiGlycan helps user to gather glycan profile information from LC-MS Spectra. It also reports quantity of specific glycan composition. We've developed two different versions of MultiGlycan: one for MALDI, and the other one for ESI. The MALDI version deconvolutes regular and overlapping glycans using simple model matching; The ESI version extracts glycans using adduct information.
 * "Automated Annotation and Quantification of Glycans Using Liquid Chromatography Mass Spectrometry (LC-MS)." Bioinformatics, C.Y. Yu, A. Mayampurath, Y. Hu, Y. Mechref and H. Tang, Apr 2013 ==


 * == GlycoFragwork: GlycoFragwork analyzes multiple pre-aligned LC-MS/MS datasets, and reports a list (termed as a 'glycomap') of identified intact glycopeptides with their mass, elution time and abundance link] ==


 * == GlycanSeq: Glycopeptide sequencing tool link] ==