...are still under construction.


SugarQBits

SugarQBits is a collection of free software tools that enable the automated identification of glycopeptides using generic MS/MS Search Engines (e.g. MASCOT, Sequest-HT/Comet, X!Tandem, OMSSA). SugarQBits is a revamped version of the original SugarQb. While SugarQb was developed as a collection of software tools ("nodes") to the Proteome Discoverer environment (Thermo), SugarQBits are implemented in the cross-platform programming language Perl. The individual SugarQBits are stand-alone scripts that can be freely arranged to process any MS/MS data in the .mgf file format.

Disclaimer

The original SugarQb nodes (and their portations to PD 2.1 and 2.3) are still freely available to all researchers at "PD Nodes" of the Protein Chemistry Facility IMP/IMBA/GMI at the Vienna Biocenter, Austria.
For further information on the SugarQb algorithms and their use within PD, please refer to:


SugarQBits_DD.pl

SugarQBits_DD is a simple charge-deconvolution and deisotoping tool for MS/MS data. This algorithm lives off the mass-precision provided by modern instruments: the script accepts .mgf files and calculates the distances between peak pairs. If neighbouring peaks are found at the distance of 0.5 or 0.33 amu (+/- a user-defined absolute precision value; in amu), the charge state of these ions is considered as 2+ or 3+, respectively, and 1+ masses are calculated accordingly. Charge states > 3+ are currently not considered. Peaks of charge-state 2+ and 3+ are removed from the spectrum, and replaced by their corresponding 1+ masses with their original peak intensity values preserved. The charge-decovoluted and deisotoped spectra are stored in a new file ("_DD.mgf"). Of note, in conjunction with MS1toPseduoMGF.pl it can also be used to charge-deconvolute and deisotope MS1 data.

SugarQBits_GF.pl

SugarQBits_GF accepts .mgf files and simply extracts all spectra that contain a user-defined m/z value (+/- a user-defined absolute precision value, in amu) into a new .mgf file ("_GF.mgf"). In the context of a glycoproteomics workflow this tool can e.g. be used to focus further analysis on MS/MS spectra that contain the notorious HexNAc oxonium ion (m/z = 204.0867 amu).

SugarQBits_RepX.pl

SugarQBits_RepX accepts .mgf files and extracts the intensity values of a list of user-defined m/z value (+/- a user-defined absolute precision value, in amu) into a .csv file ("_RepIntensities.csv"), and removes them from a "cleaned" copy of the input .mgf-file ("_RepX.mgf"). This script can e.g. be used to extract intensity values of TMT-reporter ions, prior to peptide identification; or even for the reconstruction of extracted MS1 ion chromatograms.

SugarQBits_Kassonade.pl

SugarQBits_Kassonade is the central SugarQBit in glycoproteomics workflows. Similar to SugarQb, the script accepts .mgf files, tries to identify Y1 (i.e. peptide + HexNAc) ions and re-adjusts the spectrum precursor mass information accordingly. SugarQBits_Kassonade, however, works as an "open" glyco-search tool, as it not longer requires the use of a user-defined glycan mass list. The beta-version script can be obtained from j.stadlmann(at)boku.ac.at.

MS1toPseduoMGF.pl

MS1toPseduoMGF converts MS1 data (in the .ms1-file format) into the .mgf-file format.

MS2Oxoplot.pl

MS2Oxoplot is an abbreviated version of SugarQBits_RepX, merely extracting the intensity values of a list of user-defined m/z value (+/- a user-defined absolute precision value, in amu) into a .csv file ("_RepIntensities.csv"). It does not generate a reporter ion "cleaned" .mgf-file version.

SugarQBits are part of: