6 research outputs found
<i>MMSAT</i>: Automated Quantification of Metabolites in Selected Reaction Monitoring Experiments
Selected reaction monitoring (SRM) is a mass spectrometry-based
approach commonly used to increase analytical sensitivity and selectively
for specific compounds in complex metabolomic samples. While the goal
of well-designed SRM methods is to monitor for unique precursor–product
ion pairs, in practice this is not always possible due to the diversity
of the metabome and the resolution limits of mass spectrometers that
are capable of SRM. Isobaric or near-isobaric precursor ions with
different chromatographic properties but identical product ions often
arise in complex samples. Without analytical standards, such metabolites
will go undetected by conventional data analysis methods. Furthermore,
a single SRM method may include simultaneous monitoring of tens to
hundreds of different metabolites across multiple samples making quantification
of all detected ions a challenging task. To facilitate the analysis
of SRM data from complex metabolomic samples, we have developed the
Metabolite Mass Spectrometry Analysis Tool (<i>MMSAT</i>). <i>MMSAT</i> is a web-based tool that objectively quantifies
every metabolite peak detected in a set of samples and aligns peaks
across multiple samples to enable quantitative comparison of each
metabolite between samples. The analysis incorporates quantification
of multiple peaks/ions that have different chromatographic retention
times but are detected within a single SRM transition. We compare
the performance of <i>MMSAT</i> against existing tools using
a human glioblastoma tissue extract and illustrate its ability to
automatically quantify multiple precursors within each of three different
transitions. The Web-interface and source code is avaliable at http://www.cancerresearch.unsw.edu.au/crcweb.nsf/page/MMSAT
Table S2
Excel spreadsheet of labile disulphide bonds present in some molecules of a protein crystal but absent in others (same PDB, sheet 1), or present in some structures of a protein but absent in others (different PDB, sheet 2)
Table S1
Excel spreadsheet of unique disulphides in a culled set of X-ray structures described by G. Wang and R. Dunbrack, Jr. (file pdbaanr)
Supplementary material from Identification of allosteric disulfides from labile bonds in X-ray structures
Table S3, Figures S1-S
Table S2 from Identification of allosteric disulfides from labile bonds in X-ray structures
Excel spreadsheet of labile disulphide bonds present in some molecules of a protein crystal but absent in others (same PDB, sheet 1), or present in some structures of a protein but absent in others (different PDB, sheet 2)
Table S1 from Identification of allosteric disulfides from labile bonds in X-ray structures
Excel spreadsheet of unique disulphides in a culled set of X-ray structures described by G. Wang and R. Dunbrack, Jr. (file pdbaanr)