Assists users to detect candidate proteins whose abundances are post-transcriptionally controlled by the anaphase promoting complex/cyclosome (APC/C). PSS is a program utilizing abundance profiles from quantitative proteomics experiments with the isobaric mass tagging (IMT) strategy. It introduces advances in exploratory data analysis that enables protein-level inference based on peptide-level measurements.
Calculates chemical formulas for fragment ions where the structure of the molecular ion is known. FFC is able to cope with general molecular rearrangement reactions occurring during GC/MS measurements.
Assists users in the automatization of species identification. This algorithm is a machine learning approach that aims to reduce the manual work required for analyzing high-throughput collagen peptide mass fingerprints (PMFs) data of ancient bone samples. This method was able to reach taxonomic resolution at family/sub-family levels within the vertebrata.
Processes liquid chromatography-high resolution mass spectrometry (LC-HRMS) data from analysis of adducted human serum albumin (HAS) peptides. adductomicsR is an R package that uses a model spectrum for a peptide to obtain masses of putative adducts and quantitates adduct levels. It provides plots of mass spectra, allowing the assessment of validity of each putative adduct. The software can correct for retention-time drift, discover and quantify putative adducts along with those for a housekeeping peptide and internal standard.
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