Concordia University

Software available to CBAMS users

Instrument operation

Xcalibur (v2.2) and MassLynx (v4.1) software for instrument control and data processing on the Thermo Scientific and Waters systems, respectively. These operating systems provide a fundamental platform for MS method setup, data acquisition, processing and reporting. MassLynx also offers a protein deconvolution tool for processing ESI data obtained on any mass spectrometer.


Proteome discoverer software (v2.1 SP1) is used to identify and quantify proteins in complex biological samples. This software simplifies a wide range of proteomics workflows, from protein and peptide identification to PTM analysis to metabolic labeling or isobaric mass tagging for quantitation. It supports multiple database search algorithms (SEQUEST, Z-Core, Mascot, etc.) and multiple dissociation techniques (CID, HCD, ETD) for more comprehensive analyses.

ProSight lite software (v1.2) is designed for top-down proteomics data analysis. It matches a single candidate protein sequence and its modifications against a set of mass spectrometric observations.


Compound discoverer software (v2.0) is de novo metabolite characterization software for the high-resolution Orbitrap MS platform. This software provides structure-based compound library, transformation library including dealkylation and dearylation predictions and phase I and II metabolism transformation products, improved multiple mass defect filtering, fragment ion search (FISh) scoring and fragment ion structure annotations and isotope pattern tracing to aid in the characterization of unknown endogenous and exogenous metabolites, metabolome annotation efforts and biomarker discovery.


LipidSearch software (v4.1) is designed to provide automated lipid identification and relative quantitative analysis and help to elucidate unknown lipid structures on the basis of high resolution accurate mass using unique database searching and scoring algorithms. LipidSearch software has lipid database containing >1.5 million lipid ions and their predicted fragment ions. The software algorithms support all common lipidomics workflows including shotgun, LC-MS, precursor ion scanning and neutral loss experiments.

Experimental design and data analysis

MODDE software (v10.1) for Design of Experiments (DOE) and quality analytics.

SIEVE software (v2.2) is used to process metabolomics data obtained on the Orbitrap platform and performs all steps of data processing including retention time alignment, peak picking, integration and simple statistical and pathway analysis.

SIMCA software (v14) for multivariate statistical analysis.

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