Research Tools & Softwares

Data Processing and Analysis Software

1. Proteome Discoverer (Thermo Fisher Scientific) - For protein identification and quantification from mass spectrometry data.

2. MaxQuant - A popular open-source software for quantitative proteomics.

3. MASCOT (Matrix Science) - A widely used search engine for identifying proteins by peptide mass fingerprinting.

4. PEAKS (Bioinformatics Solutions Inc.) - For de novo sequencing, protein identification, and quantification.

5. Skyline - Open-source software for targeted proteomics, including MRM/PRM data analysis.

6. MassHunter (Agilent Technologies) - For data acquisition and analysis, including qualitative and quantitative analysis.

7. MSFragger - Fast database search engine for shotgun proteomics.

8. Byonic (Protein Metrics) - For identifying peptides with modifications and analyzing glycoproteomics data.

Quantification Software

1. Label-Free Quantification (LFQ)

   • Progenesis QI (Waters Corporation) - For label-free quantification of small molecules and proteins.

   • Spectronaut (Biognosys) - For processing data-independent acquisition (DIA) data.

2. Label-Based Quantification

   • iTRAQ/TMT Quantification

     • IsobarQuant - For quantifying isobaric tag data (iTRAQ, TMT).

     • MaxQuant - Also supports label-based quantification.

   • SILAC Quantification

     • MSQuant - For quantifying stable isotope labeling by amino acids in cell culture (SILAC) data.

Metabolomics Software

1. MetaboAnalyst - A web-based tool for metabolomics data analysis and interpretation.

2. XCMS - An R-based software for processing and analyzing untargeted metabolomics data.

3. MS-DIAL - For untargeted metabolomics, lipidomics, and MS imaging.

4. MZmine - An open-source framework for processing and visualizing mass spectrometry-based molecular profile data

Structural Analysis & Annotation

1. MS/MS Fragmentation Tools

   • ProteinProspector - For protein characterization and post-translational modification (PTM) analysis.

   • pFind - For peptide and protein identification from MS/MS data.

   • Maestro (Sciex) - For automated protein and peptide identification.

2. Glycomics

   • GlycoWorkbench - For the annotation of glycan structures from MS data.

   • GlycoMod - For calculating the composition of glycopeptides from mass spectrometric data.

3. Lipidomics

   • LipidSearch (Thermo Fisher Scientific) - For identifying and quantifying lipids.

   • LipidXplorer - An open-source software for shotgun lipidomics.

Statistical Analysis and Visualization

1. Perseus - A platform for statistical analysis of proteomics data, often used in conjunction with MaxQuant.

2. R packages - Including MSnbase, Proteomics, and Metabolomics, which offer various tools for data processing and analysis in R.

3. Principal Component Analysis (PCA) Tools - Often integrated into other software for dimensionality reduction and visualization.

Imaging Software

1. SCiLS Lab (Bruker Daltonics) - For analyzing mass spectrometry imaging (MSI) data.

2. MALDI-MSI - An open-source toolbox for visualization and analysis of MSI data.