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Protein identification
• Digestion with trypsin or alternative enzymes
• Sample preparation with RPLC and retention time determination in chromatogram
• Peptide fragmentation (HCD) and m/z determination in MS/MS spectrum
• Peptide/protein identification with database searching software
Protein characterization
• Post-translational modifications (PTMs): phosphorylation, deamidation, methylation, nitration, acylation
• Other: cleavage site determination, amino acid substitution, disulfide crosslinking, chemical modifications
Quantitative proteomics
• Label-free quantitative LC-MS/MS
• Quantification of whole proteome in samples
• >100 sampling capacity
• Effecient and reproducible on-pellet digestion
• Separation on long nano LC column
• High-resolution MS on Orbitrap Fusion Lumos
• Accurate quantification models
Data analysis packages
• Protein/peptide & PTM identification: Proteome Discoverer (SEQUEST/MASCOT), MSGF+, PEAKS, Maxquant
• Peptide filtering & protein grouping: IDPicker, Scaffold
• Proteome-wide quantitative analysis: SIEVE, Skyline, DIANN, MaxQuant
Consultation
• Consultation on project design, data analysis and data interpretation is available upon request. Please contact lab staff.
• Consultation is strongly recommended for new users or for new projects.
• Consultation areas include de novo peptide sequencing, database interrogation, database searching, search results exporting and reporting, manual inspection of MS and MS/MS spectra data for validation of identification and quantitation analysis.