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 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.


Update date: December, 2022