Services

• Digestion with rypsin or alternative enzymes

• Sample preparation with RPLC and retention time determination in chromatogram

• Peptide fragmentation (CID/HCD/ETD) and m/z determination in MS/MS spectrum

• Peptide/protein identification with database searching software

• Label-free quantitative LC-MS/MS by IonStar

• 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

• Post-translational modifications (PTMs): phosphorylation, deamidation, methylation, nitration, acylation

• Other: cleavage site determination, amino acid substitution, disulfide crosslinking, chemical modifications

• Protein/peptide & PTM identification: Proteome Discoverer (SEQUEST/MASCOT), MSGF+, PEAKS, Maxquant

• Peptide filtering & protein grouping: IDPicker, Scaffold

• Proteome-wide quantitative analysis: SIEVE, Skyline, 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.