Protein identification

Identification of proteins by bottom-up LC-MS/MS (peptide mapping)

Looking for a precise and reliable method for protein identification? We offer comprehensive bottom-up LC-MS/MS proteomic analysis, including peptide mapping for accurate protein composition determination and detection of post-translational modifications in biological samples. Our approach is based on untargeted proteomic analysis (shotgun proteomics), which allows for broad profiling of protein content in test material – from simple solutions to complex biological matrices.

What is the bottom-up method?

The bottom-up method is a commonly used approach that involves enzymatic digestion of proteins (usually using trypsin), followed by analysis of the resulting peptides using LC-MS/MS mass spectrometry. The experimental data (MS/MS spectra) are matched to protein sequences stored in reputable databases such as UniProt and NCBI.

In advanced studies where confidence in the amino acid composition of the protein is crucial, we use rich EAD (Electron-Activated Dissociation) fragmentation, thanks to the use of an advanced ZenoTOF 7600 (SCIEX) instrument that has 2 collision chambers: CID and EAD. This makes it possible to distinguish even difficult-to-identify amino acids, such as leucine vs. isoleucine. This increases the sensitivity, accuracy and specificity of the analysis, which is crucial for advanced scientific and industrial research.

Offer Scope:

✅ Protein identification – qualitative analysis

• Sample preparation: denaturation, reduction, alkylation, enzymatic digestion

• Matching MS/MS data with theoretical sequences from databases (PEAKS Studio, DIA-NN, Skyline)

• Detection of post-translational modifications (PTMs): phosphorylation, oxidation, acetylation, deamidation and many others

• Mutation detection – sequence variants

• Evaluation of sequence coverage (protein sequence coverage)

• Calculation of Score and FDR values determining the certainty of identification

✅ Comparative analysis of proteins

• Determination of the composition of the protein mixture

• Comparison of samples to assess differences in protein expression

• Use of acquisition strategies: DDA (IDA), DIA (SWATH)

✅ Types of samples analyzed

• Samples from the solution

• Gel samples

• Lyophilized samples

• Complex biological matrices including sample preparation (by prior arrangement)

• other types of samples provided by the customer