ModifiComb, a New Proteomic Tool for Mapping Substoichiometric Post-translational Modifications, Finding Novel Types of Modifications, and Fingerprinting Complex Protein Mixtures

• Published in: Molecular & cellular proteomics Vol. 5; no. 5; pp. 935 - 948
• Main Authors: Savitski, Mikhail M., Nielsen, Michael L., Zubarev, Roman A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.05.2006; American Society for Biochemistry and Molecular Biology
• Subjects: Adult; Algorithms; Amino Acid Sequence; Escherichia coli - chemistry; False Positive Reactions; Humans; Male; Medicin och hälsovetenskap; Methylation; Molecular Sequence Data; Peptide Mapping - methods; Protein Processing, Post-Translational; Proteins - analysis; Proteins - chemistry; Proteomics - methods; Reproducibility of Results; Saliva - chemistry; Time Factors; Triose-Phosphate Isomerase - chemistry; Tumor Cells, Cultured
• ISSN: 1535-9476; 1535-9484
• DOI: 10.1074/mcp.T500034-MCP200

A major challenge in proteomics is to fully identify and characterize the post-translational modification (PTM) patterns present at any given time in cells, tissues, and organisms. Here we present a fast and reliable method (“ModifiComb”) for mapping hundreds types of PTMs at a time, including novel and unexpected PTMs. The high mass accuracy of Fourier transform mass spectrometry provides in many cases unique elemental composition of the PTM through the difference ΔM between the molecular masses of the modified and unmodified peptides, whereas the retention time difference ΔRT between their elution in reversed-phase liquid chromatography provides an additional dimension for PTM identification. Abundant sequence information obtained with complementary fragmentation techniques using ion-neutral collisions and electron capture often locates the modification to a single residue. The (ΔM, ΔRT) maps are representative of the proteome and its overall modification state and may be used for database-independent organism identification, comparative proteomic studies, and biomarker discovery. Examples of newly found modifications include +12.000 Da (+C atom) incorporation into proline residues of peptides from proline-rich proteins found in human saliva. This modification is hypothesized to increase the known activity of the peptide.