[In vitro protein phosphorylation as a template for SRM method development]

Comparison of heat-stable peptides using a multiple-reaction monitoring method to identify beef muscle tissue

Nowadays, proteomics is widely used as an analytical control method. A new method for determining animal tissue species-specificity based on a combination of two effective methods of food analysis, liquid chromatography (LC) and mass spectrometry (MS), was used in this work. Using this approach, it became possible to detect peptides. This work presents a comparison of species-specific, heat-stable peptides for the identification of beef. The objects of the study were native and boiled model mixtures containing beef with concentrations of 8% (w/w) and 16% (w/w). Pork was also added to the recipe to control for false-positive results. A high-performance liquid chromatography technique with mass spectrometric detection (LC-MS/MS) was used. Analysis of finished samples takes 25 minutes and is adapted to detect marker peptides. From the processing of the obtained data, three beef marker peptides were identified that were accepted as the best candidates. Two peptide prototypes, NDMAAQYK and YLEFISDAIIHVLHAK from the myoglobin protein and SNVSDAVAQSAR from the triosephosphate isomerase protein, were selected as potential biomarkers. For all samples, the signal-to-noise ratio (S/N) was set above 10. Temperature was not found to affect the structure and detection of marker peptides in samples with a muscle tissue concentration of 8% (w/w) at p <0.05. This approach is universally applicable for comparing biomarkers of other types of meat and to identify the most suitable candidates.

[Use of de novo sequencing for proteins identification]

Three de novo sequencing programs (Novor, PEAKS and PepNovo+) have been used for identification of 48 individual human proteins constituting the Universal Proteomics Standard Set 2 (UPS2) ("Sigma-Aldrich", USA). Experimental data have been obtained by tandem mass spectrometry. The MS/MS was performed using pure UPS2 and UPS2 mixtures with E. coli extract and human plasma samples. Protein detection was based on identification of at least two peptides of 9 residues in length or one peptide containing at least 13 residues. Using these criteria 13 (Novor), 20 (PEAKS) and 11 (PepNovo+) proteins were detected in pure UPS2 sample. Protein identifications in mixed samples were comparable or worse. Better results (by ~20%) were obtained using prediction included high quality identified fragment (TAG) containing at least 7 residues and unidentified additional masses at N- and C-termini (PepNovo+). The latter approach confidently recognized mass-spectrometric artefacts (and probably PTM). Atypical mass changes missed in UNIMOD DB were found (PepNovo+) to be statistically significant at the C-terminus (+23.02, +26.04 and +27.03). Using peptides containing these modifications and milder detection threshold 41 of 48 UPS2 proteins were identified.

Is myelin basic protein a potential biomarker of brain cancer?

Myelin basic protein is a potential biomarker for the central nervous system diseases in which the myelin sheath is destroyed. Using pseudo-selected reaction monitoring and the method of standard additions, we have measured the myelin basic protein level in the cerebrospinal fluid of patients with neurotrauma (n = 6), chronic neurodegenerative diseases (n = 2) and brain cancer (n = 5). Myelin basic protein was detected only in four out of five cerebrospinal fluid samples of patients with brain cancer. The cerebrospinal fluid myelin basic protein level ranged from 3.7 to 8.8 ng ml^-1. We suggest that monitoring of myelin basic protein in cerebrospinal fluid can serve as a diagnostic test for the brain cancer.