Mass-Spectrometry Based Characterisation of Infant Whole Saliva Peptidome

MALDI(+) FT-ICR Mass Spectrometry (MS) Combined with Machine Learning toward Saliva-Based Diagnostic Screening for COVID-19

Rapid identification of existing respiratory viruses in biological samples is of utmost importance in strategies to combat pandemics. Inputting MALDI FT-ICR MS (matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry) data output into machine learning algorithms could hold promise in classifying positive samples for SARS-CoV-2. This study aimed to develop a fast and effective methodology to perform saliva-based screening of patients with suspected COVID-19, using the MALDI FT-ICR MS technique with a support vector machine (SVM). In the method optimization, the best sample preparation was obtained with the digestion of saliva in 10 μL of trypsin for 2 h and the MALDI analysis, which presented a satisfactory resolution for the analysis with 1 M. SVM models were created with data from the analysis of 97 samples that were designated as SARS-CoV-2 positives versus 52 negatives, confirmed by RT-PCR tests. SVM1 and SVM2 models showed the best results. The calibration group obtained 100% accuracy, and the test group 95.6% (SVM1) and 86.7% (SVM2). SVM1 selected 780 variables and has a false negative rate (FNR) of 0%, while SVM2 selected only two variables with a FNR of 3%. The proposed methodology suggests a promising tool to aid screening for COVID-19.

EndoProteoFASP as a Tool to Unveil the Peptidome-Protease Profile: Application to Salivary Diagnostics

In the quest to fully comprehend the proteolytic events leading to the generation of the salivary peptidome, we have developed a method for the sequential elution of salivary peptides throughout progressive endogenous proteolysis. By screening the time-dependent changes in the salivary peptidome we can predict the activity pattern of salivary proteases responsible for such peptide fingerprint and identify susceptible protein targets. Herein, we describe a step-by-step tutorial based on a filter-aided sample preparation (FASP) method, taking advantage of the endogenous salivary proteases armamentarium (endoProteoFASP), to produce new peptides from the salivary proteins, adding to those present in the sample at the time of collection. In this protocol, the different sets of peptides retrieved after sample elution are identified following a liquid chromatography-tandem mass spectrometry approach. The likelihood of a large set of endogenous proteases (collected from several public sources) to be responsible for the generation of such peptides can be predicted by the analysis of the cleavage site specificity by Proteasix ( http://proteasix.cs.man.ac.uk /) algorithm. The attained peptidome-protease profile can be useful to elucidate the peptidome dynamics and the proteolytic events underpinning pathophysiological phenomena taking place locally within the oral cavity. This may help clinicians to diagnose oral pathologies and develop preventive therapeutic plans.

One decade of salivary proteomics: current approaches and outstanding challenges

Efforts have been made in the last decade towards the complete characterization of saliva proteome using gel-based and gel-free approaches. The combination of these strategies resulted in the increment of the dynamic range of saliva proteome, which yield in the identification of more than 3,000 different protein species. Comparative protein profiling using isotope labeling and label free approaches has been used for the identification of novel biomarkers for oral and related diseases. Although progresses have been made in saliva proteome characterization, the comparative profiling in different pathophysiological conditions is still at the beginning if compared to other bodily fluids. The potential biomarkers identified so far lack specificity once common differentially expressed proteins were detected in the saliva of patients with distinct diseases. In addition, recent research works focused on saliva peptidome profiling already allowed a better understanding of peptides' physiological role in oral cavity. This review provides an overview of the major achievements in saliva proteomics giving emphasis to methodological concerns related with saliva collection, treatment and analysis, as well as the main advantages and pitfalls underlying salivary proteomic strategies and potential clinical outcomes.

Human infant saliva peptidome is modified with age and diet transition

In order to describe developmental changes in human salivary peptidome, whole saliva was obtained from 98 infants followed longitudinally at 3 and 6months of age. Data on teeth eruption and diet at the age of 6months were also recorded. Salivary peptide extracts were characterised by label-free MALDI-MS. Peptides differentially expressed between the two ages, and those significantly affected by teeth eruption or introduction of solid foods were identified by MALDI TOF-TOF and LC ESI MS-MS. Out of 81 peaks retained for statistical analysis, 26 were overexpressed at the age of 6months. Exposure to solid foods had a more pronounced effect on profiles (overexpression of nine peaks) than teeth eruption (overexpression of one peak). Differential peaks corresponded to fragments of acidic and basic PRPs, statherin and histatin. Comparison with existing knowledge on adult saliva peptidome revealed that proteolytic processing of salivary proteins is qualitatively quite comparable in infants and in adults. However, age and diet are modulators of salivary peptidome in human infants.