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Additional file 1: Table S1. Identified proteins in CM in the group of controls and in patients affected by endometriosis.

In the present study, we show that the heterogeneous mixture of glycoforms of the basic salivary proline-rich protein 3M, encoded by PRB3-M locus, is a major component of the acidic soluble fraction of human whole saliva in the first years of life. Reversed-phase high-performance liquid chromatography with high-resolution electrospray ionization mass spectrometry analysis of the intact proteoforms before and after N-deglycosylation with Peptide-N-Glycosidase F and tandem mass spectrometry sequencing of peptides obtained after Endoproteinase GluC digestion allowed the structural characterization of the peptide backbone and identification of N- and O-glycosylation sites. The heterogeneous mixture of the proteoforms derives from the combination of 8 different neutral and sialylated glycans O-linked to Threonine 50, and 33 different glycans N-linked to Asparagine residues at positions 66, 87, 108, 129, 150, 171, 192, and 213.

In the present study, we show that the heterogeneous mixture of glycoforms of the basic salivary proline-rich protein 3M, encoded by PRB3-M locus, is a major component of the acidic soluble fraction of human whole saliva in the first years of life. Reversed-phase high-performance liquid chromatography with high-resolution electrospray ionization mass spectrometry analysis of the intact proteoforms before and after N-deglycosylation with Peptide-N-Glycosidase F and tandem mass spectrometry sequencing of peptides obtained after Endoproteinase GluC digestion allowed the structural characterization of the peptide backbone and identification of N- and O-glycosylation sites. The heterogeneous mixture of the proteoforms derives from the combination of 8 different neutral and sialylated glycans O-linked to Threonine 50, and 33 different glycans N-linked to Asparagine residues at positions 66, 87, 108, 129, 150, 171, 192, and 213.

Alzheimer's disease (AD) is a progressive form of dementia characterized by increased production of amyloid-β plaques and hyperphosphorylated tau protein, mitochondrial dysfunction, elevated oxidative stress (OS), reduced protein clearance among others. Several studies showed systemic modifications of immune and inflammatory systems due, in part, to decreased levels of T cells in peripheral blood during AD. Considering that oxidative stress, both in the brain and in the periphery, can influence the activation and differentiation of T cells, we investigated the nitro-oxidized proteome of blood T cells derived from AD patients compared to non-demented subjects (NSD) by using a redox proteomic approach. We identified eleven proteins showing increasing levels of 3-nitrotyrosine (3-NT) in AD T cells compared with NSD. These proteins are involved in energy metabolism, transcriptional regulation and antioxidant response and can help to clarify molecular mechanism that impact on the reduced T cells differentiation in AD. Our results highlight the role of peripheral OS in T cells related to immune-senescence during AD pathology focusing on the specific target of protein nitration that can be suitable to further therapies.

In 1620 Francis Bacon published the Novum Organum, opening a new era in the experimental research of natural phenomena based on the principle of induction. When describing this principle, he anticipated the effects of advances in science, engineering, and technology. Such a principle opposed to the a priori deductive knowledge has been the corner stone for proteomics investigations based on the unsupervised observation of protein modulation in a given biological background. This approach has led to contrasting evidence in the scientific literature from the last 20 years, primarily based on the discoveries of unexpected molecular association, to the complexity of protein modulation and often to the strong will of the investigators to potentially extend the application of their experimental observation beyond the given experimental framework. A wellknown example of this experience is available in the quest for protein biomarker discovery in clinical proteomics campaigns. Unfortunately inductive methods may only provide a probability for a given argument in a well-defined framework and their wide extension has been proved by a number of philosophers, e.g. Karl Popper and Bertrand Russell, to potentially lead to false conclusions. Although the introduction of a priori based proteomics investigations by applying targeted SRM (Selective Reaction Monitoring) design on proteotypic transition brought a new impulse, many researchers still prefer inductive experimental methods in order to obtain novel evidences. Inductive proteomics still provides a passage through the Pillars of Hercules, which for the ancients, symbolized the limits of possible human explorations. Beyond the pillars lay the edge of current knowledge. Thus, their crossing represents our aim toward new uncharted biological molecular mechanisms. These open-platform investigations are presently achieving a higher experimental confidence, providing large dataset collections for a more rigorous description of the experimental framework for the application of the reported results. In this themed issue dedicated to proteomics we have a clear example of such an extended description. The paper from Claudia Desiderio et al., dedicated to ‘Integrated proteomic platforms for the comparative characterization ofmedulloblastoma and pilocytic astrocytoma pediatric brain tumors’ (DOI: 10.1039/ C5MB00076A), provides a good example of such a definition. Following the research on medulloblastoma, Maurizio Ronci et al. (DOI: 10.1039/C5MB00034C) addressed the protein determinants associated with the stemness phenotype in hedgehog models. Glioblastoma response to nitric oxide releasing compounds is addressed in the paper by Roberta Leone et al. (DOI: 10.1039/ C4MB00725E) by applying 2DE-DIGE approaches. Redox modifications of proteins are further addressed in a welldefined model for microglia exposure to beta amyloid peptide in the work of Virginia Correani et al. (DOI: 10.1039/C4MB00703D) and in the paper by Claudia D’Anna et al. (DOI: 10.1039/C5MB00188A) on the impact of cigarette smoke on fibroblasts. While clinical proteomics investigations based on bottom-up approaches have been proving their limits, top-down proteomics investigations represent a fundamental approach to achieve the high specificity required. The current FDA 510k and CE-IVD approved proteomics-based platforms for clinical microbiology (MALDI Biotyper and Vitek MS) are in fact both based on a top-down experimental set-up. In this light, the work from Monica Sanna et al. (DOI: 10.1039/C4MB00719K) may a Department of Experimental Medicine and Surgery, University of Rome ‘‘Tor Vergata’’, Via Montpellier 1, Rome, Italy. E-mail: andrea.urbani@uniroma2.it b IRCCS-Fondazione S. Lucia, Rome, Italy c Section of Proteomics, Istituto Sperimentale Italiano L. Spallanzani, University of Milano, Milano, Italy d Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy e Dipartimento di Scienze Ambientali, Universita della Tuscia, Viterbo, Italy f Department of Life Sciences, University of Siena, Italy g Department of Theoretical and Applied Sciences, and Center of Neuroscience, University of Insubria, Busto Arsizio, Italy h Institute of Biochemistry and Clinical Biochemistry, Faculty of Medicine, Catholic University, Piazza A. Gemelli, Rome, Italy. E-mail: massimo.castagnola@icrm.cnr.it i Istituto di Chimica del Riconoscimento Molecolare, CNR, Rome, Italy DOI: 10.1039/c5mb90021b

The combination of top-down and bottom-up platforms was utilized for the LC-MS proteomic characterization of the intracystic fluid of adamantinomatous craniopharyngioma pediatric brain tumor disease. Proteins and peptides characterization was achieved by high-resolution LC-ESI-LTQ-Orbitrap-MS analysis while low-resolution LC-ESI-IT-MS was applied for the complete screening of the samples and the evaluation of the protein distribution within patients. Top-down analyses were applied to liquid/liquid extracted samples while bottom-up analyses were performed after trypsin digestion of both untreated and pretreated samples. The two proteomic approaches were complementary for the characterization of the proteome of craniopharyngioma intracystic fluid. Proteins and peptides involved in inflammation, mineralization processes and lipid transport were identified, in agreement with the calcium flecks, cholesterol granules and bone residues characteristic of this fluid. Apolipoprotein A-I, A-II, C-I and J, hemoglobin fragments, ubiquitin, α-2-HS-glycoprotein or fetuin A, α-1-antichymotrypsin, vitamin D binding protein, and α-1-acid glycoprotein were characterized. These data could be relevant for the comprehension of the processes involved in the pathogenesis of the disease and the development of the cyst and could contribute to the individuation of therapeutic targets for the reduction of the cyst volume delaying and/or avoiding invasive surgical treatments.