Tandem MS Experiments Research Articles

Hydrophilic interaction liquid chromatography–electrospray ionization-tandem mass spectrometry of a complex mixture of native and oxidized phospholipids

A mixture of native and oxidized phospholipids (PLs), generated by the soybean lipoxygenase type V-catalyzed partial oxidation of a lipid extract obtained from human platelets, was analyzed by Hydrophilic Interaction Liquid Chromatography-ElectroSpray Ionization-Tandem Mass Spectrometry (HILIC–ESI-MS/MS). The complexity of the resulting mixture was remarkable, considering that the starting lipid extract, containing (as demonstrated in a previous study) about 130 native PLs, was enriched with enzymatically generated hydroperoxylated derivatives and chemically generated hydroxylated forms of PLs bearing polyunsaturated side chains. Nonetheless, the described analytical approach proved to be very powerful; indeed, focusing on phosphatidylcolines (PCs), the most abundant PL class in human platelets, about fifty different native/oxidized species could be identified in a single HILIC–ESI-MS/MS run. Low-energy collision induced dissociation tandem MS (CID-MS/MS) experiments on chromatographically separated species showed single neutral losses of H2O2 and H2O to be typical fragmentation pathways of hydroperoxylated PCs, whereas a single H2O loss was observed for hydroxylated ones. Moreover, diagnostic losses of n-hexanal or n-pentanol were exploited to recognize PCs hydroperoxylated on the last but five carbon atom of a ɷ-6 polyunsaturated side chain. Despite the low resolution of the 3D ion trap mass analyzer used, the described HILIC–ESI-MS/MS approach appears very promising for the identification of oxidized lipids in oxidatively stressed complex biological systems.

An Efficient Approach to Evaluate Reporter Ion Behavior from MALDI-MS/MS Data for Quantification Studies Using Isobaric Tags.

Protein quantification, identification, and abundance determination are important aspects of proteome characterization and are crucial in understanding biological mechanisms and human diseases. Different strategies are available to quantify proteins using mass spectrometric detection, and most are performed at the peptide level and include both targeted and untargeted methodologies. Discovery-based or untargeted approaches oftentimes use covalent tagging strategies (i.e., iTRAQ, TMT), where reporter ion signals collected in the tandem MS experiment are used for quantification. Herein we investigate the behavior of the iTRAQ 8-plex chemistry using MALDI-TOF/TOF instrumentation. The experimental design and data analysis approach described is simple and straightforward, which allows researchers to optimize data collection and proper analysis within a laboratory. iTRAQ reporter ion signals were normalized within each spectrum to remove peptide biases. An advantage of this approach is that missing reporter ion values can be accepted for purposes of protein identification and quantification without the need for ANOVA analysis. We investigate the distribution of reporter ion peak areas in an equimolar system and a mock biological system and provide recommendations for establishing fold-change cutoff values at the peptide level for iTRAQ data sets. These data provide a unique data set available to the community for informatics training and analysis.

Tandem Native Mass-Spectrometry on Antibody-Drug Conjugates and Submillion Da Antibody-Antigen Protein Assemblies on an Orbitrap EMR Equipped with a High-Mass Quadrupole Mass Selector.

Native mass spectrometry is emerging as a powerful tool for the characterization of intact antibodies and antibody-based therapeutics. Here, we demonstrate new possibilities provided by the implementation of a high mass quadrupole mass selector on the recently introduced Orbitrap Exactive EMR mass spectrometer. This configuration allows precursor ion selection, and thus tandem mass spectrometry experiments, even on analytes with masses in the hundreds of kilodaltons. We apply tandem mass spectrometry to localize the drug molecules in the therapeutic antibody-drug conjugate brentuximab vedotin, which displays a heterogeneous drug load. Our tandem MS data reveal that drug conjugation takes place nonhomogeneously to cysteine residues both on the light and heavy chains. Next, we analyzed how many antigens bind to IgG hexamers, based on a recently described antibody mutant IgG1-RGY that forms hexamers and activates complement in solution. The fully saturated IgG1-RGY-antigen complexes displayed a stoichiometry of IgG:CD38 of 6:12, possessing a molecular weight of about 1.26 MDa and demonstrating that IgG assembly does not hamper antigen binding. Through tandem MS experiments, we retrieve information about the spatial arrangement and stoichiometry of the subunits within this complex. These examples underscore the potential of this further modified Orbitrap-EMR instrument especially for the in-depth characterization by native tandem mass spectrometry of antibodies and antibody-based constructs.

Characterization of quillaja bark extracts and evaluation of their purity using liquid chromatography–high resolution mass spectrometry

In the course of development of semi-preparative liquid chromatographic methods for the isolation of individual quillaja saponins from Quillaja saponaria (L.), some commercially available quillaja bark extracts revealed a distinctive and characteristic pattern of additional peaks in the chromatogram that could not be attributed to saponins commonly present in quillaja. To identify these peaks, analytical procedures based on HPLC coupled with high resolution MS detection were optimized which allowed the identification of the additional saponins Mi saponin A, Mi saponin B, Mi saponin C, madhucoside A and madhucoside B. These compounds are known to be the main saponins of the Indian plant Madhuca longifolia (L.). Tandem MS experiments were performed for the unambiguous assignment of the sapogenin. Madhuca saponins yielded a characteristic fragment of protobassic acid, whereas quillaja saponins showed a fragment of quillaic acid as expected. In addition, samples from madhuca seed kernels were analysed to verify the origin of the characteristic chromatographic peak pattern observed frequently in commercially available quillaja bark extracts.

Insights on the mechanism of thioredoxin reductase inhibition by Gold N-heterocyclic carbene compounds using the synthetic linear Selenocysteine containing C-terminal peptide hTrxR(488-499): An ESI-MS investigation

Gold-based drugs typically behave as strong inhibitors of the enzyme thioredoxin reductase (hTrxR), possibly as the consequence of direct Gold(I) coordination to its active site selenocysteine. To gain a deeper insight into the molecular basis of enzyme inhibition and prove gold-selenocysteine coordination, the reactions of three parent Gold(I) NHC compounds with the synthetic C-terminal dodecapeptide of hTrxR containing Selenocysteine at position 498, were investigated by electrospray ionization mass spectrometry (ESI-MS). Formation of 1:1 Gold-peptide adducts, though in highly different amounts, was demonstrated in all cases. In these adducts the same [Au-NHC]+ moiety is always associated to the intact peptide. Afterward, tandem MS experiments, conducted on a specific Gold-peptide complex, pointed out that Gold is coordinated to the selenolate group. The relatively large strength of the Gold-selenolate coordinative bond well accounts for potent enzyme inhibition typically afforded by these Gold(I) compounds. In a selected case, the time course of enzyme inhibition was explored. Interestingly, enzyme inhibition turned out to show up very quickly and reached its maximum just few minutes after mixing. Overall, the present results offer some clear insight into the process of thioredoxin reductase inhibition by Gold-based compounds.

Structural Characterisation of Malonyl Flavonols in Leek (Allium porrum L .) Using High-performance Liquid Chromatography and Mass Spectrometry

Vegetables contain a variety of phytochemicals that have the ability to modify enzymatic and chemical reactions, and therefore may have a positive influence on human health. In particular kaempferol is known to possess anti-carcinogenic activity. The purpose of this work was to determine the structure of glycosylated kaempferol derivatives, acylated with malonic acid on the sugar portion. A methanolic extract of the leaves of Allium porrum L. was submitted to fractionation procedures through semi-preparative HPLC/UV-MS techniques. The collected fractions were evaluated by accurate tandem mass spectrometry experiments using an electrospray ionisation (ESI) quadrupole time-of-flight instrument. Isolated compounds were hydrolysed in order to obtain information on the ester moieties. The structures of five compounds not previously reported in leek were determined. The molecules are mono-hexose, di-hexose and coumaroyl, feruloyl and caffeoyl acylated di-hexose derivatives of kaempferol. The common characteristic of the structures relies on the presence of the malonyl moiety on the primary alcoholic function of the sugar immediately linked to the aglycone. Accurate tandem MS experiments and basic hydrolysis treatments revealed a sequence of the acylated glycosidic moieties. A set of secondary metabolites of the aerial part of Allium porrum L. (leek) was identified and characterised by ESI/MS(2) . Knowledge of the presence of these first-reported compounds in leek could provide the means for fully understanding of the metabolism of this plant in relation to the biosynthesis of the phenolics.

A Differentially Pumped Dual Linear Quadrupole Ion Trap (DLQIT) Mass Spectrometer: A Mass Spectrometer Capable of MSn Experiments Free From Interfering Reactions

A novel differentially pumped dual linear quadrupole ion trap (DLQIT) mass spectrometer was designed and built to facilitate tandem MS experiments free from interfering reactions. The instrument consists of two differentially pumped Thermo Scientific linear quadrupole ion trap (LQIT) systems that have been connected via an ion transfer octupole encased in a machined manifold. Tandem MS experiments can be performed in the front trap and then the resulting product ions can be transferred via axial ejection into the back trap for further, independent tandem MS experiments in a differentially pumped area. This approach allows the examination of consecutive collision-activated dissociation (CAD) and ion-molecule reactions without unwanted side reactions that often occur when CAD and ion-molecule reactions are examined in the same space. Hence, it greatly facilitates investigations of ion structures. In addition, the overall lower pressure of the DLQIT, as compared to commercial LQIT instruments, results in a reduction of unwanted side reactions with atmospheric contaminants, such as water and oxygen, in CAD and ion-molecule experiments.

Generation of a Dynamic System of Three‐Dimensional Tetrahedral Polycatenanes

Generation of a Dynamic System of Three‐Dimensional Tetrahedral Polycatenanes

Measurements of Calf Muscle Oxygenation during Standing and Exercise in Patients with Chronic Venous Insufficiency

Background: Varicose vein tissues have been shown to have differential metabolic profiles as compared with non-varicose veins, suggesting a metabolic component of the disease. Vein wall stretch has been suggested as a potential etiological factor in the development of varicose veins. However, the relation between vein wall stretch and the metabolic profile of the vein wall is unclear. The aim of the study was to determine whether vein wall stretch alters the metabolic profile of the vein wall. Methods: Segments of male rat inferior vena cava (IVC) were suspended in tissue bath under 0.5 g basal tension for 1 hour, and a control contraction to phenylephrine (PHE, 10 5 M) and KCl (96 mM) was elicited. The veins were then exposed to normal 0.5 g or high 2 g tension for short 4 or prolonged 18 hours (five vein segments in each group). The veins were frozen, then hydrophilic and organic metabolites were extracted using a bilayer extraction method. Aqueous and organic extracts obtained from stretched (2 g tension) and non-stretched (0.5 g basal tension) IVC segments were run on 1-dimensional H Nuclear Magnetic Resonance (NMR) spectroscopy (800 MHz) and liquid-chromatography coupled to Mass Spectrometry (LC-MS) LCT QTOF premier (Waters Corporation, Milford, MA), respectively. Spectra acquired from NMR and chromatograms from LC-MS were mathematically modelled and statistically analysed using multivariate statistical models including MATLAB (Mathworks ) and SIMPCA-P + 12.0 (UMETRICS Sweden). 2-Dimensional NMR and tandem MS experiments were performed on selected samples for structural elucidation of molecules. Results: H NMR spectra of aqueous extracts of stretched and nonstretched veins for 4 hrs revealed the presence of several metabolites including leucine, isoleucine, valine, creatine, myo-inositol, choline, glucose, and aspartate. There was no significant difference in aqueous or lipid metabolic profiles of non-stretched and stretched IVC segments for 4 hours. Univariate analysis revealed increased concentrations of leucine, isoleucine, and valine metabolites in IVC segments stretched as compared with nonstretched for 18 hours (P value range, 0.01-0.004). Orthogonal partial least square-discriminatory (OPLS-DA) identified triglycerides moieties as a differentiating markers and were present in higher concentrations in stretched segments as compared with non-stretched vein segments for 18 hours (P value range, 0.01-0.003). Conclusions: We have shown, for the first time, a complete metabolic profile of aqueous and organic extracts from rat veins subjected to normal (0.5 g) and high (2 g) mechanical stretch. Elucidation of cellular pathways linked to these differential metabolites may disclose cellular mechanisms affected by stretch and may improve our understanding about varicose vein disease.

Investigating the Chemical Changes of Chlorogenic Acids during Coffee Brewing: Conjugate Addition of Water to the Olefinic Moiety of Chlorogenic Acids and Their Quinides

Coffee is one of the most popular and consumed beverages in the world and is associated with a series of benefits for human health. In this study we focus on the reactivity of chlorogenic acids, the most abundant secondary metabolites in coffee, during the coffee brewing process. We report on the hydroxylation of the chlorogenic acid cinnamoyl substituent by conjugate addition of water to form 3-hydroxydihydrocaffeic acid derivatives using a series of model compounds including monocaffeoyl and dicaffeoylquinic acids and quinic acid lactones. The regiochemistry of conjugate addition was established based on targeted tandem MS experiments. Following conjugate addition of water a reversible water elimination yielding cis-cinnamoyl derivatives accompanied by acyl migration products was observed in model systems. We also report the formation of all of these derivatives during the coffee brewing process.

Characterization of Protein Glycosylation in Francisella tularensis subsp. holarctica: IDENTIFICATION OF A NOVEL GLYCOSYLATED LIPOPROTEIN REQUIRED FOR VIRULENCE

FTH_0069 is a previously uncharacterized strongly immunoreactive protein that has been proposed to be a novel virulence factor in Francisella tularensis. Here, the glycan structure modifying two C-terminal peptides of FTH_0069 was identified utilizing high resolution, high mass accuracy mass spectrometry, combined with in-source CID tandem MS experiments. The glycan observed at m/z 1156 was determined to be a hexasaccharide, consisting of two hexoses, three N-acetylhexosamines, and an unknown monosaccharide containing a phosphate group. The monosaccharide sequence of the glycan is tentatively proposed as X-P-HexNAc-HexNAc-Hex-Hex-HexNAc, where X denotes the unknown monosaccharide. The glycan is identical to that of DsbA glycoprotein, as well as to one of the multiple glycan structures modifying the type IV pilin PilA, suggesting a common biosynthetic pathway for the protein modification. Here, we demonstrate that the glycosylation of FTH_0069, DsbA, and PilA was affected in an isogenic mutant with a disrupted wbtDEF gene cluster encoding O-antigen synthesis and in a mutant with a deleted pglA gene encoding pilin oligosaccharyltransferase PglA. Based on our findings, we propose that PglA is involved in both pilin and general F. tularensis protein glycosylation, and we further suggest an inter-relationship between the O-antigen and the glycan synthesis in the early steps in their biosynthetic pathways.

RRKM modeling of collision activated reaction/collision induced dissociation experiments: Energy profile determination for phenylethyne incorporation on palladium (II)–phosphinous acid complex

We have recently reported a detailed ESI-collision activated reaction/collision activated reaction (ESI-CAR/CAR) and ESI-collision activated reaction/collision induced dissociation (ESI-CAR/CID) mass spectrometric investigation, combined with quantum chemistry calculations, to elucidate the reaction mechanism of [2+1] cycloaddition between alkyne and norbornadiene using a Pd(II) complex as catalyst. The coordination mode of alkyne on the metal was shown to be an essential preliminary step of the reaction, but mass spectrometric results were difficult to rationalize according to changes in the experimental conditions. In this work we present a detailed RRKM modeling of these experiments using MassKinetics software. We demonstrate how essential kinetic modeling is in order to interpret these experiments: both for phenomenological aspects (understand spectra and changes in their pattern due to energetic modifications) and as a link between quantum chemistry results and tandem MS experiments. Complete energy profile for isomerization and decomposition processes of [Pd[(t-Bu)(Ph)PO]2H+PhCCH]+ complexes has been determined through kinetic modeling of experimental data.Detailed modeling procedure is presented; approximations discussed and validated for quantitative comparison with quantum chemistry calculations. Agreement between isomerization barriers determined with kinetic modeling of experimental data and those determined through quantum chemistry was found to be within few kcal/mol supporting the validity of the approach and assumptions made in the model.

Human Urinary Glycoproteomics; Attachment Site Specific Analysis of N- and O-Linked Glycosylations by CID and ECD

Urine is a complex mixture of proteins and waste products and a challenging biological fluid for biomarker discovery. Previous proteomic studies have identified more than 2800 urinary proteins but analyses aimed at unraveling glycan structures and glycosylation sites of urinary glycoproteins are lacking. Glycoproteomic characterization remains difficult because of the complexity of glycan structures found mainly on asparagine (N-linked) or serine/threonine (O-linked) residues. We have developed a glycoproteomic approach that combines efficient purification of urinary glycoproteins/glycopeptides with complementary MS-fragmentation techniques for glycopeptide analysis. Starting from clinical sample size, we eliminated interfering urinary compounds by dialysis and concentrated the purified urinary proteins by lyophilization. Sialylated urinary glycoproteins were conjugated to a solid support by hydrazide chemistry and trypsin digested. Desialylated glycopeptides, released through mild acid hydrolysis, were characterized by tandem MS experiments utilizing collision induced dissociation (CID) and electron capture dissociation fragmentation techniques. In CID-MS(2), Hex(5)HexNAc(4)-N-Asn and HexHexNAc-O-Ser/Thr were typically observed, in agreement with known N-linked biantennary complex-type and O-linked core 1-like structures, respectively. Additional glycoforms for specific N- and O-linked glycopeptides were also identified, e.g. tetra-antennary N-glycans and fucosylated core 2-like O-glycans. Subsequent CID-MS(3), of selected fragment-ions from the CID-MS(2) analysis, generated peptide specific b- and y-ions that were used for peptide identification. In total, 58 N- and 63 O-linked glycopeptides from 53 glycoproteins were characterized with respect to glycan- and peptide sequences. The combination of CID and electron capture dissociation techniques allowed for the exact identification of Ser/Thr attachment site(s) for 40 of 57 putative O-glycosylation sites. We defined 29 O-glycosylation sites which have, to our knowledge, not been previously reported. This is the first study of human urinary glycoproteins where "intact" glycopeptides were studied, i.e. the presence of glycans and their attachment sites were proven without doubt.

Proteomics Analyses of Human Optic Nerve Head Astrocytes Following Biomechanical Strain

We investigate the role of glial cell activation in the human optic nerve caused by raised intraocular pressure, and their potential role in the development of glaucomatous optic neuropathy. To do this we present a proteomics study of the response of cultured, optic nerve head astrocytes to biomechanical strain, the magnitude and mode of strain based on previously published quantitative models. In this case, astrocytes were subjected to 3 and 12% stretches for either 2 h or 24 h. Proteomic methods included nano-liquid chromatography, tandem mass spectrometry, and iTRAQ labeling. Using controls for both stretch and time, a six-plex iTRAQ liquid chromatography- tandem MS (LC/MS/MS) experiment yielded 573 proteins discovered at a 95% confidence limit. The pathways included transforming growth factor β1, tumor necrosis factor, caspase 3, and tumor protein p53, which have all been implicated in the activation of astrocytes and are believed to play a role in the development of glaucomatous optic neuropathy. Confirmation of the iTRAQ analysis was performed by Western blotting of various proteins of interest including ANXA 4, GOLGA2, and αB-Crystallin.

From {Bi22O26} to Chiral Ligand‐Protected {Bi38O45}‐Based Bismuth Oxido Clusters

The reaction of [Bi(22)O(26)(OSiMe(2)tBu)(14)] (1) in THF with salicylic acid gave [Bi(22)O(24)(HSal)(14)] (2) first, which was converted into [Bi(38)O(45)(HSal)(22)(OH)(2)(DMSO)(16.5)]·DMSO·H(2)O (3·DMSO·H(2)O) after dissolution and crystallization from DMSO. Single-crystal X-ray diffraction analysis and ESI mass spectrometry associated with infrared multi-photon dissociation (IRMPD) tandem MS experiments confirm the formation of the large and quite stable bismuth oxido cluster 3. The reaction of compound 2 with the butoxycarbonyl(BOC)-protected amino acids phenylalanine and valine (BOC-PheOH and BOC-ValOH), respectively, resulted in the formation of chiral [Bi(38)O(45)(BOC-AA)(22)(OH)(2)] (AA=deprotonated amino acid), as shown by a combination of different analytical techniques such as elemental analysis, dynamic light scattering, circular dichroism spectroscopy, and ESI mass spectrometry.

Analysis of Major Phospholipid Species and Ergosterol in Fermenting Industrial Yeast Strains Using Atmospheric Pressure Ionization Ion-Trap Mass Spectrometry

Knowledge of the individual lipid species that are associated with ethanol tolerance in Saccharomyces cerevisiae is necessary to understand potential mechanisms of how this organism uses these molecules to mitigate the toxic effects of ethanol. Three industrial yeast strains with varying degrees of ethanol tolerance were examined utilizing normal phase high-performance liquid chromatography and atmospheric pressure ionization-ion-trap mass spectrometry methods to quantitatively determine phospholipid and ergosterol levels at numerous fermentation time points. Both high and low Brix fermentations were performed to assess the sugar utilization capabilities of the strains. The results indicated that the strain with the most robust fermentation characteristics had the highest phosphatidylinositol levels and lowest phosphatidylcholine levels. Examination of the phospholipid structural data from tandem MS experiments indicated that the levels of several phospholipid species were unique to the slowest fermenting strain. The relation of ergosterol and other phospholipids to ethanol tolerance is also discussed.

Formation and Fragmentation of Radical Peptide Anions: Insights from Vacuum Ultra Violet Spectroscopy

We have studied the photodissociation of gas-phase deprotonated caerulein anions by vacuum ultraviolet (VUV) photons in the 4.5 to 20 eV range, as provided by the DESIRS beamline at the synchrotron radiation facility SOLEIL (France). Caerulein is a sulphated peptide with three aromatic residues and nine amide bonds. Electron loss is found to be the major relaxation channel at every photon energy. However, an increase in the fragmentation efficiency (neutral losses and peptide backbone cleavages) as a function of the energy is also observed. The oxidized ions, generated by electron photodetachment were further isolated and activated by collision (CID) in a MS(3) scheme. The branching ratios of the different fragments observed by CID as a function of the initial VUV photon energy are found to be independent of the initial photon energy. Thus, there is no memory effect of the initial excitation energy on the fragmentation channels of the oxidized species on the time scale of our tandem MS experiment. We also report photofragment yields as a function of photon energy for doubly deprotonated caerulein ions, for both closed-shell ([M-2H](2-)) non-radical ions and open-shell ([M-3H](2-•)) radical ions. These latter ions are generated by electron photodetachment from [M-3H](3-) precursor ions. The detachment yield increases monotonically with the energy with the appearance of several absorption bands. Spectra for radical and non-radical ions are quite similar in terms of observed bands; however, the VUV fragmentation yield is enhanced by the presence of a radical in caerulein peptides.

Structure of singly hydrated, protonated phospho-tyrosine

Tandem mass spectrometry is a powerful analytical technique for distinguishing phosphorylated from non-phosphorylated peptides, and also to locate the phosphorylated site. It is however desirable to further extend the tandem MS capacities via the development of structure specific activation techniques. This work is part of an ongoing project which aims at characterizing the environment of the phosphate group using tunable IRMPD. The effect of microsolvation of protonated phospho-tyrosine on the phosphate environment has been investigated using a combination of tandem MS experiments and quantum chemical calculations. Infrared spectra have been recorded in the 900–1900 cm −1 and 2500–3750 cm −1 regions using a free electron laser and a tabletop laser, respectively. Water is found to form a hydrogen bonded bridge between the otherwise nearly isolated phosphate and ammonium groups. Theoretical and experimental results also provide consistent evidences for two weaker hydrogen bonds between the two other NH bonds with the π-aromatic ring and the carboxylic CO. The MP2 calculated IR absorption spectrum of the lowest energy structure allows for a clear band assignment. As compared to intramolecular direct interaction between the phosphate and the ammonium, the two hydrogen bonds associated with the water bridge between these groups are found to have a larger impact on their IR structure-specific probes. This is reflected by the red-shift of the P O stretch, and also the blue shift of the umbrella mode of the ammonium. Special attention is paid to the 2500–3750 cm −1 spectral range. While the phosphate OH stretching modes are not affected by the addition of water, the red shifts of the three ammonium NH stretches are found to be significant and quite different for their three types of non-covalent interactions.

Identification of polyphenolic compounds in red and white grape varieties grown in R. Macedonia and changes of their content during ripening

The composition of polyphenols in the skin, seed and pulp extracts of the grapes of Vranec and Smederevka varieties, and Merlot and Chardonnay as well, was analyzed by liquid chromatography-diode array detection-mass spectrometry (HPLC-DAD-MS) and MS/MS techniques. Thirty-one phenolic compounds, including anthocyanins, flavonols and flavan-3-ols, as well as phenolic acids derivatives, have been identified in the extracts prepared from the grapes at physiological maturity, by mass spectrometry applying electrospray ionization operated in alternating ion mode and by performing tandem MS experiments in the ion trap mass analyzer. Grapes were analyzed at three different phases: (i) veraison, (ii) physiological ripeness and (iii) late harvest, in order to follow the evolution of polyphenolic content during berry development, applying spectrophotometric methods. Vranec had a higher polyphenolic content compared to Merlot due to the higher levels of total phenolics and flavonoids in the skins and seeds as well as a higher content of flavan-3-ols and anthocyanins in the skins, allowing discriminating the varieties. HPLC-DAD-MS analysis presented significantly higher relative amounts of anthocyanin monoglucosides and p-coumaroylglucosides in Vranec grapes. Smederevka seeds had a higher amount of flavan-3-ols than Chardonnay, while a higher content of total phenolics and flavonoids was found in the skins of the Chardonnay variety. Anthocyanin content in both red varieties increased during the berry ripening, while flavan-3-ols in seeds were mainly accumulated in the veraison phase followed by decrease of the content with ripening.

A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas.

Human blood plasma can be obtained relatively noninvasively and contains proteins from most, if not all, tissues of the body. Therefore, an extensive, quantitative catalog of plasma proteins is an important starting point for the discovery of disease biomarkers. In 2005, we showed that different proteomics measurements using different sample preparation and analysis techniques identify significantly different sets of proteins, and that a comprehensive plasma proteome can be compiled only by combining data from many different experiments. Applying advanced computational methods developed for the analysis and integration of very large and diverse data sets generated by tandem MS measurements of tryptic peptides, we have now compiled a high-confidence human plasma proteome reference set with well over twice the identified proteins of previous high-confidence sets. It includes a hierarchy of protein identifications at different levels of redundancy following a clearly defined scheme, which we propose as a standard that can be applied to any proteomics data set to facilitate cross-proteome analyses. Further, to aid in development of blood-based diagnostics using techniques such as selected reaction monitoring, we provide a rough estimate of protein concentrations using spectral counting. We identified 20,433 distinct peptides, from which we inferred a highly nonredundant set of 1929 protein sequences at a false discovery rate of 1%. We have made this resource available via PeptideAtlas, a large, multiorganism, publicly accessible compendium of peptides identified in tandem MS experiments conducted by laboratories around the world.