Comparison of LFQ and IPTL for Protein Identification and Relative Quantification.

(1) Background: Mass spectrometry-based quantitative proteome profiling is most commonly performed by label-free quantification (LFQ), stable isotopic labeling with amino acids in cell culture (SILAC), and reporter ion-based isobaric labeling methods (TMT and iTRAQ). Isobaric peptide termini labeling (IPTL) was described as an alternative to these methods and is based on crosswise labeling of both peptide termini and MS2 quantification. High quantification accuracy was assumed for IPTL because multiple quantification points are obtained per identified MS2 spectrum. A direct comparison of IPTL with other quantification methods has not been performed yet because IPTL commonly requires digestion with endoproteinase Lys-C. (2) Methods: To enable tryptic digestion of IPTL samples, a novel labeling for IPTL was developed that combines metabolic labeling (Arg-0/Lys-0 and Arg-d4/Lys-d4, respectively) with crosswise N-terminal dimethylation (d4 and d0, respectively). (3) Results: The comparison of IPTL with LFQ revealed significantly more protein identifications for LFQ above homology ion scores but not above identity ion scores. (4) Conclusions: The quantification accuracy was superior for LFQ despite the many quantification points obtained with IPTL.

An Approach for Triplex-IPTL.

Isobaric peptide termini labeling (IPTL) is an approach for quantitative proteomics based on crosswise isotopic labeling of peptides at the N- and C-terminus. The labeling reagents are chosen in isotopic variations that the resulting mass of all labels per peptide is isobaric, but the individual label on each peptide terminus is different. Therefore, the quantitative difference of the peptide signal can be determined by the fragment ions of the corresponding MS2 spectra. Here, we describe an approach for triplex-IPTL to allow the comparison of three proteomes. This approach is based on digestion of the proteins by endoproteinase Lys-C, followed by three combinations of selective dimethylation of the peptide N-termini and subsequent dimethylation of the lysine residues at the C-termini. Data analysis is performed using Mascot for database searches and the freely available software package IsobariQ for quantification.

Predominant cleavage of proteins N-terminal to serines and threonines using scandium(III) triflate.

Proteolytic digestion prior to LC-MS analysis is a key step for the identification of proteins. Digestion of proteins is typically performed with trypsin, but certain proteins or important protein sequence regions might be missed using this endoproteinase. Only few alternative endoproteinases are available and chemical cleavage of proteins is rarely used. Recently, it has been reported that some metal complexes can act as artificial proteases. In particular, the Lewis acid scandium(III) triflate has been shown to catalyze the cleavage of peptide bonds to serine and threonine residues. Therefore, we investigated if this compound can also be used for the cleavage of proteins. For this purpose, several single proteins, the 20S immune-proteasome (17 proteins), and the Universal Proteomics Standard UPS1 (48 proteins) were analyzed by MALDI-MS and/or LC-MS. A high cleavage specificity N-terminal to serine and threonine residues was observed, but also additional peptides with deviating cleavage specificity were found. Scandium(III) triflate can be a useful tool in protein analysis as no other reagent has been reported yet which showed cleavage specificity within proteins to serines and threonines.

Absolute two-point quantification of proteins using dimethylated proteotypic peptides.

Absolute targeted proteomics typically employs known amounts of synthetic stable isotopically labeled peptides which are mixed with the analyte and analysed by LC-MS to determine the concentration of proteins. In order to obtain more data, we evaluated the use of two different stable isotopes of the same peptide as spike-in for absolute quantification. For this purpose, peptide labeling by reductive amination was applied, which is a mild reaction for dimethylation of amine groups with very high yield. Three different forms can be generated with e.g., light and heavy labels for spike-in peptides, and medium label for endogenous peptides. The method was studied with peptides of apolipoprotein A-I, apolipoprotein B-100, and leucine-rich alpha-2-glycoprotein without and with serum. In serum, the endogenous protein concentrations were measured across four orders of magnitude by the two-point quantification method. Less than 20% of coefficient of variation (CV) values and strong correlation with R2 of 0.99 across three analytical replicates was observed. Most importantly, the two-point quantification method allows an internal quality control of the spike-in peptide as strong deviations in ratios calculated between the first and second reference indicate a methodical error. Because of the significant lower costs than synthetically stable isotopically labeled peptides, this approach might be particularly interesting for the absolute quantification of multiple proteins.

Author Correction: Large-scale intact glycopeptide identification by Mascot database search.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Large-scale intact glycopeptide identification by Mascot database search.

Workflows capable of determining glycopeptides in large-scale are missing in the field of glycoproteomics. We present an approach for automated annotation of intact glycopeptide mass spectra. The steps in adopting the Mascot search engine for intact glycopeptide analysis included: (i) assigning one letter codes for monosaccharides, (ii) linearizing glycan sequences and (iii) preparing custom glycoprotein databases. Automated annotation of both N- and O-linked glycopeptides was proven using standard glycoproteins. In a large-scale study, a total of 257 glycoproteins containing 970 unique glycosylation sites and 3447 non-redundant N-linked glycopeptide variants were identified in 24 serum samples. Thus, a single tool was developed that collectively allows the (i) elucidation of N- and O-linked glycopeptide spectra, (ii) matching glycopeptides to known protein sequences, and (iii) high-throughput, batch-wise analysis of large-scale glycoproteomics data sets.

Factor VII deficiency: Unveiling the cellular and molecular mechanisms underlying three model alterations of the enzyme catalytic domain.

Activated factor (F) VII is a vitamin K-dependent glycoprotein that initiates blood coagulation upon interaction with tissue factor. FVII deficiency is the most common of the rare congenital bleeding disorders. While the mutational pattern has been extensively characterized, the pathogenic molecular mechanisms of mutations, particularly at the intracellular level, have been poorly defined. Here, we aimed at elucidating the mechanisms underlying altered FVII biosynthesis in the presence of three mutation types in the catalytic domain: a missense change, a microdeletion and a frameshift/elongation, associated with severe or moderate to severe phenotypes. Using CHO-K1 cells transiently transfected with expression vectors containing the wild-type FVII cDNA (FVIIwt) or harboring the p.I289del, p.G420V or p.A354V-p.P464Hfs mutations, we found that the secretion of the FVII mutants was severely decreased compared to FVIIwt. The synthesis rate of the mutants was slower than the FVIIwt and delayed, and no degradation of the FVII mutants by proteasomes, lysosomes or cysteine proteases was observed. Confocal immunofluorescence microscopy studies showed that FVII variants were localized into the endoplasmic reticulum (ER) but were not detectable within the Golgi apparatus. These findings suggested that a common pathogenic mechanism, possibly a defective folding of the mutant proteins, was triggered by the FVII mutations. The misfolded state led to impaired trafficking of these proteins causing ER retention, which would explain the low to very low FVII plasma levels observed in patients carrying these mutations.

Purely ultrasonic enzyme extraction from activated sludge in an ultrasonic cleaning bath.

Enzymes are important in biological wastewater treatment systems, since they are responsible for breakdown of macro- and micropollutants, thereby making the pollutants available for metabolism. Enzyme activity has been investigated in particular in activated sludge processes, since the activated sludge technology is the most important and widely spread wastewater treatment technology used today. Various methods have been used to extract enzymes from activated sludge in order to measure their activity, these include stirring with additives like detergents and cation exchange resins, ultrasonication (with probes) and combinations of the three [1], [2], [3]. In this article we describe a method for purely ultrasonic enzyme extraction from activated sludge using low power ultrasound generated by an ultrasonic bath and no additives. The method essentially consists of: •Sonication of the sludge sample using a glass beaker and an ultrasonic bath.•Filtration of the sample in order to obtain the enzyme extract.•Measurement of enzyme activity by fluorescence spectrometry using a substrate that yields a fluorescent product.

Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches.

Alternative splicing is a mechanism in eukaryotes by which different forms of mRNAs are generated from the same gene. Identification of alternative splice variants requires the identification of peptides specific for alternative splice forms. For this purpose, we generated a human database that contains only unique tryptic peptides specific for alternative splice forms from Swiss-Prot entries. Using this database allows an easy access to splice variant-specific peptide sequences that match to MS data. Furthermore, we combined this database without alternative splice variant-1-specific peptides with human Swiss-Prot. This combined database can be used as a general database for searching of LC-MS data. LC-MS data derived from in-solution digests of two different cell lines (LNCaP, HeLa) and phosphoproteomics studies were analyzed using these two databases. Several nonalternative splice variant-1-specific peptides were found in both cell lines, and some of them seemed to be cell-line-specific. Control and apoptotic phosphoproteomes from Jurkat T cells revealed several nonalternative splice variant-1-specific peptides, and some of them showed clear quantitative differences between the two states.

Application of the half decimal place rule to increase the peptide identification rate.

RATIONALE: Many MS2 spectra in bottom-up proteomics experiments remain unassigned. To improve proteome coverage, we applied the half decimal place rule (HDPR) to remove non-peptidic molecules. The HDPR considers the ratio of the digits after the decimal point to the full molecular mass and results in a relatively small permitted mass window for most peptides. METHODS: First, the HDPR mass filter was calculated for the human and other proteomes. Subsequently, the HDPR was applied to three technical replicates of an in-solution tryptic digest of HeLa cells which were analysed by liquid chromatography/mass spectrometry (LC/MS) using a quadrupole-orbitrap mass spectrometer (Q Exactive). In addition, the same sample was analysed three times with a fixed exclusion list. The exclusion list was based on only choosing doubly charged ions for fragmentation. RESULTS: The peptide spectrum match (PSM) rate increased by 2-4% applying HDPR filters from 0.1-0.25 Da and 75-150 ppm, respectively. Excluding all MS2 events by applying an HDPR filter of doubly charged ions, we were able to improve PSMs by 0.9% and the PSM rate by 2.5%. CONCLUSIONS: An algorithm to filter precursors based on the HDPR was established to improve the targeting of the acquisition of MS2 spectra in data-dependent acquisition (DDA) experiments. According to our data, a total gain of PSMs of 1-5% might be achievable if the HPDR filter would already be applied during MS data acquisition. Copyright © 2016 John Wiley & Sons, Ltd.

The Proinflammatory Potential of Nitrogen Dioxide and Its Influence on the House Dust Mite Allergen Der p 1.

Asthma and allergies are both major global health problems with an increasing prevalence, and environmental data implicate an influence of air pollutants on their development. The present study focuses on the influence of nitrogen dioxide (NO2) and the major allergen of the house dust mite Der p 1 on human nasal epithelial cells of nonallergic patients in vitro. Nasal epithelial mucosa samples of 11 donors were harvested during nasal air passage surgery and cultured as an air-liquid interface. Exposure to 0.1, 1 and 10 ppm NO2 or synthetic air as a control was performed for 1 h. Subsequently, the cells were exposed to Der p 1 for 24 h. The release of interleukin (IL)-6 and IL-8 was measured by ELISA, and the production of IL-6 mRNA and IL-8 mRNA was measured by RT-PCR. NO2 exposure resulted in a concentration-dependent release of IL-6, but not IL-8 release. The coexposure of 0.1 ppm NO2 and Der p 1, or 1 ppm NO2 and Der p 1 significantly increased both IL-6 and IL-8 release. Exposure to NO2, Der p 1, or their combination, did not significantly influence the production of IL-6 or IL-8 mRNA. In conclusion, NO2 increases the release of inflammatory cytokines in human nasal epithelial cells, especially in coexposure with Der p 1, as a mechanism of allergotoxicology.

Tracer tests and uncertainty propagation to design monitoring setups in view of pharmaceutical mass flow analyses in sewer systems.

The development of a strategic approach to manage pollution of surface waters with pharmaceutical residues is in centre of interest in Europe. In this context a lack of reliable standard procedures for sampling and subsequent assessment of pharmaceutical mass flows in the water cycle has been identified. Authoritative assessment of relevant substance concentrations and flows is essential for environmental risk assessments and reliable efficiency analysis of measures to reduce or avoid emissions of drugs to water systems. Accordingly, a detailed preparation of monitoring campaigns including an accuracy check for the sampling configuration provides important information on the reliability of the gathered data. It finally supports data analysis and interpretation for evaluations of the efficiency of measures as well as for cost benefit assessments. The precision of mass flow balances is expected to be particularly weak when substances with high short-term variations and rare upstream emissions are considered. This is especially true for substance flow analysis in sewers close to source because of expectable highly dynamic flow conditions and emission patterns of pollutants. The case study presented here focusses on the verification of a monitoring campaign in a hospital sewer in Luxembourg. The results highlight the importance for a priori accuracy checks and provide a blueprint for well-designed monitoring campaigns of pharmaceutical trace pollutants on the one hand. On the other hand, the study provides evidence that the defined and applied continuous flow proportional sampling procedure enables a representative monitoring of short-term peak loads of the x-ray contrast media iobitridol close to source.

The impact of carbon-13 and deuterium on relative quantification of proteins using stable isotope diethyl labeling.

RATIONALE: Stable isotopic labeling techniques are useful for quantitative proteomics. A cost-effective and convenient method for diethylation by reductive amination was established. The impact using either carbon-13 or deuterium on quantification accuracy and precision was investigated using diethylation. METHODS: We established an effective approach for stable isotope labeling by diethylation of amino groups of peptides. The approach was validated using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and nanospray liquid chromatography/electrospray ionization (nanoLC/ESI)-ion trap/orbitrap for mass spectrometric analysis as well as MaxQuant for quantitative data analysis. RESULTS: Reaction conditions with low reagent costs, high yields and minor side reactions were established for diethylation. Furthermore, we showed that diethylation can be applied to up to sixplex labeling. For duplex experiments, we compared diethylation in the analysis of the proteome of HeLa cells using acetaldehyde-(13) C(2)/(12) C(2) and acetaldehyde-(2) H(4)/(1) H(4). Equal numbers of proteins could be identified and quantified; however, (13) C(4)/(12) C(4) -diethylation revealed a lower variance of quantitative peptide ratios within proteins resulting in a higher precision of quantified proteins and less falsely regulated proteins. The results were compared with dimethylation showing minor effects because of the lower number of deuteriums. CONCLUSIONS: The described approach for diethylation of primary amines is a cost-effective and accurate method for up to sixplex relative quantification of proteomes. (13) C(4)/(12) C(4) -diethylation enables duplex quantification based on chemical labeling without using deuterium which reduces identification of false-negatives and increases the quality of the quantification results.

Consolidation of proteomics data in the Cancer Proteomics database.

Cancer is a class of diseases characterized by abnormal cell growth and one of the major reasons for human deaths. Proteins are involved in the molecular mechanisms leading to cancer, furthermore they are affected by anti-cancer drugs, and protein biomarkers can be used to diagnose certain cancer types. Therefore, it is important to explore the proteomics background of cancer. In this report, we developed the Cancer Proteomics database to re-interrogate published proteome studies investigating cancer. The database is divided in three sections related to cancer processes, cancer types, and anti-cancer drugs. Currently, the Cancer Proteomics database contains 9778 entries of 4118 proteins extracted from 143 scientific articles covering all three sections: cell death (cancer process), prostate cancer (cancer type) and platinum-based anti-cancer drugs including carboplatin, cisplatin, and oxaliplatin (anti-cancer drugs). The detailed information extracted from the literature includes basic information about the articles (e.g., PubMed ID, authors, journal name, publication year), information about the samples (type, study/reference, prognosis factor), and the proteomics workflow (Subcellular fractionation, protein, and peptide separation, mass spectrometry, quantification). Useful annotations such as hyperlinks to UniProt and PubMed were included. In addition, many filtering options were established as well as export functions. The database is freely available at http://cancerproteomics.uio.no.

Identification of prostate cancer biomarkers in urinary exosomes.

Exosomes have recently appeared as a novel source of non-invasive cancer biomarkers since tumour-specific molecules can be found in exosomes isolated from biological fluids. We have here investigated the proteome of urinary exosomes by using mass spectrometry to identify proteins differentially expressed in prostate cancer patients compared to healthy male controls. In total, 15 control and 16 prostate cancer samples of urinary exosomes were analyzed. Importantly, 246 proteins were differentially expressed in the two groups. The majority of these proteins (221) were up-regulated in exosomes from prostate cancer patients. These proteins were analyzed according to specific criteria to create a focus list that contained 37 proteins. At 100% specificity, 17 of these proteins displayed individual sensitivities above 60%. Even though several of these proteins showed high sensitivity and specificity for prostate cancer as individual biomarkers, combining them in a multi-panel test has the potential for full differentiation of prostate cancer from non-disease controls. The highest sensitivity, 94%, was observed for transmembrane protein 256 (TM256; chromosome 17 open reading frame 61). LAMTOR proteins were also distinctly enriched with very high specificity for patient samples. TM256 and LAMTOR1 could be used to augment the sensitivity to 100%. Other prominent proteins were V-type proton ATPase 16 kDa proteolipid subunit (VATL), adipogenesis regulatory factor (ADIRF), and several Rab-class members and proteasomal proteins. In conclusion, this study clearly shows the potential of using urinary exosomes in the diagnosis and clinical management of prostate cancer.

Assessment of HEMA and TEGDMA induced DNA damage by multiple genotoxicological endpoints in human lymphocytes.

OBJECTIVES: Residual unbound resin monomers of 2-hydroxyethyl methacrylate (HEMA) and triethylene glycol dimethacrylate (TEGDMA) are known to diffuse in the saliva and through dentin and pulp into the blood and may affect cellular integrity. The current study was performed to investigate the genotoxic potential of both monomers in distinctly lower concentrations than known to cause cytotoxic damage. METHODS: Lymphocytes from 10 healthy volunteers were treated with HEMA (10µM-1mM) and TEGDMA (1µM-100µM) for 24h. Cell viability, apoptosis and influence on cell cycle kinetics were assessed by flowcytometry. DNA damage was determined by the alkali version of the comet assay in combination with the FPG protein and by the cytokinesis-block micronucleus (CBMN) test. Additionally, the chromosome aberration (CA) test and sister chromatid exchange (SCE) test were performed. RESULTS: A slight decrease in cell viability was detected only at the highest concentration of TEGDMA. Genotoxic effects were measurable in the comet assay at 1mM of HEMA and 100µM of TEGDMA, with and without FPG protein, but not in the CBMN test or the cell cycle analysis. Contrary to these findings, a significant dose-dependent increase in the frequency of CAs and SCEs could be demonstrated in all tested concentrations. SIGNIFICANCE: This is the first time clastogenic responses to HEMA and TEGDMA have been detected in concentrations distinctly lower than those reported for causing cytotoxic or even genotoxic effects. These findings underline the importance of using test batteries with different genotoxicological endpoints to describe the multiple effects of both resin monomers.

Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes.

Transcription factors are abundant Sumo targets, yet the global distribution of Sumo along the chromatin and its physiological relevance in transcription are poorly understood. Using Saccharomyces cerevisiae, we determined the genome-wide localization of Sumo along the chromatin. We discovered that Sumo-enriched genes are almost exclusively involved in translation, such as tRNA genes and ribosomal protein genes (RPGs). Genome-wide expression analysis showed that Sumo positively regulates their transcription. We also discovered that the Sumo consensus motif at RPG promoters is identical to the DNA binding motif of the transcription factor Rap1. We demonstrate that Rap1 is a molecular target of Sumo and that sumoylation of Rap1 is important for cell viability. Furthermore, Rap1 sumoylation promotes recruitment of the basal transcription machinery, and sumoylation of Rap1 cooperates with the target of rapamycin kinase complex 1 (TORC1) pathway to promote RPG transcription. Strikingly, our data reveal that sumoylation of Rap1 functions in a homeostatic feedback loop that sustains RPG transcription during translational stress. Taken together, Sumo regulates the cellular translational capacity by promoting transcription of tRNA genes and RPGs.

Nicotine causes genotoxic damage but is not metabolized during long-term exposure of human nasal miniorgan cultures.

Human nasal miniorgan cultures (MOC) are a useful tool in ecogenotoxicology. Repetitive exposure to nicotine showed reversible DNA damage, and stable CYP2A6 expression was demonstrated in nasal MOC in previous investigations. The aim of the present study was to evaluate the genotoxic effect of nicotine in nasal MOC after chronic nicotine exposure, and to monitor possible metabolism capacities. MOC were dissected from human nasal mucosa and cultured under standard cell culture conditions. MOC were exposed to nicotine for 3 weeks at concentrations of 1 µM and 1 mM. The concentrations were chosen based on nicotine plasma levels in heavy smokers, and possible concentrations used in topical application of nicotine nasal spray. DNA damage was assessed by the comet assay at days 7, 14 and 21. Concentrations of nicotine and cotinine were analyzed in cell culture medium by gas chromatography/mass spectrometry to determine a possible metabolism of nicotine by MOC. Distinct DNA damage in MOC could be demonstrated after 1 week of exposure to 1 µM and 1 mM nicotine. This effect decreased after 2 and 3 weeks with no statistically relevant DNA migration. No nicotine metabolism could be detected by changes in nicotine and cotinine concentrations in the supernatants. This is the first time genotoxic effects have been evaluated in nasal MOC after chronic nicotine exposure for up to 3 weeks. Genotoxic effects were present after 1 week of culture with a decrease over time. Down-regulation of nicotinic acetylcholine receptors, which are expressed in nasal mucosa, may be a possible explanation. The lack of nicotine metabolism in this model could be explained by the functional loss of CYP2A6 during chronic nicotine exposure. Further investigations are necessary to provide a more detailed description of the underlying mechanisms involved in DNA damage by nicotine.

Nicotine derived genotoxic effects in human primary parotid gland cells as assessed in vitro by comet assay, cytokinesis-block micronucleus test and chromosome aberrations test.

Genotoxic effects of nicotine were described in different human cells including salivary gland cells. Based on the high nicotine concentration in saliva of smokers or patients using therapeutic nicotine patches, the current study was performed to evaluate the genotoxic potential of nicotine in human salivary gland cells. Therefore, primary salivary gland cells from 10 patients undergoing parotid gland surgery were exposed to nicotine concentrations between 1 µM and 1000 µM for 1 h in the absence of exogenous metabolic activation. The acinar phenotype was proven by immunofluorescent staining of alpha-amylase. Genotoxic effects were evaluated using the Comet assay, the micronucleus test and the chromosome aberration test. Cytotoxicity and apoptosis were determined by trypan blue exclusion test and Caspase-3 assay. Nicotine was able to induce genotoxic effects in all three assays. The chromosome aberration test was the most sensitive and increases in numerical and structural (chromatid-type and chromosome-type) aberrations were seen at ≥1 µM, whereas increases in micronuclei frequency were detected at 10 µM and DNA damage as measured in the Comet assay was noted at >100 µM. No cytotoxic damage or influence of apoptosis could be demonstrated. Nicotine as a possible risk factor for tumor initiation in salivary glands is still discussed controversially. Our results demonstrated the potential of nicotine to induce genotoxic effects in salivary gland cells. These results were observed at saliva nicotine levels similar to those found after oral or transdermal exposure to nicotine and suggest the necessity of careful monitoring of the use of nicotine in humans.