Estimation of influential points in any data set from coefficient of determination and its leave-one-out cross-validated counterpart

Coefficient of determination (R2) and its leave-one-out cross-validated analogue (denoted by Q2 or Rcv 2) are the most frequantly published values to characterize the predictive performance of models. In this article we use R2 and Q2 in a reversed aspect to determine uncommon points, i.e. influential points in any data sets. The term (1 - Q2)/(1 - R2) corresponds to the ratio of predictive residual sum of squares and the residual sum of squares. The ratio correlates to the number of influential points in experimental and random data sets. We propose an (approximate) F test on (1 - Q2)/(1 - R2) term to quickly pre-estimate the presence of influential points in training sets of models. The test is founded upon the routinely calculated Q2 and R2 values and warns the model builders to verify the training set, to perform influence analysis or even to change to robust modeling. Graphical Abstract: [Figure not available: see fulltext.] © 2013 Springer Science+Business Media Dordrecht

Determination of 24 primary aromatic amines in aqueous food simulants by combining solid phase extraction and salting-out assisted liquid?liquid extraction with liquid chromatography tandem mass spectrometry

Carcinogenic primary aromatic amines (PAAs) can be released from improperly manufactured food packaging materials. The limit for the sum of PAAs is set to 10 ?gkg- 1 in Commission Regulation No. 10/2011 (FCM Regulation). However, a lower individual limit, 2 ?gkg- 1 has been recently introduced for the carcinogenic PAAs in Commission Regulation No. 2020/1245. As the majority of the previously published methods are no longer compliant with the current regulation, a UHPLC-MS/MS method was developed to enable food packaging compliance testing for PAAs not only from 3% (w/v) acetic acid, but also from 10% (v/v) ethanol food simulant. Since the latest amendment of the FCM Regulation refers to the list of the 22 restricted PAAs of EU Regulation No. 1907/2006, these PAAs were selected as target compounds along with aniline and p-toluidine, the most common impurities of azo colorants and isocyanates. An enrichment factor of 20 could be achieved combining solid phase extraction with salting-out assisted liquid?liquid extraction. The method was successfully validated and applied on real samples. Limit of quantitation (LOQ) and limit of detection (LOD) values were 0.15 ?gL-1 and 0.05 ?gL-1 for both food simulants, respectively; except for 2,4-diaminotoluene, aniline and 4,4?-oxydianiline. However, even these compounds had lower LOD values than the new individual limit of 2 ?gkg- 1. Cumulative LOD values for both food simulants (1.6 ?gL-1 and 1.5 ?gL-1 for 3% (w/v) acetic acid and 10% (v/v) ethanol, respectively) were lower than the 10 ?gkg- 1 specified in the FCM Regulation. Accuracy values were between 70 and 118% for both food simulants for the majority of PAAs. Both within-day and between-day precision values were below 20%. This method proved to be suitable for daily routine analysis enabling compliance testing of food packaging materials according to the latest regulations. The method was successfully applied for the analysis of plastic kitchenware samples

Shotgun Lipidomic Profiling of the NCI60 Cell Line Panel Using Rapid Evaporative Ionization Mass Spectrometry

Rapid evaporative ionization mass spectrometry (REIMS) was used for the rapid mass spectrometric profiling of cancer cell lines. Spectral reproducibility was assessed for three different cell lines, and the extent of interclass differences and intraclass variance was found to allow the identification of these cell lines based on the REIMS data. Subsequently, the NCI60 cell line panel was subjected to REIMS analysis, and the resulting data set was investigated for its distinction of individual cell lines and different tissue types of origin. Information content of REIMS spectral profiles of cell lines were found to be similar to those obtained from mammalian tissues although pronounced differences in relative lipid intensity were observed. Ultimately, REIMS was shown to detect changes in lipid content of cell lines due to mycoplasma infection. The data show that REIMS is an attractive means to study cell lines involving minimal sample preparation and analysis times in the range of seconds. © 2016 American Chemical Society

The surgical intelligent knife distinguishes normal, borderline and malignant gynaecological tissues using rapid evaporative ionisation mass spectrometry (REIMS)

Background Survival from ovarian cancer (OC) is improved with surgery, but surgery can be complex and tumour identification, especially for borderline ovarian tumours (BOT), is challenging. The Rapid Evaporative Ionisation Mass Spectrometric (REIMS) technique reports tissue histology in real-time by analysing aerosolised tissue during electrosurgical dissection. Methods Aerosol produced during diathermy of tissues was sampled with the REIMS interface. Histological diagnosis and mass spectra featuring complex lipid species populated a reference database on which principal component, linear discriminant and leave-one-patient-out cross-validation analyses were performed. Results A total of 198 patients provided 335 tissue samples, yielding 3384 spectra. Cross-validated OC classification vs separate normal tissues was high (97·4% sensitivity, 100% specificity). BOT were readily distinguishable from OC (sensitivity 90.5%, specificity 89.7%). Validation with fresh tissue lead to excellent OC detection (100% accuracy). Histological agreement between iKnife and histopathologist was very good (kappa 0.84, P < 0.001, z = 3.3). Five predominantly phosphatidic acid (PA(36:2)) and phosphatidyl-ethanolamine (PE(34:2)) lipid species were identified as being significantly more abundant in OC compared to normal tissue or BOT (P < 0.001, q < 0.001). Conclusions The REIMS iKnife distinguishes gynaecological tissues by analysing mass-spectrometry-derived lipidomes from tissue diathermy aerosols. Rapid intra-operative gynaecological tissue diagnosis may improve surgical care when histology is unknown, leading to personalised operations tailored to the individual

Phase separated ribosome-nascent chain complexes in genotoxic stress response

Assemblysomes are EDTA- and RNase-resistant ribonucleoprotein (RNP) complexes of paused ribosomes with protruding nascent polypeptide chains. They have been described in yeast and human cells for the proteasome subunit Rpt1, and the disordered N-terminal part of the nascent chain was found to be indispensable for the accumulation of the Rpt1-RNP into assemblysomes. Motivated by this, to find other assemblysome-associated RNPs we used bioinformatics to rank subunits of Saccharomyces cerevisiae protein complexes according to their N-terminal disorder propensity. The results revealed that gene products involved in DNA repair are enriched among the top candidates. The Sgs1 DNA helicase was chosen for experimental validation. We found that indeed nascent chains of Sgs1 form EDTA-resistant RNP condensates, assemblysomes by definition. Moreover, upon exposure to UV, SGS1 mRNA shifted from assemblysomes to polysomes, suggesting that external stimuli are regulators of assemblysome dynamics. We extended our studies to human cell lines. The BLM helicase, ortholog of yeast Sgs1, was identified upon sequencing assemblysome-associated RNAs from the MCF7 human breast cancer cell line, and mRNAs encoding DNA repair proteins were overall enriched. Using the radiation-resistant A549 cell line, we observed by transmission electron microscopy that 1,6-hexanediol, an agent known to disrupt phase-separated condensates, depletes ring ribosome structures compatible with assemblysomes from the cytoplasm of cells and makes the cells more sensitive to X-ray treatment. Taken together these findings suggest that assemblysomes may be a component of the DNA damage response from yeast to human