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Mass spectrometry-based proteomics provides a holistic snapshot of the entire protein set of living cells on a molecular level. Currently, only a few deep learning approaches exist that involve peptide fragmentation spectra, which represent partial sequence information of proteins. Commonly, these approaches lack the ability to characterize less studied or even unknown patterns in spectra because of their use of explicit domain knowledge. Here, to elevate unrestricted learning from spectra, we introduce ‘ad hoc learning of fragmentation’ (AHLF), a deep learning model that is end-to-end trained on 19.2 million spectra from several phosphoproteomic datasets. AHLF is interpretable, and we show that peak-level feature importance values and pairwise interactions between peaks are in line with corresponding peptide fragments. We demonstrate our approach by detecting post-translational modifications, specifically protein phosphorylation based on only the fragmentation spectrum without a database search. AHLF increases the area under the receiver operating characteristic curve (AUC) by an average of 9.4% on recent phosphoproteomic data compared with the current state of the art on this task. Furthermore, use of AHLF in rescoring search results increases the number of phosphopeptide identifications by a margin of up to 15.1% at a constant false discovery rate. To show the broad applicability of AHLF, we use transfer learning to also detect cross-linked peptides, as used in protein structure analysis, with an AUC of up to 94%.
We report the results of a Versailles Project on Advanced Materials and Standards (VAMAS) interlaboratory study on the measurement of the shell thickness and chemistry of nanoparticle coatings. Peptide-coated gold particles were supplied to laboratories in two forms: a colloidal suspension in pure water and particles dried onto a silicon wafer. Participants prepared and analyzed these samples using either X-ray photoelectron spectroscopy (XPS) or low energy ion scattering (LEIS). Careful data analysis revealed some significant sources of discrepancy, particularly for XPS. Degradation during transportation, storage, or sample preparation resulted in a variability in thickness of 53%. The calculation method chosen by XPS participants contributed a variability of 67%. However, variability of 12% was achieved for the samples deposited using a single method and by choosing photoelectron peaks that were not adversely affected by instrumental transmission effects. The study identified a need for more consistency in instrumental transmission functions and relative sensitivity factors since this contributed a variability of 33%. The results from the LEIS participants were more consistent, with variability of less than 10% in thickness, and this is mostly due to a common method of data analysis. The calculation was performed using a model developed for uniform, flat films, and some participants employed a correction factor to account for the sample geometry, which appears warranted based upon a simulation of LEIS data from one of the participants and comparison to the XPS results.
Due to the extremely high specific surface area of nanoparticles and corresponding potential for adsorption, the results of surface analysis can be highly dependent on the history of the particles, particularly regarding sample preparation and storage. The sample preparation method has, therefore, the potential to have a significant influence on the results. This report describes an interlaboratory comparison (ILC) with the aim of assessing which sample preparation methods for ToF-SIMS analysis of nanoparticles provided the most intra- and interlaboratory consistency and the least amount of sample contamination. The BAM reference material BAM-P110 (TiO2 nanoparticles with a mean Feret diameter of 19 nm) was used as a sample representing typical nanoparticles. A total of 11 participants returned ToF-SIMS data,in positive and (optionally) negative polarity, using sample preparation methods of “stick-and-go” as well as optionally “drop-dry” and “spin-coat.” The results showed that the largest sources of variation within the entire data set were caused by adventitious hydrocarbon contamination or insufficient sample coverage, with the spin-coating protocol applied in this ILC showing a tendency toward insufficient sample coverage; the sample preparation method or the participant had a lesser influence on results.
Sialic acid (SA) is a monosaccharide usually linked to the terminus of glycan chains on the cell surface. It plays a crucial role in many biological processes, and hypersialylation is a common feature in cancer. Lectins are widely used to analyze the cell surface expression of SA.
However, these protein molecules are usually expensive and easily denatured, which calls for the development of alternative glycan-specific receptors and cell imaging technologies. In this study, SA-imprinted fluorescent core-shell molecularly imprinted polymer particles (SA-MIPs) were employed to recognize SA on the cell surface of cancer cell lines. The SA-MIPs improved suspensibility and scattering properties compared with previously used core-shell SA-MIPs. Although SA-imprinting was performed using SA without preference for the alpha-2,3- and alpha-2,6-SA forms, we screened the cancer cell lines analyzed using the lectins Maackia Amurensis Lectin I (MAL I, alpha-2,3-SA) and Sambucus Nigra Lectin (SNA, alpha-2,6-SA). Our results show that the selected cancer cell lines in this study presented a varied binding behavior with the SA-MIPs. The binding pattern of the lectins was also demonstrated. Moreover, two different pentavalent SA conjugates were used to inhibit the binding of the SA-MIPs to breast, skin, and lung cancer cell lines, demonstrating the specificity of the SA-MIPs in both flow cytometry and confocal fluorescence microscopy. We concluded that the synthesized SA-MIPs might be a powerful future tool in the diagnostic analysis of various cancer cells.
Zeolitic imidazolate frameworks (ZIFs) have been widely investigated for their use in separation, gas adsorption, catalysis, and biotechnology. Their practical applications, however, can be hampered by their structural instability in humid acidic conditions. Here, guided by density functional theory calculations, we demonstrate that the acidic stability of two polymorphic ZIFs (i.e., ZIF-8 and ZIF-L) can be enhanced by the incorporation of functional groups on polypeptides or DNA. A range of complementary synchrotron investigations into the local chemical structure and bonding environment suggest that the enhanced acidic stability arises from the newly established coordinative interactions between the Zn centers and the inserted carboxylate (for polypeptides) or phosphate (for DNA) groups, both of which have lower pKas than the imidazolate ligand. With functional biomolecular homologs (i.e., enzymes), we demonstrate a symbiotic stability reinforcement effect, i.e., the encapsulated biomolecules stabilize the ZIF matrix while the ZIF exoskeleton protects the enzyme from denaturation.
The evolution of biological complexity is associated with the emergence of bespoke immune systems that maintain and protect organism integrity. Unlike the well-studied immune systems of cells and individuals, little is known about the origins of immunity during the transition to eusociality, a major evolutionary transition comparable to the evolution of multicellular organisms from single-celled ancestors. We aimed to tackle this by characterizing the immune gene repertoire of 18 cockroach and termite species, spanning the spectrum of solitary, subsocial and eusocial lifestyles. We find that key transitions in termite sociality are correlated with immune gene family contractions. In cross-species comparisons of immune gene expression, we find evidence for a caste-specific social defence system in termites, which appears to operate at the expense of individual immune protection. Our study indicates that a major transition in organismal complexity may have entailed a fundamental reshaping of the immune system optimized for group over individual defence.
This study describes an interlaboratory comparison (ILC) among nine (9) laboratories to evaluate and validate the standard operation procedure (SOP) for single-particle (sp) ICP-TOFMS developed within the context of the Horizon 2020 project ACEnano. The ILC was based on the characterization of two different Pt nanoparticle (NP) suspensions in terms of particle mass, particle number concentration, and isotopic composition. The two Pt NP suspensions were measured using icpTOF instruments (TOFWERK AG, Switzerland).
Two Pt NP samples were characterized and mass equivalent spherical sizes (MESSs) of 40.4 ± 7 nm and 58.8 ± 8 nm were obtained, respectively. MESSs showed <16% relative standard deviation (RSD) among all participating labs and <4% RSD after exclusion of the two outliers. A good agreement was achieved between the different participating laboratories regarding particle mass, but the particle number concentration results were more scattered, with <53% RSD among all laboratories, which is consistent with results from previous ILC studies conducted using ICP-MS instrumentation equipped with a sequential mass spectrometer. Additionally, the capabilities of sp-ICP-TOFMS to determine masses on a particle basis are discussed with respect to the potential for particle density determination. Finally, because quasi-simultaneous multi-isotope and multielement determinations are a strength of ICP-TOFMS instrumentation, the precision and trueness of isotope ratio determinations were assessed. The average of 1000 measured particles yielded a precision of below ±1% for intensity ratios of the most abundant Pt isotopes, i.e. 194Pt and 195Pt, while the accuracy of isotope ratios with the lower abundant isotopes was limited by counting statistics.
Sialyl-Tn (STn or sialyl-Thomsen-nouveau) is a carbohydrate antigen expressed by more than 80% of human carcinomas. We here report a strategy for ratiometric STn detection and dual-color cancer cell labeling, particularly, by molecularly imprinted polymers (MIPs). Imprinting was based on spectroscopic studies of a urea-containing green-fluorescent monomer 1 and STn-Thr-Na (sodium salt of Neu5Acα2-6GalNAcα-O-Thr). A few-nanometer-thin green-fluorescent polymer shell, in which STn-Thr-Na was imprinted with 1, other comonomers, and a cross-linker, was synthesized from the surface of red-emissive carbon nanodot (R-CND)-doped silica nanoparticles, resulting in dual fluorescent STn-MIPs. Dual-color labeling of cancer cells was achieved since both red and green emissions were detected in two separate channels of the microscope and an improved accuracy was obtained in comparison with single-signal MIPs. The flow cytometric cell analysis showed that the binding of STn-MIPs was significantly higher (p < 0.001) than that of non-imprinted polymer (NIP) control particles within the same cell line, allowing to distinguish populations. Based on the modularity of the luminescent core–fluorescent MIP shell architecture, the concept can be transferred in a straightforward manner to other target analytes.
CCQM key comparison K-129 for the quantitative analysis of Cu(In,Ga)Se2 (CIGS) films has been performed by the Surface Analysis Working Group (SAWG) of the Consultative Committee for Amount of Substance (CCQM). The objective of this key comparison is to compare the equivalency of the National Metrology Institutes (NMIs) and Designated Institutes (DIs) for the measurement of mole fractions of Cu, In, Ga and Se in a thin CIGS film. The measurand of this key comparison is the average mole fractions of Cu, In, Ga and Se of a test CIGS alloy film in the unit of mole fraction (mol/mol). Mole fraction with the metrological unit of mol/mol can be practically converted to atomic fraction with the unit of at%.
In this key comparison, a CIGS film with certified mole fractions was supplied as a reference specimen to determine the relative sensitivity factors (RSFs) of Cu, In, Ga and Se. The mole fractions of the reference specimen were certified by isotope dilution - inductively coupled plasma/mass spectrometry (ID-ICP/MS) and are traceable to the SI. A total number counting (TNC) method was recommended as a method to determine the signal intensities of the constituent elements acquired in the depth profiles by Secondary Ion Mass Spectrometry (SIMS), X-ray Photoelectron Spectroscopy (XPS) and Auger Electron Spectroscopy (AES). Seven NMIs and one DI participated in this key comparison. The mole fractions of the CIGS films were measured by depth profiling based-SIMS, AES and XPS. The mole fractions were also measured by non-destructive X-Ray Fluorescence (XRF) Analysis and Electron Probe Micro Analysis (EPMA) with Energy Dispersive X-ray Spectrometry (EDX).
In this key comparison, the average degrees of equivalence uncertainties for Cu, In, Ga and Se are 0.0093 mol/mol, 0.0123 mol/mol, 0.0047 mol/mol and 0.0228 mol/mol, respectively. These values are much smaller than that of Fe in a Fe-Ni alloy film in CCQM K-67 (0.0330 mol/mol). This means that the quantification of multi-element alloy films is possible by depth profiling analysis using the TNC method.
A pilot study for the quantitative surface analysis of multi-element alloy films has been performed by the Surface Analysis Working Group (SAWG) of the Consultative Committee for Amount of Substance (CCQM). The aim of this pilot study is to ensure the equivalency in the measurement capability of national metrology institutes for the quantification of multi-element alloy films. A Cu(In,Ga)Se2 (CIGS) film with non-uniform depth distribution was chosen as a representative multi-element alloy film. The atomic fractions of the reference and the test CIGS films were certified by isotope dilution - inductively coupled plasma/mass spectrometry. A total number counting (TNC) method was used as a method to determine the signal intensities of the constituent elements, which are compared with their certified atomic fractions. The atomic fractions of the CIGS films were measured by various methods, such as Secondary Ion Mass Spectrometry (SIMS), Auger Electron Spectroscopy (AES), X-ray Photoelectron Spectroscopy (XPS), X-Ray Fluorescence (XRF) analysis and Electron Probe Micro Analysis (EPMA) with Energy Dispersive X-ray Spectrometry (EDX). Fifteen laboratories from eight National Metrology Institutes (NMIs), one Designated Institute (DI) and six non-NMIs participated in this pilot study. Although the average atomic fractions of 18 data sets showed rather poor relative standard deviations of about 5.5 % to 6.8 %, they were greatly improved to about 1.5 % to 2.2 % by excluding 5 strongly deviating data sets from the average atomic fractions. In this pilot study, the average expanded uncertainties of SIMS, XPS, AES, XRF and EPMA were 3.84%, 3.68%, 3.81%, 2.88% and 2.90%, respectively. These values are much better than those in the key comparison K-67 for composition of a Fe-Ni alloy film. As a result, the quantification of CIGS films using the TNC method was found to be a good candidate as a subject for a CCQM key comparison.