Improved Sample Preparation Method for Protein and Peptide Identification from Human Hair.

A fast and sensitive direct extraction (DE) method developed in our group can efficiently extract proteins in 30 min from a 5 cm-long hair strand. Previously, we coupled DE to downstream analysis using gel electrophoresis followed by in-gel digestion, which can be time-consuming. In searching for a better alternative, we found that a combination of DE with a bead-based method (SP3) can lead to significant improvements in protein discovery in human hair. Since SP3 is designed for general applications, we optimized it to process hair proteins following DE and compared it to several other in-solution digestion methods. Of particular concern are genetically variant peptides (GVPs), which can be used for human identification in forensic analysis. Here, we demonstrated improved GVP discovery with the DE and SP3 workflow, which was 3 times faster than the previous in-gel digestion method and required significantly less instrument time depending on the number of gel slices processed. Additionally, it led to an increased number of identified proteins and GVPs. Among the tested in-solution digestion methods, DE combined with SP3 showed the highest sequence coverage, with higher abundances of the identified peptides. This provides a significantly enhanced means for identifying proteins and GVPs in human hair.

Inferring the Nominal Molecular Mass of an Analyte from Its Electron Ionization Mass Spectrum.

The performance of three algorithms for predicting nominal molecular mass from an analyte's electron ionization mass spectrum is presented. The Peak Interpretation Method (PIM) attempts to quantify the likelihood that a molecular ion peak is contained in the mass spectrum, whereas the Simple Search Hitlist Method (SS-HM) and iterative Hybrid Search Hitlist Method (iHS-HM) leverage results from mass spectral library searching. These predictions can be employed in combination (recommended) or independently. The methods were tested on two sets of query mass spectra searched against libraries that did not contain the reference mass spectra of the same compounds: 19,074 spectra of various organic molecules searched against the NIST17 mass spectral library and 162 spectra of small molecule drugs searched against SWGDRUG version 3.3. Individually, each molecular mass prediction method had computed precisions (the fraction of positive predictions that were correct) of 91, 89, and 74%, respectively. The methods become more valuable when predictions are taken together. When all three predictions were identical, which occurred in 33% of the test cases, the predicted molecular mass was almost always correct (>99%).

On the challenge of unambiguous identification of fentanyl analogs: Exploring measurement diversity using standard reference mass spectral libraries.

Fentanyl analogs are a class of designer drugs that are particularly challenging to unambiguously identify due to the mass spectral and retention time similarities of unique compounds. In this paper, we use agglomerative hierarchical clustering to explore the measurement diversity of fentanyl analogs and better understand the challenge of unambiguous identifications using analytical techniques traditionally available to drug chemists. We consider four measurements in particular: gas chromatography retention indices, electron ionization mass spectra, electrospray ionization tandem mass spectra, and direct analysis in real time mass spectra. Our analysis demonstrates how simultaneously considering data from multiple measurement techniques increases the observable measurement diversity of fentanyl analogs, which can reduce identification ambiguity. This paper further supports the use of multiple analytical techniques to identify fentanyl analogs (among other substances), as is recommended by the Scientific Working Group for the Analysis of Seized Drugs (SWGDRUG).

NIST Mass Spectrometry Data Center standard reference libraries and software tools: Application to seized drug analysis.

The standard reference libraries and associated custom software provided by the National Institute of Standards and Technology's Mass Spectrometry Data Center (NIST MSDC) are described with a focus on assisting the seized drug analyst with the identification of fentanyl-related substances (FRS). These tools are particularly useful when encountering novel substances when no certified sample is available. The MSDC provides three standard reference mass spectral libraries, as well as six software packages for mass spectral analysis, reference library searching, data interpretation, and measurement uncertainty estimation. Each of these libraries and software packages are described with references to the original publications provided. Examples of fentanyl identification by gas chromatography-mass spectrometry (GC-MS) and by direct analysis in real-time (DART) mass spectrometry are given. A link to online tutorials is provided.

Comprehensive Analysis of Tryptic Peptides Arising from Disulfide Linkages in NISTmAb and Their Use for Developing a Mass Spectral Library.

This work presents methods for identifying and then creating a mass spectral library for disulfide-linked peptides originating from the NISTmAb, a reference material of the humanized IgG1k monoclonal antibody (RM 8671). Analyses involved both partially reduced and non-reduced samples under neutral and weakly basic conditions followed by nanoflow liquid chromatography tandem mass spectrometry (LC-MS/MS). Spectra of peptides containing disulfide bonds are identified by both MS1 ion and MS2 fragment ion data in order to completely map all the disulfide linkages in the NISTmAb. This led to the detection of 383 distinct disulfide-linked peptide ions, arising from fully tryptic cleavage, missed cleavage, irregular cleavage, complex Met/Trp oxidation mixtures, and metal adducts. Fragmentation features of disulfide bonds under low-energy collision dissociation were examined. These include (1) peptide bond cleavage leaving disulfide bonds intact; (2) disulfide bond cleavage, often leading to extensive fragmentation; and (3) double cleavage products resulting from breakages of two peptide bonds or both peptide and disulfide bonds. Automated annotation of various complex MS/MS fragments enabled the identification of disulfide-linked peptides with high confidence. Peptides containing each of the nine native disulfide bonds were identified along with 86 additional disulfide linkages arising from disulfide bond shuffling. The presence of shuffled disulfides was nearly completely abrogated by refining digest conditions. A curated spectral library of 702 disulfide-linked peptide spectra was created from this analysis and is publicly available for free download. Since all IgG1 antibodies have the same constant regions, the resulting library can be used as a tool for facile identification of "hard-to-find" disulfide-bonded peptides. Moreover, we show that one may identify such peptides originating from IgG1 proteins in human serum, thereby serving as a means of monitoring the completeness of protein reduction in proteomics studies. Data are available via ProteomeXchange with identifier PXD023358.

Mass Spectral Library of Acylcarnitines Derived from Human Urine.

We describe the creation of a mass spectral library of acylcarnitines and conjugated acylcarnitines from the LC-MS/MS analysis of six NIST urine reference materials. To recognize acylcarnitines, we conducted in-depth analyses of fragmentation patterns of acylcarnitines and developed a set of rules, derived from spectra in the NIST17 Tandem MS Library and those identified in urine, using the newly developed hybrid search method. Acylcarnitine tandem spectra were annotated with fragments from carnitine and acyl moieties as well as neutral loss peaks from precursors. Consensus spectra were derived from spectra having similar retention time, fragmentation pattern, and the same precursor m/z and collision energy. The library contains 157 different precursor masses, 586 unique acylcarnitines, and 4 332 acylcarnitine consensus spectra. Furthermore, from spectra that partially satisfied the fragmentation rules of acylcarnitines, we identified 125 conjugated acylcarnitines represented by 987 consensus spectra, which appear to originate from Phase II biotransformation reactions. To our knowledge, this is the first report of conjugated acylcarnitines. The mass spectra provided by this work may be useful for clinical screening of acylcarnitines as well as for studying relationships among fragmentation patterns, collision energies, structures, and retention times of acylcarnitines. Further, these methods are extensible to other classes of metabolites.

Sensitive Method for the Confident Identification of Genetically Variant Peptides in Human Hair Keratin.

Recent reports have demonstrated that genetically variant peptides derived from human hair shaft proteins can be used to differentiate individuals of different biogeographic origins. We report a method involving direct extraction of hair shaft proteins more sensitive than previously published methods regarding GVP detection. It involves one step for protein extraction and was found to provide reproducible results. A detailed proteomic analysis of this data is presented that led to the following four results: (i) A peptide spectral library was created and made available for download. It contains all identified peptides from this work, including GVPs that, when appropriately expanded with diverse hair-derived peptides, can provide a routine, reliable, and sensitive means of analyzing hair digests; (ii) an analysis of artifact peptides arising from side reactions is also made using a new method for finding unexpected modifications; (iii) detailed analysis of the gel-based method employed clearly shows the high degree of cross-linking or protein association involved in hair digestion, with major GVPs eluting over a wide range of high molecular weights while others apparently arise from distinct non-cross-linked proteins; and (v) finally, we show that some of the specific GVP identifications depend on the sample preparation method.

Combining Fragment-Ion and Neutral-Loss Matching during Mass Spectral Library Searching: A New General Purpose Algorithm Applicable to Illicit Drug Identification.

A mass spectral library search algorithm that identifies compounds that differ from library compounds by a single "inert" structural component is described. This algorithm, the Hybrid Similarity Search, generates a similarity score based on matching both fragment ions and neutral losses. It employs the parameter DeltaMass, defined as the mass difference between query and library compounds, to shift neutral loss peaks in the library spectrum to match corresponding neutral loss peaks in the query spectrum. When the spectra being compared differ by a single structural feature, these matching neutral loss peaks should contain that structural feature. This method extends the scope of the library to include spectra of "nearest-neighbor" compounds that differ from library compounds by a single chemical moiety. Additionally, determination of the structural origin of the shifted peaks can aid in the determination of the chemical structure and fragmentation mechanism of the query compound. A variety of examples are presented, including the identification of designer drugs and chemical derivatives not present in the library.

Mass Spectral Library Quality Assurance by Inter-Library Comparison.

A method to discover and correct errors in mass spectral libraries is described. Comparing across a set of highly curated reference libraries compounds that have the same chemical structure quickly identifies entries that are outliers. In cases where three or more entries for the same compound are compared, the outlier as determined by visual inspection was almost always found to contain the error. These errors were either in the spectrum itself or in the chemical descriptors that accompanied it. The method is demonstrated on finding errors in compounds of forensic interest in the NIST/EPA/NIH Mass Spectral Library. The target list of compounds checked was the Scientific Working Group for the Analysis of Seized Drugs (SWGDRUG) mass spectral library. Some examples of errors found are described. A checklist of errors that curators should look for when performing inter-library comparisons is provided. Graphical Abstract ᅟ.

Analysis of human plasma metabolites across different liquid chromatography/mass spectrometry platforms: Cross-platform transferable chemical signatures.

RATIONALE: The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different liquid chromatography/mass spectrometry (LC/MS) platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. METHODS: Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC/MS platforms using reversed-phase chromatography and different chromatographic scales (conventional HPLC, UHPLC and nanoLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). RESULTS: Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (relative standard deviation (RSD) <2%); however, substantial differences were found in the LC/MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. CONLUSIONS: Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable.

Metabolite profiling of a NIST Standard Reference Material for human plasma (SRM 1950): GC-MS, LC-MS, NMR, and clinical laboratory analyses, libraries, and web-based resources.

Recent progress in metabolomics and the development of increasingly sensitive analytical techniques have renewed interest in global profiling, i.e., semiquantitative monitoring of all chemical constituents of biological fluids. In this work, we have performed global profiling of NIST SRM 1950, "Metabolites in Human Plasma", using GC-MS, LC-MS, and NMR. Metabolome coverage, difficulties, and reproducibility of the experiments on each platform are discussed. A total of 353 metabolites have been identified in this material. GC-MS provides 65 unique identifications, and most of the identifications from NMR overlap with the LC-MS identifications, except for some small sugars that are not directly found by LC-MS. Also, repeatability and intermediate precision analyses show that the SRM 1950 profiling is reproducible enough to consider this material as a good choice to distinguish between analytical and biological variability. Clinical laboratory data shows that most results are within the reference ranges for each assay. In-house computational tools have been developed or modified for MS data processing and interactive web display. All data and programs are freely available online at http://peptide.nist.gov/ and http://srmd.nist.gov/ .

Continuous flow enzyme-catalyzed polymerization in a microreactor.

Enzymes immobilized on solid supports are increasingly used for greener, more sustainable chemical transformation processes. Here, we used microreactors to study enzyme-catalyzed ring-opening polymerization of ε-caprolactone to polycaprolactone. A novel microreactor design enabled us to perform these heterogeneous reactions in continuous mode, in organic media, and at elevated temperatures. Using microreactors, we achieved faster polymerization and higher molecular mass compared to using batch reactors. While this study focused on polymerization reactions, it is evident that similar microreactor based platforms can readily be extended to other enzyme-based systems, for example, high-throughput screening of new enzymes and to precision measurements of new processes where continuous flow mode is preferred. This is the first reported demonstration of a solid supported enzyme-catalyzed polymerization reaction in continuous mode.

The effect of 3D hydrogel scaffold modulus on osteoblast differentiation and mineralization revealed by combinatorial screening.

Cells are known to sense and respond to the physical properties of their environment and those of tissue scaffolds. Optimizing these cell-material interactions is critical in tissue engineering. In this work, a simple and inexpensive combinatorial platform was developed to rapidly screen three-dimensional (3D) tissue scaffolds and was applied to screen the effect of scaffold properties for tissue engineering of bone. Differentiation of osteoblasts was examined in poly(ethylene glycol) hydrogel gradients spanning a 30-fold range in compressive modulus ( approximately 10 kPa to approximately 300 kPa). Results demonstrate that material properties (gel stiffness) of scaffolds can be leveraged to induce cell differentiation in 3D culture as an alternative to biochemical cues such as soluble supplements, immobilized biomolecules and vectors, which are often expensive, labile and potentially carcinogenic. Gel moduli of approximately 225 kPa and higher enhanced osteogenesis. Furthermore, it is proposed that material-induced cell differentiation can be modulated to engineer seamless tissue interfaces between mineralized bone tissue and softer tissues such as ligaments and tendons. This work presents a combinatorial method to screen biological response to 3D hydrogel scaffolds that more closely mimics the 3D environment experienced by cells in vivo.

Single-walled carbon nanotubes: geno- and cytotoxic effects in lung fibroblast V79 cells.

With the development of nanotechnology, there is a tremendous growth of the application of nanomaterials, which increases the risk of human exposure to these nanomaterials through inhalation, ingestion, and dermal penetration. Among different types of nanoparticles, single-walled carbon nanotubes (SWCNT) with extremely small size (1 nm in diameter) exhibit extraordinary properties and offer possibilities to create materials with astounding features. Since the release of nanoparticles in an enclosed environment is of great concern, a study of possible genotoxic effects is important. Our previous data showed that pharyngeal aspiration of SWCNT elicited pulmonary effects in C57BL/6 mice that was promoted by a robust, acute inflammatory reaction with early onset resulting in progressive interstitial fibrogenic response and the formation of granulomas. In the present study, the genotoxic potential of SWCNT was evaluated in vitro. The genotoxic effects of nanoparticles were examined using three different test systems: the comet assay and micronucleus (MN) test in a lung fibroblast (V79) cell line, and the Salmonella gene mutation assay in strains YG1024/YG1029. Cytotoxicity tests showed loss of viability in a concentration- and time-dependent manner after exposure of cells to SWCNT. Results from the comet assay demonstrated the induction of DNA damage after only 3 h of incubation with 96 microg/cm2 of SWCNT. The MN test indicated some but not significant micronucleus induction by SWCNT in the V79 cell line at the highest concentrations tested. With two different strains of Salmonella typhimurium, no mutations were found following SWCNT exposure.

Reactive MALDI mass spectrometry: application to high mass alkanes and polyethylene.

A molecular solid of fullerene (C(60)) intercalated with cobalt cyclopentadienyl dicarbonyl (CoCp(CO)(2)) was shown to be an effective matrix for matrix-assisted laser desorption/ionization mass spectrometry (MALDI) of large alkanes (demonstrated up to C(94)H(190)) and polyethylenes that otherwise cannot be produced as intact ions in the gas phase.

[Determination and analysis of silica particles surface alumino-silicate occlusion].

OBJECTIVE: To investigate the methods of determining aluminum silicate coated on the surface of silica particles and analyze the role of surface occlusion on development of silicosis. METHODS: Respirable dust samples were collected on filters using 2 L/min flow in tungsten mines and pottery factories of Jiangxi province, and tin mines of Guanxi province. Dust particles were analyzed by a multiple-voltage scanning electron microscopy-energy dispersive X-ray spectroscopy (MVSEM-EDS) using 20 KeV and 5 KeV electron beam accelerating voltages. Changes in the silicon to aluminum X-ray line intensity ratio between the two voltages are compared particle by particle. This provided an index that distinguishes a silica particle that was homogeneously aluminum-contaminated from a clay coated silica particle. RESULTS: The total of 3,982 dust particles from 47 dust samples of seven pottery factories, three tin mines and three tungsten mines were analyzed in this study. Significant difference of aluminum silicate coated on the surface of silica particle was shown between particles from pottery factories and tin mines. The average sample percentage of respirbale-sized silica particles alumino-silicate occlusion in the pottery factories (45%) was higher than that in the tin mines (18%) and tungsten mines (13%). CONCLUSION: Higher percentages silica particles alumino-silicate occlusion is observed in the pottery factories than that in metal mines. These surface analysis results help to understand differences in risk of silicosis when exposure is normalized to cumulative respirable surface silica dust.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry interlaboratory comparison of mixtures of polystyrene with different end groups: statistical analysis of mass fractions and mass moments.

A matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) interlaboratory comparison was conducted on mixtures of synthetic polymers having the same repeat unit and closely matching molecular mass distributions but with different end groups. The interlaboratory comparison was designed to see how well the results from a group of experienced laboratories would agree on the mass fraction, and molecular mass distribution, of each polymer in a series of binary mixtures. Polystyrenes of a molecular mass near 9000 u were used. Both polystyrenes were initiated with the same butyl initiator; however, one was terminated with -H (termed PSH) and the other was terminated with -CH2CH2OH (termed PSOH). End group composition of the individual polymers was checked by MALDI-TOF MS and by nuclear magnetic resonance (NMR). Five mixtures were created gravimetrically with mass ratios between 95:5 and 10:90 PSOH/PSH. Mixture compositions where measured by NMR and by Fourier transform infrared spectrometry (FT-IR). NMR and FT-IR were used to benchmark the performance of these methods in comparison to MALDI-TOF MS. Samples of these mixtures were sent to any institution requesting it. A total of 14 institutions participated. Analysis of variance was used to examine the influences of the independent parameters (participating laboratory, MALDI matrix, instrument manufacturer, TOF mass separation mode) on the measured mass fractions and molecular mass distributions for each polymer in each mixture. Two parameters, participating laboratory and instrument manufacturer, were determined to have a statistically significant influence. MALDI matrix and TOF mass separation mode (linear or reflectron) were found not to have a significant influence. Improper mass calibration, inadequate instrument optimization with respect to high signal-to-noise ratio across the entire mass range, and poor data analysis methods (e.g., baseline subtraction and peak integration) seemed to be the greatest obstacles in the correct application of MALDI-TOF MS to this problem. Each of these problems can be addressed with proper laboratory technique.

A 13C CP/MAS and 31P NMR study of the interactions of dipalmitoylphosphatidylcholine with respirable silica and kaolin.

The interaction of silica and kaolin with dipalmitoylphosphatidylcholine (DPPC) has been studied using 13C and 31P solid state nuclear magnetic resonance spectroscopy. These studies explore the molecular interactions of these respirable dusts with a model lung surfactant species to characterize silica toxicity in mixed systems. The choline head group of DPPC was found to remain mobile when adsorbed on kaolin, in contrast to an immobile head group on silica. Further, glycerol carbon intensities were greatly diminished relative to that of choline carbons, a result attributed to broadening effects. These preliminary findings suggest that silica toxicity may not be related to choline mobility as previously noted.