Spectra Library Search Research Articles

Supercritical carbon dioxide extraction of red cypress sawdust: A comparison of solvent extraction vs. steam distillation methods

By using a supercritical carbon dioxide extraction (SFE-CO2) technique, We extracted several fragrances from red cypress sawdust under a condition of 3500 psi and 35°C. The extracts were then analyzed by a gas chromatography/mass spectrometry (GC/MS). After a Wiley mass spectrum library search, We identified most of the major peaks in the GC/MS total ion chromatogram, which are borneol, myrtenol, β-elemene, β-selinene, S-cadinene, and α-pinene, etc. for a total of 26 different compounds. In comparison with n-hexane extraction, ether extraction, steam distillation, and head space sampling techniques, we concluded that(1) the polarity of CO2 under the condition of 3500 psi and 35°C is between ether and water; and(2) most of the fragrances in the cypress sawdust are polar compounds.

Methods to Calculate Spectrum Similarity.

Scoring functions that assess spectrum similarity play a crucial role in many computational mass spectrometry algorithms. These functions are used to compare an experimentally acquired fragmentation (MS/MS) spectrum against two different types of target MS/MS spectra: either against a theoretical MS/MS spectrum derived from a peptide from a sequence database, or against another, previously acquired MS/MS spectrum. The former is typically encountered in database searching, while the latter is used in spectrum clustering and spectral library searching. The comparison between acquired versus theoretical MS/MS spectra is most commonly performed using cross-correlations or probability derived scoring functions, while the comparison of two acquired MS/MS spectra typically makes use of a normalized dot product, especially in spectrum library search algorithms. In addition to these scoring functions, Pearson's or Spearman's correlation coefficients, mean squared error, or median absolute deviation scores can also be used for the same purpose. Here, we describe and evaluate these scoring functions with regards to their ability to assess spectrum similarity for theoretical versus acquired, and acquired versus acquired spectra.

Broad screening and identification of β-agonists in feed and animal body fluid and tissues using ultra-high performance liquid chromatography-quadrupole-orbitrap high resolution mass spectrometry combined with spectra library search

Broad screening and identification of β-agonists in feed, serum, urine, muscle and liver samples was achieved in a quick and highly sensitive manner using ultra high performance liquid chromatography-quadrupole-orbitrap high resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS) combined with a spectra library search. Solid-phase extraction technology was employed for sample purification and enrichment. After extraction and purification, the samples were analyzed using a Q-Orbitrap high-resolution mass spectrometer under full-scan and data-dependent MS/MS mode. The acquired mass spectra were compared with an in-house library (compound library and MS/MS mass spectral library) built with TraceFinder Software which contained the M/Z of the precursor ion, chemical formula, retention time, character fragment ions and the entire MS/MS spectra of 32 β-agonist standards. Screening was achieved by comparing 5 key mass spectral results and positive matches were marked. Using the developed method, the identification results from 10 spiked samples and 238 actual samples indicated that only 2% of acquired mass spectra produced false identities. The method validation results showed that the limit of detection ranged from 0.021–3.854μgkg−1and 0.015–1.198ngmL−1 for solid and liquid samples, respectively.

Detection, quantification, and identification of dermorphin in equine plasma and urine by LC–MS/MS for doping control

Dermorphin is a unique opioid peptide that is 30-40 times more potent than morphine. It was misused and went undetected in horse racing until 2011 when intelligence obtained from a few North American race tracks suggested its use. To prevent such misuse, a reliable analytical method became necessary for detection and identification of dermorphin in post-race horse samples. This paper describes the first liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for such a purpose. Equine plasma and urine samples were pre-treated with ethylenediamine tetra-acetic acid and urea prior to solid-phase extraction (SPE) on Oasis MCX cartridges. Resulting eluates were dried under vacuum and analyzed by LC-MS/MS for dermorphin. The matrix effect, SPE efficiency, intra-day and inter-day accuracy and precision, and stability of the analyte were assessed. The limit of detection was 10 pg/mL in plasma and 20 pg/mL in urine, and the limit of confirmation was 20 pg/mL in plasma and 50 pg/mL in urine. Dermorphin in plasma is stable at ambient temperature, but its diastereomer is unstable. With isotopically labeled dermorphin as an internal standard, the quantification range was 20-10,000 pg/mL in plasma and 50-20,000 pg/mL in urine. The intra-day and inter-day accuracy was from 91 % to 100 % for the low, intermediate, and high concentrations. The intra-day and inter-day coefficients of variation were less than 12 %. The method differentiates dermorphin from its diastereomer. This method is very specific for identification of dermorphin in equine plasma and urine, as assessed by BLAST search and targeted SEQUEST search, and by MS/MS spectrum library search. The method has been successfully applied to analysis of samples collected following dermorphin administration to research horses and of official post-race samples.

QuickMod: A Tool for Open Modification Spectrum Library Searches

MS2 library spectra are rich in reproducible information about peptide fragmentation patterns compared to theoretical spectra modeled by a sequence search tool. So far, spectrum library searches are mostly applied to detect peptides as they are present in the library. However, they also allow finding modified variants of the library peptides if the search is done with a large precursor mass window and an adapted Spectrum-Spectrum Match (SSM) scoring algorithm. We perform a thorough evaluation on the use of library spectra as opposed to theoretical peptide spectra for the identification of PTMs, analyzing spectra of a well-annotated modification-rich test data set compiled from public data repositories. These initial studies motivate the development of our modification tolerant spectrum library search tool QuickMod, designed to identify modified variants of the peptides listed in the spectrum library without any prior input from the user estimating the modifications present in the sample. We built the search algorithm of QuickMod after carefully testing different SSM similarity scores. The final spectrum scoring scheme uses a support vector machine (SVM) on a selection of scoring features to classify correct and incorrect SSM. After identification of a list of modified peptides at a given False Discovery Rate (FDR), the modifications need to be positioned on the peptide sequence. We present a rapid modification site assignment algorithm and evaluate its positioning accuracy. Finally, we demonstrate that QuickMod performs favorably in terms of speed and identification rate when compared to other software solutions for PTM analysis.

A Simulated MS/MS Library for Spectrum-to-spectrum Searching in Large Scale Identification of Proteins

Identifying peptides from mass spectrometric fragmentation data (MS/MS spectra) using search strategies that map protein sequences to spectra is computationally expensive. An alternative strategy uses direct spectrum-to-spectrum matching against a reference library of previously observed MS/MS that has the advantage of evaluating matches using fragment ion intensities and other ion types than the simple set normally used. However, this approach is limited by the small sizes of the available peptide MS/MS libraries and the inability to evaluate the rate of false assignments. In this study, we observed good performance of simulated spectra generated by the kinetic model implemented in MassAnalyzer (Zhang, Z. (2004) Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 76, 3908-3922; Zhang, Z. (2005) Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. Anal. Chem. 77, 6364-6373) as a substitute for the reference libraries used by the spectrum-to-spectrum search programs X!Hunter and BiblioSpec and similar results in comparison with the spectrum-to-sequence program Mascot. We also demonstrate the use of simulated spectra for searching against decoy sequences to estimate false discovery rates. Although we found lower score discrimination with spectrum-to-spectrum searches than with Mascot, particularly for higher charge forms, comparable peptide assignments with low false discovery rate were achieved by examining consensus between X!Hunter and Mascot, filtering results by mass accuracy, and ignoring score thresholds. Protein identification results are comparable to those achieved when evaluating consensus between Sequest and Mascot. Run times with large scale data sets using X!Hunter with the simulated spectral library are 7 times faster than Mascot and 80 times faster than Sequest with the human International Protein Index (IPI) database. We conclude that simulated spectral libraries greatly expand the search space available for spectrum-to-spectrum searching while enabling principled analyses and that the approach can be used in consensus strategies for large scale studies while reducing search times.

Simultaneous determination and spectra correction of air toxic organic compounds using pls and ann in ftir spectroscopy

In this paper, the residual spectra library search was used to correct the spectrum containing one interferent. Two groups of which each sample contained no or one interferent were supplied to amplify the above method. PLS was used to identify the interferents and correct the spectra, the corrected spectra information was sent into the PLS(Partial Least Squares) and ANN(Artificial Neural Network) prediction step. The concentration of each component in the unknown mixtures was determined using two different prediction method. The RSD%(mean relative standard deviation) for the two groups was calculated respectively. The prediction results of PLS and ANN was compared to illustrate which one is better in solving this problem.

Determination of Panthenol, Cholecalciferol and Tocopherol in Cosmetic Products by Gas Chromatography‐Mass Spectrometry in SIM Mode

A novel simple method to detect vitamins in cosmetic products by gas chromatography-mass spectrometry (GC-MS) has been developed. Three vitamins (panthenol, cholecalciferol and tocopherol) were used for this study. Vitamins were prepared by dissolving in tetrahydrofuran (ThF), and silylated with bis-trimethylsilyltri-fluoroacetamide- trichloromethylsilane (BSTFA). Silylated vitamins were separated on a fused-silica capillary column coated with DB-5. The identification of each vitamin was accomplished by retention time and mass spectrum library search with a computer, and the quantitation was made in the selected-ion monitoring (SIM) mode of GC-MS. SIM mode had given sensitivity to determine 50 pg of panthenol, 285 pg of cholecalciferol and 130 pg of tocopherol. Linearity was maintained over the range 0.005-0.20% for each vitamin. Each cosmetic product (i.e. hair tonic and lotion) was found to contain amounts of the vitamins. This method was sensitive and gave 77.5-99.9% recovery of each vitamin from these cosmetic products. From these results, we concluded that silylation with BSTFA followed by GC-MS analysis allows the simple, convenient and exact determination of panthenol, cholecalciferol and tocopherol.

Elimination of Interferents Influence in Simultaneous Determination of Organic Gases Using PLS with FTIR Spectroscopy*

The most serious problem in multivariate calibration analysis is that the prediction samples may contain the interferents which are not modeled in the calibration step. Then how to detect the interferents and eliminate their influence is significantly important in order to obtain the correct compositional analysis results. The so-called residual spectra library search is supplied and an iterative loop regression algorithm to successfully correct the spectrum containing two interferents is developed in this paper. Three groups of which each sample contains no, one or two interferents are supplied to amplify the above method. The mean relative standard deviation (RSD) for the three groups are 0.163, 0.375, 0.355%, respectively. There are no comparable difference among these RSDs, which proves the validation of the method provided in this paper. The results specify that PLS with FTIR spectroscopy is a powerful tool to resolve both the multicomponent simultaneous determination and the identification of interferents when combined with additional diagnostic and corrected procedure. *The project was supported by National Natural Science Foundation of China and Ph.D Foundation of National Education Committee.

Separation and characterization of steroids in biomass vacuum pyrolysis oils

Large-scale thermochemical conversion under vacuum of various common wood species yielded a series of steroids which have rarely been reported in plants. Heating under vacuum accelerates the removal of extractives from the plant biological matrices without any significant modification. Gravity-flow column liquid chromatography on silica gel, thin-layer chromatography and high-resolution gas chromatography interfaced with a mass spectrometer were the principal methods used for the separation and quantitative analysis of the steroids. Identification was based on the NBS mass spectra library search file and comparison with the gas chromatographic retention times of the authentic compounds. Steroid distributions of softwood and hardwood species were compared.

Scope and limitations of a general unknown screening by gas chromatography—mass spectrometry in acute poisoning

The gold standard for the diagnosis of acute poisoning is toxicological analysis. Because information on the incorporated toxic substance provided by the patient or his relatives is known from experience to be unreliable in about 40% of all intoxications, a screening procedure that covers most relevant drugs and toxicants is required rather than an analytical procedure optimized for the identification of a single class of substances. The special task for a general unknown screening procedure is to identify a toxic substance among endogenous or food-derived substances as well as environmental toxicants in a biological matrix on an emergency basis. Because the unknown toxic substance may vary considerably in its physicochemical properties and its concentration range, a universally applicable screening procedure is required. Although gas chromatography-mass spectrometry has been used for three decades, it still offers many unique advantages in terms of sensitivity, specificity, reliability, and coverage of a large number of toxic substances. Because the procedure has to be kept as simple and as short as possible, compromises have to be made with respect to extraction, derivatization, and mass-spectral techniques. The specimen of choice for a general unknown screening is-if available-urine. The standard mode of ionization is electron impact. The identification of unknown substances is highly challenging because, in our experience, previously unknown metabolites may be detected rather frequently in acute poisoning. Although an automated mass spectra library search considerably facilitates the identification process, expert knowledge on the identification of substances not included in the library as well as knowledge in clinical toxicology and metabolism is indispensable.

Determination of salicylate- and benzophenone-type sunscreen agents in cosmetic products by gas chromatography-mass spectrometry

A novel simple method to detect salicylate- and benzophenone-type sunscreen agents in cosmetic products by gas chromatography-mass spectrometry (GC-MS) has been developed. Seven sunscreen agents (two salicylate-type and five benzophenone-type) were used for this study. Sunscreen agents and cosmetic product solutions were prepared by dissolving in dimethylformamide, and silylated with bis-trimethylsilyltrifluoroacetamide-trichloro-methylsilane (BSTFA). Silylated sunscreen agents were separated on a cross-linked methyl silicone gum column. The identification of each sunscreen agent was accomplished by retention time and mass spectrum library search with a computer, and the quantitation was made in the selected-ion monitoring (SIM) mode of GC-MS. Silylation increased the detection limits of all sunscreen agents about 20–170-fold. Linearity was maintained over the range 1–300 μg ml for each sunscreen agent. Each cosmetic product (i.e. sun lotion, sun cream and sun cream foundation) was found to contain amounts of the sunscreen agents. This method was sensitive and gave 95.2–104.1% recovery of each sunscreen agent from these cosmetic products. From these results, we concluded that silylation with BSTFA followed by GC-MS analysis allows the simple, convenient and exact determination of sunscreen agents from cosmetic products.

Identification of tryptophan and tyrosine residues in peptides separated by capillary electrophoresis by their second-derivative spectra using diode-array detection

The use of diode-array detection allows the non-destructive identification of tryptophan and tyrosine residues in complex peptide mixtures separated by capillary electrophoresis. Second-order derivative spectra of both amino acids show significant differences while zero-order spectra are overlapping to a great extent. A mixture of peptides containing tryptophan and/or tyrosine residues was used to evaluate this method. Tryptic peptide maps of carbonic anhydrase and of the bacterial chaperonin protein GroEL, and of an autodigest of trypsin were characterized for tryptophan- and tyrosine-containing peptides. Automated spectra library search was performed successfully.

Pyrolysis—gas chromatography/mass spectrometry in the characterization of glycated albumin

Pyrolysis-GC/MS has been employed to characterize the products arising from the interaction between glucose and albumin. The pyrolysis products of genuine bovine serum albumin and glycated bovine serum albumin have been compared, after an extensive study devoted to the optimization of the pyrolysis conditions. Clear differences between the pyrograms of glycated and non-glycated samples have been found, confirming the validity of such an analytical approach. The structures of some components, characteristic of glycation, have been tentatively assigned on the basis of a mass spectra library search.

Automated screening for drug metabolites with high-performance liquid chromatography UV-visible diode array detection and spectra library search

Automated screening for drug metabolites with high-performance liquid chromatography UV-visible diode array detection and spectra library search

Optimization of search algorithms for a mass spectra library

The SISCOM mass spectra library search is mainly an interpretative system producing a “hit list” of similar spectra based on six comparison factors. This paper deals with extension of the system; the aim is exact identification (retrieval) of those reference spectra in the SISCOM hit list that correspond to the unknown compounds or components of the mixture. Thus, instead of a similarity measure, a decision (retrieval) function is needed to establish the identity of reference and unknown compounds by comparison of their spectra. To facilitate estimation of the weightings of the different variables in the retrieval function, pattern recognition algorithms were applied. Numerous statistical evaluations of three different library collections were made to check the quality of data bases and to derive appropriate variables for the retrieval function.

A quality index for spectra library search methods

For an objective judgement of spectra library search methods it is necessary to quantify the success of these methods. Therefore, a procedure for calculating a factor to measure the success of a library search method is described. As an example, the application of the method to low-resolution mass spectra is described.