Chemical substructure identification by mass spectral library searching

A library-search procedure that identifies structural features of an unknown compound from its electron-ionization mass spectrum is described. Like other methods, this procedure first retrieves library compounds whose spectra are most similar to the spectrum of an unknown compound. It then deduces structural features of the unknown compound from the chemical structures of the retrievals. Unlike other methods, the significance of each retrieved spectrum is weighted according to its similarity to the spectrum of the unknown compound. Also, a “peaks-in-common” screening step serves to reduce search times and an optimized dot product function provides the match factor. If the molecular weight of the unknown compound is provided, the identification of certain substructures can be improved by including “neutral loss” peaks. Correlations between the presence of a substructure in a test compound and its presence among library retrievals were derived from the results of searching the NIST/EPA/NIH reference library with a 7891 compound test set. These correlations allow the estimation of probabilities of substructure occurrence and absence in an unknown compound from the results of a library search. This method may be viewed as an optimization of the “K-nearest neighbor” method of Isenhour and co-workers, with improvements that arise from spectrum screening, peak scaling, an optimal distance measure, a relative-distance weighting scheme, and a larger reference library.     

Evaluating electron ionization mass spectral library search results

As the size of various collections of electron ionization mass spectra gets larger, there is a continuing and increasing propensity to rely on the results of computerized library searches. The results of these computerized searches do not necessarily account for a spectrum that is produced by the mixture of two or more different compounds. Sometimes the submitted spectrum is not that of a compound whose spectrum is in the library. The quality of the spectrum submitted to the library is often such that the numerical confidence level reported for the search result is so low that it will cause the result to be disregarded. When the sample spectrum is matched against library spectra that have been condensed, the search result can be misleading. Three different examples of mass spectral search results are examined: one, with a high confidence level that the unknown has been identified, but the results are incorrect; one, where the spectrum of the unknown compound is not in the library; one, where consideration of the numerical search results would cause a positive identity not to be confirmed.     

Optimization and testing of mass spectral library search algorithms for compound identification

Five algorithms proposed in the literature for library search identification of unknown compounds from their low resolution mass spectra were optimized and tested by matching test spectra against reference spectra in the NIST-EPA-NIH Mass Spectral Database. The algorithms were probability-based matching (PBM), dot-product, Hertz et al. similarity index, Euclidean distance, and absolute value distance. The test set consisted of 12,592 alternate spectra of about 8000 compounds represented in the database. Most algorithms were optimized by varying their mass weighting and intensity scaling factors. Rank in the list of candidatc compounds was used as the criterion for accuracy. The best performing algorithm (75% accuracy for rank 1) was the dot-product function that measures the cosine of the angle between spectra represented as vectors. Other methods in order of performance were the Euclidean distance (72%), absolute value distance (68%) PBM (65%), and Hertz et al. (64%). Intensity scaling and mass weighting were important in the optimized algorithms with the square root of the intensity scale nearly optimal and the square or cube the best mass weighting power. Several more complex schemes also were tested, but had little effect on the results. A modest improvement in the performance of the dot-product algorithm was made by adding a term that gave additional weight to relative peak intensities for spectra with many peaks in common.     

Discovery of mass spectral characteristics and automatic identification of wax esters from gas chromatography mass spectrometry data

The mass spectral characteristics of wax esters were systemically summarized and interpreted through data mining of their standard mass spectra taken from NIST standard mass spectral library. Combining with the rules of retention indices described in the previous study, an automatic system was subsequently developed to identify the structural information for wax esters from GC/MS data. After tested and illustrated by both simulated and real GC/MS data, the results indicate that this system could identify wax esters except the polyunsaturated ones and the mass spectral characteristics are useful and effective information for identification of wax esters.     

A mass spectral library based on chemical ionization and collision-induced dissociation

Antibodies were purified from normal rabbit, sheep, goat, rat, human and bovine serum using preparative electrophoresis on a Gradiflow in a single-step process using an asymmetrical cartridge with three different pore size polyacrylamide membranes. Recoveries in each case were over 80% and were higher than those obtained using affinity chromatography on protein A, protein G or protein L. Degree of purity was at least comparable with these methods. These results suggest that preparative electrophoresis can be considered a general method for the purification of research quantities of antibodies from multiple serum sources and may be particularly useful where the reactivity with protein A, G or L is unknown.     

Computer-assisted library search system for identification of unknown mass spectra

The library search system described identifies a single component or two components in the unknown pure or mixture mass spectra by comparing them with a large data base of reference spectra. A preliminary search is based on the spectral interpretation and the main search is based on the probability of peak appearance. The performance of this system was tested on 254 pure spectra and 88 mixture spectra. The percentages of successful search by using the NIH/EPA/MSDC data base were 75% for the pure spectra, and 63% for both the first and second components in mixture spectra. The percentages of successful search improved to 94% for the first components of the mixture spectra and 77% for both first and second components of the mixture spectra, when conditions for measurement of reference spectra were the same as those for the unknown spectra.     

Development of a dedicated peptide tandem mass spectral library for conservation science

In recent years, the use of liquid chromatography tandem mass spectrometry (LC–MS/MS) on tryptic digests of cultural heritage objects has attracted much attention. It allows for unambiguous identification of peptides and proteins, and even in complex mixtures species-specific identification becomes feasible with minimal sample consumption. Determination of the peptides is commonly based on theoretical cleavage of known protein sequences and on comparison of the expected peptide fragments with those found in the MS/MS spectra. In this approach, complex computer programs, such as Mascot, perform well identifying known proteins, but fail when protein sequences are unknown or incomplete. Often, when trying to distinguish evolutionarily well preserved collagens of different species, Mascot lacks the required specificity. Complementary and often more accurate information on the proteins can be obtained using a reference library of MS/MS spectra of species-specific peptides. Therefore, a library dedicated to various sources of proteins in works of art was set up, with an initial focus on collagen rich materials. This paper discusses the construction and the advantages of this spectral library for conservation science, and its application on a number of samples from historical works of art.     

Estimating probabilities of diabetes mellitus using neural networks

Classification problems are often encountered in medical diagnosis. This paper presents an introduction to classification theory and shows how artificial neural networks can be used for classification. We also map out a bootstrapped procedure for interval estimation of posterior probabilities. The entire procedure is illustrated using the diabetes mellitus data in Pima Indians.     

Tune compounds for electrospray ionisation/in-source collision-induced dissociation with mass spectral library searching

Haloperidol, paracetamol, metronidazole and metamizole have been tested as tune compounds for electrospray ionisation in-source collision-induced dissociation MS (ESI-CID-MS) with two different mass spectrometers (Sciex API 365 and Agilent 1100 MSD SL). The different electrospray sources of API 365 and MSD 1100 SL consist of an orifice with nitrogen curtain gas and a capillary interface, respectively. In-source CID occurs in both interfaces in front of the skimmers, which separate a region with a vacuum of approximately 300 Pa and the high vacuum (<10(-3) Pa). Comparison of the breakdown curves of selected tune compounds, depending on collision energy (orifice or fragmentor voltage), showed, that very similar fragmentation can be obtained with both instruments, when adjusting the fragmentor voltage of the MSD 1100 SL to higher values than the orifice voltage of the API 365. For three energy levels--low, medium and high--the corresponding voltages were 20, 50 and 80 V for the API 365 and 110, 190, 230 V for the MSD 1100 SL. These voltages resulted in the most similar spectra for haloperidol and paracetamol with both instruments. The comparison of ESI-CID-MS of all tune compounds at three energy levels showed, that - despite variations in relative ion abundances - all significant ions were present in one of the three CID spectra. Therefore, mass spectral library searching of an ESI-CID-MS library set-up with one of the two instruments should be possible with the other instrument after adjusting the CID energies by means of at least two tune compounds such as haloperidol and paracetamol, metronidazole or metamizole.     

Simple modification of a protein database for mass spectral identification of N-linked glycopeptides

We describe an algorithm which modifies a protein database such that during a database search deamidation is limited to asparagines strictly contained within the N-glycosylation consensus sequence. The modified database was evaluated using a dataset created from the shotgun proteomic analysis of N-linked glycopeptides from human blood serum. We demonstrate that the application of the modified database eliminates incorrect glycopeptide assignments, reduces the peptide false-discovery rate, and eliminates the need for manual validation of glycopeptide identifications.     

荧光衍生-高效液相色谱分离及质谱鉴定芳香胺

含氮杂环光致发光分子经柱前衍生化,采用荧光检测及柱后在线质谱鉴定对废水中胺类化合物进行了测定.衍生物荧光激发和发射波长分别为λex=275 nm,λem=380 nm.在pH 8.0的硼酸钠缓冲液中,于40 ℃下衍生反应40 min后获得稳定的荧光产物.在Hypersil BDS C18柱上,采用梯度洗脱对5种芳香胺衍生物进行了优化分离.采用大气压化学电离源(APCI Source)正离子模式进行在线的柱后质谱定性,实现了5种芳香胺衍生物的快速、准确测定.方法具有良好的重现性,线性回归系数大于0.9998,检出限在71～81 fmol水平.     

Average peptide score: a useful parameter for identification of proteins derived from database searches of liquid chromatography/tandem mass spectrometry data

The quantity and variable quality of data that can be generated from liquid chromatography (LC)/mass spectrometry (MS)-based proteomics analyses creates many challenges in interpreting the spectra in terms of the actual proteins in a complex sample. In spite of improvements in algorithms that match putative peptide sequences to MS/MS spectra, the assembly of these lists of possible or probable peptides into a 'correct' set of proteins is still problematic. We have observed a trend in a simple relationship, derived from standard database search outputs, which can be useful in assessing the quality of a MS/MS-based protein identification. Specifically, the ratio of the protein score and number of non-redundant peptides, or average peptide score (APS), can facilitate initial filtering of database search results in addition to providing a useful measure of confidence for the proteins identified. This parameter has been applied to results from the analysis of multi-protein complexes derived from pull-down experiments analyzed using a two-dimensional LC/MS/MS workflow. In particular, the complex list of protein identifications derived from a drug affinity pull-down with immobilized ampicillin and an E. coli lysate was greatly simplified by applying the APS as a filter, allowing for facile identification of the penicillin-binding proteins known to interact with ampicillin. Furthermore, an APS threshold can be used for any data sets derived from electrospray ionization (ESI)- or matrix-assisted laser desorption/ionization (MALDI)-MS/MS experiments and is also not specific to any database search program.     

A quantitative measure of the reliability of searches of spectral libraries

A quantitative measure of library search reliability has been developed. Applications of the quantitative reliability metric (QRM) for evaluating the reliability of library searches for unknown target spectra and the use of this measure to detect the failure of a library search caused by noise, contaminant peaks and missing library spectra are discussed. The effects of noise and composite infrared spectra of mixtures on the QRM are examined for test sets of 561 infrared spectra. The QRM is also used to evaluate the performance of a search of an infrared library compressed by eigenvector projection.     

Development of fast atom bombardment mass spectral methods for the identification of carcinogen-nucleoside adducts

An analytical strategy using fast atom bombardment (FAB) ionization and tandem mass spectrometry has been developed to determine the molecular weight and major fragment ions, and to provide limited structural characterization of low picomole levels of carcinogen-nucleoside adducts. This strategy consists of three main components: (1) the sensitivity for analysis by FAB combined with mass spectrometry is increased via chemical derivatization; (2) the nucleoside adducts are selectively detected by using constant neutral loss scans; and (3) structurally characteristic fragments are obtained by using daughter ion scans. Trimethylsilyl derivatized arylamine-nucleoside adducts have been detected at levels as low as a few picomoles by using this approach. After experimental determination of the mass of the BH ₂ ⁺ fragment ion, daughter ion spectra have been used to probe the structure specificity associated with collision-activated decomposition of this fragment. With model C-8 substituted arylamine adducts [N-(deoxyguanosin-8-yl)-4-aminobiphenyl, N-(deoxyadenosin--yl)-4-aminobiphenyl, and N-(deoxyguanosin-8-yl)-2-aminofluorene], nucleoside-specific and carcinogen-specific fragmentation have been observed in daughter ion spectra.     

A combined forward—reverse library search system for the identification of low-resolution mass spectra

A combined forward—reverse library search routine for low-resolution mass spectra is described. The routine requires binary-coded spectra. Masses and peak intensities are used for spectral comparison. On the basis of three possible search strategies, this routine is adaptable to analytical problems. The program was tested for 25 000 spectra from the ISAS, MSDC and EPA mass spectra libraries. The program is written completely in FORTRAN IV.     

Chromatographic and mass spectral methods of identification for the side-chain and ring regioisomers of methylenedioxymethamphetamine

The popular drug of abuse 3,4-methylenedioxymethamphetamine (MDMA) is one of a total of 10 regioisomeric 2,3- and 3,4-methylenedioxyphenethylamines of MW 193 that yields regioisomeric fragment ions with equivalent mass (m/z 58 and 135/136) in the electron-impact (EI) mass spectrum. Thus, these 10 methylenedioxyphenethylamines are uniquely isomeric; they have the same molecular weight and equivalent major fragments in their mass spectra. The specific identification of one of these compounds (i.e., Ecstasy or 3,4-MDMA) in a forensic drug sample depends upon the analyst's ability to eliminate the other regioisomers as possible interfering or coeluting substances. This study reports the synthesis, chemical properties, spectral characterization, and chromatographic analysis of these 10 unique regioisomers. The ten 2,3- and 3,4-regioisomers of MDMA are synthesized from commercially available precursor chemicals. In the EI mass spectra, the side-chain regioisomers show some variation in the relative intensity of the major ions, with the exception of only one or two minor ions that might be considered side-chain specific fragments. The position of substitution for the methylenedioxy ring is not easily determined by mass spectral techniques, and the ultimate identification of any one of these amines with the elimination of the other nine must depend heavily upon chromatographic methods. The chromatographic separation of these 10 uniquely regioisomeric amines are studied using reversed-phase liquid chromatographic methods with gradient elution and gas chromatographic techniques with temperature program optimization.