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PubMed2000

A statistical basis for testing the significance of mass spectrometric protein identification results.

A method for testing the significance of mass spectrometric (MS) protein identification results is presented. MS proteolytic peptide mapping and genome database searching provide a rapid, sensitive, and potentially accurate means for identifying proteins. Database search algorithms detect the matching between proteolytic peptide masses from an MS peptide map and theoretical proteolytic peptide masses of the proteins in a genome database. The number of masses that matches is used to compute a score, S, for each protein, and the protein that yields the best score is assumed as the identification result. There is a risk of obtaining a false result, because masses determined by MS are not unique; i.e., each mass in a peptide map can match randomly one or several proteins in a genome database. A false result is obtained when the score, S, due to random matching cannot be discerned from the score due to matching with a real protein in the sample. We therefore introduce the frequency function, f(S), for false (random) identification results as a basis for testing at what significance level, alpha, one can reject a null hypothesis, H0: "the result is false". The significance is tested by comparing an experimental score, S(E), with a critical score, S(C), required for a significant result at the level alpha. If S(E) > or = S(C), H0 is rejected. f(S) and S(C) were obtained by simulations utilizing random tryptic peptide maps generated from a genome database. The critical score, S(C), was studied as a function of the number of masses in the peptide map, the mass accuracy, the degree of incomplete enzymatic cleavage, the protein mass range, and the size of the genome. With S(C) known for a variety of experimental constraints, significance testing can be fully automated and integrated with database searching software used for protein identification.

Genome↗

PubMed2000

Raman spectroscopic method for identification of clinically relevant microorganisms growing on solid culture medium.

Routine clinical microbiological identification of pathogenic microorganisms is largely based on nutritional and biochemical tests. In the case of severely ill patients, the unavoidable time delay associated with such identification procedures can be fatal. We present a novel identification method based on confocal Raman microspectroscopy. With this approach it is possible to obtain Raman spectra directly from microbial microcolonies on the solid culture medium, which have developed after only 6 h of culturing for the most commonly encountered organisms. Due to the limited thickness of microcolonies, some of the underlying culture medium is sampled together with the bacteria. Spectra measured at different depths in a microcolony contain different amounts of the medium signal. A mathematical routine, involving vector algebra, is described for the nonsubjective correction of spectra for variable signal contributions of the medium. To illustrate the possibilities of our approach for the identification of microorganisms, Raman spectra were collected from 6-h microcolonies of five bacterial strains on solid culture medium. The classification results show that confocal Raman microspectroscopy has great potential as a powerful new tool in clinical diagnostic microbiology.

Bacteriological Techniques↗

PubMed2000

Site-specific mass tagging with stable isotopes in proteins for accurate and efficient protein identification.

Proteolytic peptide mass mapping as measured by mass spectrometry provides a major approach for the identification of proteins. A protein is usually identified by the best match between the measured and calculated m/z values of the proteolytic peptides. A unique identification is, however, heavily dependent upon the mass accuracy and sequence coverage of the fragment ions generated by peptide ionization. Without ultrahigh instrumental accuracy, it is possible to increase the specificity of the assignments of particular proteolytic peptides by the incorporation of selected amino acid residue(s) enriched with stable isotope(s) into the protein sequence. Here we report this novel method of generating residue-specific mass-tagged proteolytic peptides for accurate and efficient protein identification. Selected amino acids are labeled with 13C/15N/2H and incorporated into proteins in a sequence-specific manner during cell culturing. Each of these labeled amino acids carries a defined mass change encoded in its monoisotopic distribution pattern. Through their characteristic patterns, the peptides with mass tags can then be readily distinguished from other peptides in mass spectra. This method of identifying unique proteins can also be extended to protein complexes and will significantly increase data search specificity, efficiency, and accuracy for protein identifications.

Amino Acid Sequence↗

PubMed2000

DNA identification of commercial ginseng samples.

An investigation was performed with the objective of developing a DNA-based protocol for the identification of commercial samples of the herbal compound ginseng. There are currently two major herbal products referred to as ginseng. They are Korean or Chinese ginseng (Panax ginseng) and American ginseng (Panax quinquefolius). The market for ginseng in the United States is estimated to be approximately $300 million annually. Current tests for ginseng species identification rely on expert botanical identification of fresh plant/root specimens or on biochemical characterization of active and marker compounds (e.g., ginsenosides). For the determination of the feasibility of ginseng identification by DNA analysis, a strategy based on the direct DNA sequence analysis of the nuclear ribosomal internal transcribed spacer region was developed. Other genetic tests included sequence analysis of the chloroplast ribulose 1,5-bisphosphate carboxylase large subunit gene and DNA fingerprinting by the rapid amplification of polymorphic DNA technique. To confirm the results, each ginseng sample was identified using high-performance liquid chromatography. All methods were successful in distinguishing American from Korean ginseng. In addition, the protocol was improved for the isolation of genomic and plastid DNA from commercial ginseng preparations by incorporating an impact homogenization step into the standard column chromatography purification procedure.

Base Sequence↗

PubMed2005

Fish species identification using PCR-RFLP analysis and lab-on-a-chip capillary electrophoresis: application to detect white fish species in food products and an interlaboratory study.

Identification of 10 white fish species associated with U.K. food products was achieved using PCR-RFLP of the mitochondrial cytochrome b gene. Use of lab-on-a-chip capillary electrophoresis for end-point analysis enabled accurate sizing of DNA fragments and identification of fish species at a level of 5% (w/w) in a fish admixture. One restriction enzyme, DdeI, allowed discrimination of eight species. When combined with NlaIII and HaeIII, specific profiles for all 10 species were generated. The method was applied to a range of products and subjected to an interlaboratory study carried out by five U.K. food control laboratories. One hundred percent correct identification of single species samples and six of nine admixture samples was achieved by all laboratories. The results indicated that fish species identification could be carried out using a database of PCR-RFLP profiles without the need for reference materials.

Animals↗

PubMed2006

Comparison of vacuum matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI (AP-MALDI) tandem mass spectrometry of 2-dimensional separated and trypsin-digested glomerular proteins for database search derived identification.

Mass spectrometric based sequencing of enzymatic generated peptides is widely used to obtain specific sequence tags allowing the unambiguous identification of proteins. In the present study, two types of desorption/ionization techniques combined with different modes of ion dissociation, namely vacuum matrix-assisted laser desorption/ionization (vMALDI) high energy collision induced dissociation (CID) and post-source decay (PSD) as well as atmospheric pressure (AP)-MALDI low energy CID, were applied for the fragmentation of singly protonated peptide ions, which were derived from two-dimensional separated, silver-stained and trypsin-digested hydrophilic as well as hydrophobic glomerular proteins. Thereby, defined properties of the individual fragmentation pattern generated by the specified modes could be observed. Furthermore, the compatibility of the varying PSD and CID (MS/MS) data with database search derived identification using two public accessible search algorithms has been evaluated. The peptide sequence tag information obtained by PSD and high energy CID enabled in the majority of cases an unambiguous identification. In contrast, part of the data obtained by low energy CID were not assignable using similar search parameters and therefore no clear results were obtainable. The knowledge of the properties of available MALDI-based fragmentation techniques presents an important factor for data interpretation using public accessible search algorithms and moreover for the identification of two-dimensional gel separated proteins.

Algorithms↗

PubMed2000

RFLP analysis of the ribosomal internal transcribed spacers and the 5.8S rRNA gene region of the genus Saccharomyces: a fast method for species identification and the differentiation of flor yeasts.

The PCR amplification and subsequent restriction analysis of the region spanning the internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene was applied to the identification of yeasts belonging to the genus Saccharomyces. This methodology has previously been used for the identification of some species of this genus, but in the present work, this application was extended to the identification of new accepted Saccharomyces species (S. kunashirensis, S. martiniae, S. rosinii, S. spencerorum, and S. transvaalensis), as well as to the differentiation of an interesting group of Saccharomyces cerevisiae strains, known as flor yeasts, which are responsible for ageing sherry wine. Among the species of the Saccharomyces sensu lato complex, the high diversity observed, either in the length of the amplified region (ranged between 700 and 875 bp) or in their restriction patterns allows the unequivocal identification of these species. With respect to the four sibling species of the Saccharomyces sensu stricto complex, only two of them, S. bayanus and S. pastorianus, cannot be differentiated according to their restriction patterns, which is in accordance with the hybrid origin (S. bayanus x S. cerevisiae) of S. pastorianus. The flor S. cerevisiae strains exhibited restriction patterns different from those typical of the species S. cerevisiae. These differences can easily be used to differentiate this interesting group of strains. We demonstrate that the specific patterns exhibited by flor yeasts are due to the presence of a 24-bp deletion located in the ITS 1 region and that this could have originated as a consequence of a slipped-strand mispairing during replication or be due to an unequal crossing-over. A subsequent restriction analysis of this region from more than 150 flor strains indicated that this deletion is fixed in flor yeast populations.

Cluster Analysis↗

PubMed2003

Application of a new method of nonlinear dynamical system identification to biochemical problems.

The system identification method for a variety of nonlinear dynamic models is elaborated. The problem of identification of an original nonlinear model presented as a system of ordinary differential equations in the Cauchy explicit form with a polynomial right part reduces to the solution of the system of linear equations for the constants of the dynamical model. In other words, to construct an integral model of the complex system (phenomenon), it is enough to collect some data array characterizing the time-course of dynamical parameters of the system. Collection of such a data array has always been a problem. However difficulties emerging are, as a rule, not principal and may be overcome almost without exception. The potentialities of the method under discussion are demonstrated by the example of the test problem of multiparametric nonlinear oscillator identification. The identification method proposed may be applied to the study of different biological systems and in particular the enzyme kinetics of complex biochemical reactions.

Enzymes↗

PubMed2004

Lineup identification by children: effects of clothing bias.

This study examined effects of clothing cues on children's identification accuracy from lineups. Four- to 14-year-olds (n = 228) saw 12 video clips of individuals, each wearing a distinctly colored shirt. After watching each clip children were presented with a target-present or target-absent photo lineup. Three clothing conditions were included. In 2 conditions all lineup members wore the same colored shirt; in the third, biased condition, the shirt color of only one individual matched that seen in the preceding clip (the target in target-present trials and the replacement in target-absent trials). Correct identifications of the target in target-present trials were most frequent in the biased condition, whereas in target-absent trials the biased condition led to more false identifications of the target replacement. Older children were more accurate than younger children, both in choosing the target from target-present lineups and rejecting target-absent lineups. These findings suggest that a simple clothing cue such as shirt color can have a significant impact on children's lineup identification accuracy.

Adolescent↗

PubMed2000

Effect of landmark identification on cephalometric measurements: guidelines for cephalometric analyses.

Identification of craniofacial landmarks, particularly condylar anatomy, on the lateral cephalometric radiograph is erratic. The accuracy of recognition is critical for proper diagnosis of malocclusion and for assessing growth and orthodontic treatment. The aim of this study was to evaluate the identification of condylion and other cephalometric landmarks commonly used, or thought to be easily identifiable. A lateral cephalograph was taken on each of 34 adult subjects. Five examiners, three orthodontists, a dental radiologist and a second-year orthodontic resident rated the condyle, along with sella (S), nasion (Na), point A (A), infradentale (I), pogonion (Pog) and menton (Me) as identifiable, non-identifiable and interpreted. In addition, distances between several of these landmarks were measured. The left condyle, subject to less magnification than the right condyle because it is closer to the film, was more identifiable than the right condyle, which had the highest rating as non-identifiable. Among other landmarks, nasion and point A were the least identifiable, Pog and Me the most. Correlation coefficients for measurements between identifiable landmarks (I-Me) were greater than coefficients for distances involving less identifiable landmarks (S-A). Interestingly, linear measurements were less variable than the identification of corresponding landmarks. These findings corroborate the previous conclusions that clearly identifiable (and the least amount of interpreted) landmarks should be used for proper evaluation of dentofacial relationships. They also suggest, on average, precision in landmark identification is more critical for research purposes than in routine clinical cephalomteric measurements, which serve only as a guide to diagnosis.

Journal Article↗

PubMed1991

Behavior identification as a mediator of dispositional inference.

According to Trope's (1986) 2-stage model, the use of situational information ("A was teased") to identify behavior ("A reacted aggressively") may result in subsequent dispositional inferences ("A is an aggressive person") that seem insensitive to situational information. Two determinants of the situational biasing effect on behavior identification were varied, namely, behavior ambiguity and order of situational and behavioral information. It was found that when behavior was ambiguous and preceded by situational information, the latter affected behavior identification but not dispositional inference; in contrast, when behavior was unambiguous or when it was followed by situational information, the latter affected dispositional inference but not behavior identification. Thus, the same conditions that allowed situational information to bias behavior identification also nullified the effect of situational information on dispositional inference.

Adult↗

PubMed1993

An empirical and meta-analytic evaluation of the phoneme identification task.

Recent studies that used Ganong's (1980) identification task have produced discrepant results. The present study sought to resolve these discrepancies by examining the influence of methodological factors on phoneme identification and differences in data analysis techniques. Three factors were examined across 2 experiments: position of target phoneme, phonetic contrast, and 2 task conditions in which stimulus quality (S/N ratio) or cognitive load varied. A meta-analysis was then performed on the results from all identification studies, including the present one, in an effort to obtain additional insight on factors that influence the task. The experiments and meta-analysis identified the importance of several methodological factors in affecting identification, most notably position of the target phoneme.

Adult↗

PubMed2001

Attentional requirements is visual detection and identification: evidence from the attentional blink.

Perception of the 2nd of 2 targets (T1 and T2) is impaired if the lag between them is short (0-500 ms). The authors used this attentional blink (AB) to index attentional requirements in detection and identification tasks, with or without backward masking of T2, in 2 stimulus domains (line orientation, coherent motion). With masking, the AB occurred because T2 was masked during the attentional dwell time created by T1 processing (Experiments 1, 2, and 3). Without masking, an AB occurred only in identification because during the attentional dwell time, T2 decayed to a level that could support simple detection but not complex identification. However, an AB occurred also in detection if T2 was sufficiently degraded (Experiment 4). The authors drew 2 major conclusions: (a) Attention is required in both identification and detection, and (b) 2 factors contribute to the AB, masking of T2 while attention is focused on T1 and decay of the T2 trace while unattended.

Attention↗

PubMed1992

Similarity, identification, and categorization: comment on Ashby and Lee (1991)

Ashby and Lee (1991) tested various models derived from the general recognition theory (GRT; Ashby & Perrin, 1988; Ashby & Townsend, 1986) on their ability to predict and interrelate similarity, categorization, and identification performance. This commentary (a) argues that contrary to Ashby and Lee's suggestion, the likelihood-based GRT cannot generally predict categorization from identification without incorporating selective attention, (b) argues that the categorization rule in the likelihood-based GRT is extremely close in spirit to Nosofsky's (1986) exemplar-based similarity model, (c) reports new model-based analyses that call into question Ashby and Lee's interpretation of their identification-confusion data, (d) raises questions about the identification and similarity models tested by Ashby and Lee, and (e) criticizes Ashby and Lee's methods of fitting and evaluating the various models.

Attention↗

PubMed1987

Attention and learning processes in the identification and categorization of integral stimuli.

The relationship between subjects' identification and categorization learning of integral-dimension stimuli was studied within the framework of an exemplar-based generalization model. The model was used to predict subjects' learning in six different categorization conditions on the basis of data obtained in a single identification learning condition. A crucial assumption in the model is that because of selective attention to component dimensions, similarity relations may change in systematic ways across different experimental contexts. The theoretical analysis provided evidence that, at least under unspeeded conditions, selective attention may play a critical role in determining the identification-categorization relationship for integral stimuli. Evidence was also provided that similarity among exemplars decreased as a function of identification learning. Various alternative classification models, including prototype, multiple-prototype, average distance, and "value-on-dimensions" models, were unable to account for the results.

Attention↗

PubMed1989

Episodic effects on picture identification: implications for theories of concept learning and theories of memory.

The effects of differences in study processing on free recall of picture names and on generalization in picture identification were investigated. Experience with degraded pictures produced poorer subsequent free recall of picture names than did naming intact pictures. For the test of picture identification, pictures that were identical to a studied picture, pictures that shared a name with a studied picture (same name), and new test pictures were presented, and the amount of clarification required to identify a picture was measured. Experience with degraded pictures produced better subsequent identification of identical test pictures but poorer later identification of same-name test pictures than did naming intact pictures. The importance of these episodic effects for theories of concept learning and theories of memory is discussed. It is argued that distinctions between memory systems (e.g., episodic-semantic) must be couched in terms of a theory of concept learning and that the data are inconsistent with a simple distinction.

Adult↗

PubMed1990

Perceptual identification, fragment completion, and free recall: concepts and data.

The effects of orthographically distinctive and orthographically common words were compared on tests of free recall, fragment completion, perceptual identification, and lexical decision. Orthographic distinctiveness is argued to effect data-driven processing and, in light of recent theory, should have little effect upon free recall but substantial effects upon fragment completion and perceptual identification. The results showed superior recall and fragment completion of orthographically distinctive words but more accurate perceptual identification of orthographically common words. Latency of lexical decision was longer for orthographically distinctive than for orthographically common words. The visual complexity of orthographically distinctive words may require more extensive sensory processing than is possible within the temporal constraints of perceptual identification tests. The effect of orthographic distinctiveness upon free recall reveals a certain inadequacy in the notion of transfer-appropriate processing.

Cues↗

PubMed2000

Differences in the coding of spatial relations in face identification and basic-level object recognition.

The purpose of this investigation was to determine if the relations among the primitives used in face identification and in basic-level object recognition are represented using coordinate or categorical relations. In 2 experiments the authors used photographs of famous people's faces as stimuli in which each face had been altered to have either 1 of its eyes moved up from its normal position or both of its eyes moved up. Participants performed either a face identification task or a basic-level object recognition task with these stimuli. In the face identification task, 1-eye-moved faces were easier to recognize than 2-eyes-moved faces, whereas the basic-level object recognition task showed the opposite pattern of results. Results suggest that face identification involves a coordinate shape representation in which the precise locations of visual primitives are specified, whereas basic-level object recognition uses categorically coded relations.

Adult↗