What is AMDIS
AMDIS program, Handbooks, Literature, Patents and Links
AMDIS publication abstracts
AMDIS (Automated Mass Spectral Deconvolution and Identification System) is a new (easy to use) sophisticated software for GC-MS data interpretation from NIST.
Publications with AMDIS (with Abstracts)
Deconvolution gas chromatography/mass spectrometry of urinary organic acids - potential for pattern recognition and automated
identification of metabolic disorders
; John M. Halket*, Anna Przyborowska, Stephen E. Stein, W. Gary Mallard,Stephen Down, Ronald A. Chalmers [LINK
]The National Institute of Standards and Technology (NIST) Automated Mass Spectral Deconvolution and Identification System (AMDIS) is applied to a selection of data files obtained from the gas chromatography/ mass spectrometry (GC/MS) analysis of
urinary organic acids. Mass spectra obtained after deconvolution are compared with a special user library containing both the mass spectra and retention indices of ethoxime-trimethylsilyl (EO-TMS) derivatives of a set of organic acids. Efficient identification of components is achieved and the potential of the procedure for automated diagnosis of inborn errors of metabolism and for related research is demonstrated.
Comparison of gas
chromatography pulsed flame photometric detection mass spectrometry, automated mass spectral deconvolution and identification system and gas chromatography tandem mass spectrometry as tools for trace level detection and identification
; Shai Dagan
, J.Chrom. A., 868, 2000, 229-247 [LINK
]The complexity of a matrix is in many cases the major
limiting factor in the detection and identification of trace level analytes. In this work, the ability to detect and identify trace level of pesticides in complex matrices was studied and compared in three, relatively new methods: (a) GC-PFPD-MS where simultaneous PFPD (pulsed flame photometric detection) and MS analysis is performed. The PFPD indicates the exact chromatographic time of suspected peaks for their MS identification and provides elemental information; (b) automatic GC-MS data
analysis using the AMDIS (Automated Mass Spectral Deconvolution and Identification System) software by the National Institute of Standards and Technology; (c) GC-MS-MS analysis. A pesticide mixture (MX-5), containing diazinon, methyl parathion, ethyl parathion, methyl trithion and ethion was spiked, in descending levels from 1 ppm to 10 ppb, into soil and sage (spice) extracts and the detection level and identification quality were evaluated in each experiment. PFPD-MS and AMDIS exhibited
similar performance, both superior to standard GC-MS, revealing and identifying compounds that did not exhibit an observable GC peak (either buried under the chromatographic background baseline or co-eluting with other interfering GC peaks). GC-MS-MS featured improved detection limits (lower by a factor of 6-8) compared to AMDIS and PFPD-MS. The GC-PFPD-MS-MS combination was found useful in several cases, where no reconstructed ion chromatogram MS-MS peaks existed, but an MS-MS spectrum could
still be extracted at the elution time indicated by PFPD. The level of identification and confirmation with MS-MS was inferior to that of the other two techniques. In comparison with the soil matrix, detection limits obtained with the loaded sage matrix were poorer by similar factors for all the techniques studied (factors of 5.8, .6.5 and 4.0 for AMDIS, PFPD-MS and MS-MS, respectively). Based on the above results, the paper discusses the trade-offs between detectivity and identification
level with the compared three techniques as well as other more traditional techniques and approaches.
1999 IFT Annual Meeting Abstract 48-6 - Effect of salt concentration on the volatile composition of cucumbers fermented with a Lactobacillus plantarum culture that does not produce carbon dioxide from malic acid
: R. F. MCFEETERS, C. S. Palma, H. P. Fleming, and F. Breidt [LINK
Pickling cucumbers (50:50 cucumber:cover solution ratio) were fermented in sealed jars with the non-malolactic culture Lactobacillus plantarum MU45.
This culture was derived from the malolactic positive MOP3 strain. Cover solutions contained 106 mM acetic acid, 36 mM calcium hydroxide and 0, 6, 9, and 12% sodium chloride. After a 2-month fermentation, brine samples were adjusted to 6% NaCl and then analyzed for volatile components by purge and trap GC-MS. Twenty-four previously identified volatile components, which included aldehydes, ketones, alcohols, and terpenes, in fermented cucumbers were quantitated. Identification of unknown components was assisted by use of an automated mass spectral deconvolution and identification system developed by the National Institute of Standards and Technology (NIST).<p>
Only four compounds analyzed quantitatively declined as salt concentration increased. None increased in concentration during fermentation, and 20 compounds did not change. A dozen additional components were identified, compared to previous analysis of fermentations in 2% NaCl, which were carried out with the L. plantarum MOP3 culture. Among the newly identified compounds, half were observed in all samples.<p>
The results indicate little effect
of salt concentration on the amounts or types of volatiles present in cucumbers after fermentation with an L. plantarum culture that does not produce carbon dioxide from malic acid. Use of such cultures will be necessary for doing fermentations in closed containers
The new Automated Mass Spectrometry Deconvolution and Identification System (AMDIS)
May/June 1998; Antony N. Davies (ISAS Dortmund) [PDF
1998 Version of the NIST/EPA/NIHMass Spectral Library—NIST98
; By O. David Sparkman [LINK
Help files compiled by James L. Little
A step towards Multi-targeted Profiling of Phytohormone levels in Plant samples
; C. Wiesner, L.Willmitzer, J,Kopka [PDF
]Multi-targeted metabolite profiling has been established for abundant solublemetabolitesfromplant samples,.To further the understanding of the regulation of primary metabolism this investigation attempts to complement the metabolite profiling technique with a
comprehensive phytohormone profile analysis. Phyto-hormones are a chemically diverse class of biomolecules. Here we report proof of concept by demonstrating that all major classes of phytohormones may be analized within a single GC/MS setup afterappropriatechemicalderivatization.
A systematic approach to biochemical profiling
; Norm Glassbrook
and John Ryals
Cur Opin Plant Biol. 4 :186- 190. 13. [LINK
]Sequencing of the Arabidopsis thaliana genome is complete. The analytical tools for determining gene function by altering and monitoring gene expression are relatively well developed, and are generating large volumes of valuable data. Recent advances in techniques for the analysis of small molecules allow researchers to apply biochemical profiling as another powerful approach to
functional genomics and metabolic research.
An Integrated Method for Spectrum Extraction and Compound Identification from GC/MS Data
; S. E. Stein; NIST; Journal of the American Society of Mass Spectrometry in Volume 10, 1999, pages 770-781. [PDF
]A method is presented for extracting individual component spectra from GC/MS data files and then using these
spectra to identify target compounds by matching spectra in a reference library. It extends a published model peak approach which uses selected ion chromatograms as models for component shape. On the basis of this shape, individual mass spectral peak abundance profiles are extracted to produce a purified spectrum. In the present work, ion-counting noise is explicitly treated and a number of characteristic features of GC/MS data are taken into account. This allows spectrum extraction to be
reliably performed down to very low signal levels and for overlapping components. A spectrum match factor for compound identification is developed that incorporates a number of new corrections, some of which employ information derived from chromatographic behavior. Test results suggest that the ability of this system to identify compounds is comparable to that of conventional analysis.
New software solutions for analytical spectroscopists;
Antony N. Davies; ISAS Dortmund; [LINK]
Analytical spectroscopists must be computer literate to effectively carry out the tasks assigned to them. This has often been resisted within organizations with insufficient funds to equip their staff properly, a lack of desire to deliver the essential training and a basic resistance amongst staff to learn the new techniques required for computer assisted analysis.
In the past these problems were compounded by seriously flawed
software which was being sold for spectroscopic applica-tions. Owing to the limited market for such complex products the analytical spectroscopist often was faced with buying incomplete and unstable tools if the price was to remain reasonable. Long product lead times meant spectrometer manufacturers often ended up offering systems running under outdated and sometimes obscure operating systems. Not only did this mean special staff training for each instrument where the knowledge gained on one
system could not be transferred to the neigh-bouring system but these spectrometers were often only capable of running in a stand-alone mode, cut-off from the rest of the laboratory environment.
Fortunately a number of developments in recent years have substantially changed this depressing picture. A true multi-tasking operating system with a simple graphical user interface, Microsoft Windows NT4, has now been widely introduced into the spectroscopic computing environment which has
provided a desktop operating system which has proved to be more stable and robust as well as requiring better programming techniques of software vendors. The opening up of the Internet has provided an easy way to access new tools for data handling and has forced a substantial re-think about results delivery (for example Chemical MIME types, IUPAC spectroscopic data exchange standards). Improved computing power and cheaper hardware now allows large spectroscopic data sets to be handled without
too many problems. This includes the ability to carry out chemometric operations in minutes rather than hours. Fast networks now enable data analysis of even multi-dimensional spectroscopic data sets remote from the measuring instrument. A strong tendency to opt for a more unified graphical user interface which is substantially more user friendly allows even inexperienced users to rapidly get acquainted with even the complex mathematical analyses.
Some examples of new spectroscopic
software products will be given to demonstrate the aforesaid points and highlight the ease of integration into a modern analytical spectroscopy workplace.
Integrated studies on plant biology using multiparallel techniques
; Oliver Fiehn
, Sebastian Kloska
and Thomas Altmann
; Curr.Opp.Biotech, 12,2001,82 [PDF
]Plant biology, especially the fields of molecular genetics and molecular physiology, is currently undergoing a change in paradigm from vertical analysis of the role(s) of one or a few genes to horizontal holistic approaches, studying the function of many or even all of the genes of an organism simultaneously. This change is leading us beyond genomes to transcriptomes, proteomes and metabalomes, and to an
understanding of life at an entirely new level. Profiling strategies are putting this change into effect through the generation of large amounts of data, requiring that current bioinformatic approaches adapt and grow in order to make the most of these data.
Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks
, Oliver Fiehn; Comp Funct Genom 2001; 2: 155-168. [PDF
]Now that complete genome sequences are available for a variety of organisms, the elucidation of gene functions involved in metabolism necessarily includes a better understanding of cellular responses upon mutations on all levels of gene products, mRNA, proteins, and metabolites. Such progress is essential since the observable properties of organisms - the phenotypes - are produced by the genotype in
juxtaposition with the environment. Whereas much has been done to make mRNA and protein profiling possible, considerably less effort has been put into profiling the end products of gene expression, metabolites. To date, analytical approaches have been aimed primarily at the accurate quantification of a number of pre-defined target metabolites, or at producing fingerprints of metabolic changes without individually determining metabolite identities. Neither of these approaches allows the
formation of an in-depth understanding of the biochemical behaviour within metabolic networks. Yet, by carefully choosing protocols for sample preparation and analytical techniques, a number of chemically different classes of compounds can be quantified simultaneously to enable such understanding. In this review, the terms describing various metabolite-oriented approaches are given, and the differences among these approaches are outlined. Metabolite target analysis, metabolite profiling,
metabolomics, and metabolic fingerprinting are considered. For each approach, a number of examples are given, and potential applications are discussed
Screening of Brazilian fruit aromas using solid-phase microextraction-gas chromatography-mass spectrometry
; Fabio Augusto , Antonio Luiz Pires Valente, Eduardo dos Santos Tada, Sandra Regina Rivellino; Journal of Chromatography A, 873 (2000) 117-127; [LINK
Manual headspace solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS) was used for the qualitative analysis of the aromas of four native Brazilian fruits: cupuassu (Theobroma grandiflorum, ´ Spreng.), caja (Spondias lutea, L.), siriguela (Spondias purpurea, L.) and graviola (Anona reticulata, L). Industrialized pulps of these fruits were used as samples, and extractions with SPME fibers coated with polydimethylsiloxane, polyacrylate,
Carbowax and Carboxen were carried out. The analytes identified included several alcohols, esters, carbonyl compounds and terpernoids. The highest amounts extracted, evaluated from the sum of peak areas, were achieved using the Carboxen fiber.
Molecular and morphologic approaches to discrimination of variability patterns in chub mackerel, Scomber japonicus
; Maria Ines Roldan , Ricardo G. Perrotta , Marti Cortey , Carles Pla; Journal of
Experimental Marine Biology and Ecology 253 (2000) 63-74 [LINK
]The systematic status and the evolutionary biology of chub mackerel (Scomber japonicus) in the South West Atlantic Ocean is confusing with an unknown degree of genetic differentiation and reproductive isolation between units. Simultaneous genetic and morphologic analyses were made on 227 fish collected from two areas of the South West Atlantic Ocean and one from the
Mediterranean Sea. The genetic analysis was based on 36 protein-coding loci, 16 of which were variable. The morphologic analyses include six morphometric length measurements and a meristic character. Correspondence between genetic and morphologic variability patterns indicates isolated Mediterranean and Southwest Atlantic subgroups of S. japonicusand, less clearly, possible additional divergence in two regional stocks within the latter group. The most conservative approach to
management is to manage the stocks independently of one another.
Resistively Heated Gas Chromatography Coupled to Quadrupole Mass Spectrometry
; Jens Dallüge, René Vreuls, Dick van Iperen, Martijn van Rijn, and Udo A.Th. Brinkman [PDF
]Earlier studies have shown that a resistive-heated capillary column is a good alternative for fast temperature-programmed
gas chromatography (GC). An assembly which can be used to upgrade existing gas chromatographs and is commercially available, is the so-called EZ Flash. The capillary column is placed inside a metal tube which can be heated, and cooled, much more rapidly than any conventional GC oven. The EZ Flash assembly generates temperature ramps up to 1200°C/min and cools down from 300 to 50°C in some 30 s. In the present study, EZ Flash was combined with quadrupole mass selective (MS) detection.
Samples were injected via a conventional split/splitless injector in both injection modes. The combination of a short column (5 m in length), a high gas flow rate and fast temperature programs typically decreased standard analysis times of 30 min to about 2.5 min. The loss of separation efficiency caused by the fast temperature gradients could be compensated by using the mass selective detector. The scan speed of a quadrupole mass spectrometer (10 spectra/s in the range m/z 50–310) was
sufficient to reconstruct the peaks properly, while still good-quality mass spectra were obtained. The approach is ideally suited for fast screening. An applications will be shown, regarding organic contamination of food samples.
The Rapid Characterisation of Complex Mixtures using a Wide Dynamic Range Benchtop GC/TOF-MS
; Jonathan Hughes, Lu Lin, Nick Bukowski [PDF
]Complex samples with components at widely differing concentration levels pose a significant challenge to analysts, when high throughput rapid analysis is required. The use of GC/TOF-MS allows rapid collection of data from components eluted from narrow-bore GC columns. The wide dynamic range of the particular instrument used enables components at percent levels and sub ppm levels to be determined in the same analytical run, thereby saving time and sample preparation effort. Full
characterisation can be achieved from complex samples using the library comparison software. The automation of this identification speeds up the sample characterization process, saving valuable time and simplifying the process.