Standardization pitfalls

A witty, straightforward guide to the pitfalls and hotly disputed issues in standard written English, illustrated with examples and including a glossary of grammatical terms and an appendix on punctuation. 

The accuracy in RBS results is -3% for areal densities and better than 1% for stoichiometric ratios. This high accuracy is obtained only when all relevant quantities are measured or evaluated carefully. Pitfalls which often prevent RBS from achieving its full accuracy are described elsewhere [3.129]. Calibration can be achieved by measuring standards obtained by either implanting into or depositing on a light element (silicon) a known amount of a much heavier element (e.g. Ta or Sb). 

Several solid materials, such as organics dissolved In plastics (,22,23), phosphors sintered with polytetrafluoroethylene (30), phosphors (31), and lumogen-T (23), have been suggested as calibration standards. But most of the publications suggesting these materials (except Ref. 31) have not Included digital data for the corrected spectra. Additional Information, precautions, and pitfalls to be aware of In the use of various standards have been summarized In Reference 11 and the references cited therein. 

It is essential to have high-quality data in place for interoperable systems to function efficiently. Standard data structures can only be used to full advantage if they are combined with standard terminology for values populating a data element. Yet there are many potential pitfalls in data collection and configuration for analysis. Some of the more common pitfalls are discussed here, but this list is by no means comprehensive. 

The applicability of all aforementioned continuous optimization techniques depends very heavily on the simplified form of the objective function and constraints. They also suffer the common drawback that the solution must be rounded to the nearest standard pipe sizes, a procedure whose pitfalls must then be eliminated by a partially enumerative search. By contrast, the discrete merge method (C8) which is an enhancement of an earlier development by Rothfarb et al. (R5), is fast, direct, compact, and flexible. 

Taylor CR, Shi S-R, Barr NJ, et al. Techniques of immunohistochemistry principles, pitfalls, and standardization. In Diagnostic Immunohistochemistry, ed. DJ Dabbs, pp. 27-29. Philadelphia Churchill Livingstone, 2002. 

Chapters conclude with a list of references followed by a bibliography. The bibliography lists general sources for the material covered in the chapter, while the references give some specific examples illustrating the application to soil. These provide the reader with additional resources and examples of how the material in the chapter is actually used in soil analysis and research. These also provide a source of standard methods and procedures of soil analysis and provide the reader with pitfalls and interferences that may be encountered in the particular analysis being discussed. 

To minimize problems with the detection and analysis of a gene that exists as a single copy on an autosomal chromosome, technology of extreme sensitivity needs to be employed. Although the standard Southern analysis combines reasonable sensitivity with greater specificity, it is labor-intensive, requiring the use of radioisotopes such as 32P, and a few days are required to complete an analysis. Several pitfalls of the Southern procedure can be eliminated by substituting the PCR technique (M4). 

The second postprocessing step is the automated enhancement of the TrEMBL annotation to bring TrEMBL entries closer to SWISS-PROT standard. There is an increasing need for reliable automatic functional annotation to cope with the rapidly increasing amount of sequence data. Most of the current approaches are still based on sequence similarity searches against known proteins. Some groups try to collect the results of different prediction tools in a simple way, e.g., PEDANT (Frishman and Mewes, 1997) or GeneQuiz (Scharf et al., 1994). However, several pitfalls of these methods have been reported (Bork and Koonin, 1998). 

Leitch, C.H.B. Lentz, D.R. 1994. The gresen approach to mass balance constraints of alteration systems methods, pitfalls, examples. In Lentz, D.R., ed) Alteration and Alteration processes associated with Ore-forming systems. Geological Association of Canada, Short Course Notes, 11, 161-192. Lentz, D.R. 1995. Preliminary evaluation of six in-house rock geochemical standards from the Bathurst Camp, New Brunswick. New Brunswick Department of Natural Resources and Energy, Minerals and Energy Division, Miscellaneous Report 18, p. 81-89. 

In the past, PTRC screening was mainly based on gas chromatography-mass spectrometry (GC-MS) [116]. The choice of GC-MS was based on a number of good reasons (separation power of GC, selectivity of detection offered by MS, inherent simplicity of information contained in a mass spectrum, availability of a well established and standardized ionization technique, electron ionization, which allowed the construction of large databases of reference mass spectra, fast and reliable computer aided identification based on library search) that largely counterbalanced the pitfalls of GC separation, i.e., the need to isolate analytes from the aqueous substrate and to derivatize polar compounds [117]. 

When disodium tartrate dihydrate is used, samples ranging from 50 to 120 mg are dissolved in methanol, and the concentration of the KF reagent is determined. Based on volume of titrant used, the weight of the sample and the percent water in the disodium tartrate dihydrate (15.66% w/w), the standardization factor can be calculated. One pitfall with this method is the solubility of the disodium tartrate dihydrate in methanol. It is recommended that the disodium tartrate dihydrate be finely divided and that a suitable extraction time be given for the solids to dissolve. 

Reference values of this approach are not different from those for other amino acid analyses. An example of a mass chromatogram, representing the plasma of a PKU patient, is shown in Fig. 2.1.1. When evaluating the results of MS/MS amino acid analyses, one has to reahze that the hquid chromatographic separation is by far less efficient that the AAA separation. For this reason, any amino acid may (partly) coelute with other amino acid(s), which potentially interferes with its mass spectromet-ric behavior. This effect is known as quenching. In order to overcome this as much as possible, stable-isotope-labeled internal standards (as many as possible) should be used. However, this matrix effect of ion suppression is the major pitfall in the MS/MS analysis of amino acids. Consequently, the MS/MS analysis of amino acids cannot be regarded as a reference method, similar to all other amino acid analytical methods. 

This application of different methods of standardization demonstrates the possibilities and the pitfalls of these methods. 

In summary LC-MS/MS has doubtlessly a high inherent potential for selectivity and accuracy. However, application of this technology is not automatically or necessarily translated into accurate results. Its pitfalls have to be recognized and must be addressed systematically. In particular interferences from in-source transformation of metabolites, differential matrix effects of analyte and internal standard and isobaric transitions can lead to inaccurate results of LC-MS/MS analyses. Further technological developments will probably help to make LC-MS/MS assays more robust towards such interferences, but clinical chemists have to remain watchful for inaccuracies also with powerful and fascinating technologies... 

Apart from the problem of nonlinearity, the calibration curve approach has another pitfall measured ion abundance ratios can change with time, leading to the possibility of significant errors since the calibration and sample measurements cannot be simultaneous (Schoeller, 1980). In order to minimize the effect of instrumental drift and to optimize precision, the National Bureau of Standards (NBS) proposed a bracketing protocol for the development of definitive (i.e., essentially bias-free and precise) IDMS methods (Cohen et al., 1980 White et al., 1982 Yap et al., 1983). It involves the measurement of each sample between measurements of calibration standards whose ion abundances most closely surround the ion abundance ratio of the sample. Measurements are made according to a strict protocol, used with samples prepared under restrictive conditions ... 

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