Limits...
the need for review and understanding of SELDI/MALDI mass spectroscopy data prior to analysis.

Grizzle WE, Semmes OJ, Bigbee W, Zhu L, Malik G, Oelschlager DK, Manne B, Manne U - Cancer Inform (2005)

Bottom Line: Also, all current mass spectroscopy systems have relatively low sensitivity compared with immunoassays (e.g., ELISA).Foremost, this low resolution results in difficulties in determining what constitutes a "peak" if a peak matching approach is used in analysis.Finally, the Ciphergen(®) system has some "noise" of the baseline which results from the accumulation of charge in the detector system.

View Article: PubMed Central - PubMed

Affiliation: University of Alabama at Birmingham, Birmingham, AL, USA. grizzle@path.uab.edu

ABSTRACT
Multiple studies have reported that surface enhanced laser desorption/ionization time of flight mass spectroscopy (SELDI-TOF-MS) is useful in the early detection of disease based on the analysis of bodily fluids. Use of any multiplex mass spectroscopy based approach as in the analysis of bodily fluids to detect disease must be analyzed with great care due to the susceptibility of multiplex and mass spectroscopy methods to biases introduced via experimental design, patient samples, and/or methodology. Specific biases include those related to experimental design, patients, samples, protein chips, chip reader and spectral analysis. Contributions to biases based on patients include demographics (e.g., age, race, ethnicity, sex), homeostasis (e.g., fasting, medications, stress, time of sampling), and site of analysis (hospital, clinic, other). Biases in samples include conditions of sampling (type of sample container, time of processing, time to storage), conditions of storage, (time and temperature of storage), and prior sample manipulation (freeze thaw cycles). Also, there are many potential biases in methodology which can be avoided by careful experimental design including ensuring that cases and controls are analyzed randomly. All the above forms of biases affect any system based on analyzing multiple analytes and especially all mass spectroscopy based methods, not just SELDI-TOF-MS. Also, all current mass spectroscopy systems have relatively low sensitivity compared with immunoassays (e.g., ELISA). There are several problems which may be unique to the SELDI-TOF-MS system marketed by Ciphergen(®). Of these, the most important is a relatively low resolution (±0.2%) of the bundled mass spectrometer which may cause problems with analysis of data. Foremost, this low resolution results in difficulties in determining what constitutes a "peak" if a peak matching approach is used in analysis. Also, once peaks are selected, the peaks may represent multiple proteins. In addition, because peaks may vary slightly in location due to instrumental drift, long term identification of the same peaks may prove to be a challenge. Finally, the Ciphergen(®) system has some "noise" of the baseline which results from the accumulation of charge in the detector system. Thus, we must be very aware of the factors that may affect the use of proteomics in the early detection of disease, in determining aggressive subsets of cancers, in risk assessment and in monitoring the effectiveness of novel therapies.

No MeSH data available.


Related in: MedlinePlus

Figure 7 demonstrates that storage of aliquots of a sample at −20°C (non-self defrost) for more than 6 months results in changes in peak amplitudes (A) and peak amplitude ratios (B vs C). Such changes were not noted on storage of an aliquot from the same original specimen for 10 months at −80°C.
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f7-cin-01-86: Figure 7 demonstrates that storage of aliquots of a sample at −20°C (non-self defrost) for more than 6 months results in changes in peak amplitudes (A) and peak amplitude ratios (B vs C). Such changes were not noted on storage of an aliquot from the same original specimen for 10 months at −80°C.

Mentions: Once the type of sample is chosen, the sampling conditions need to be standardized. The choice of sample collection and storage containers may influence spectral results. While glass sample collection tubes may activate specific proteins, plastic collection and storage containers may contaminate specimens with plastic components. Because plastics usually are poly-molecular forms (e.g., polyvinyl chloride), plastic contaminants may present as repeating spectral peaks, each separated by a standard molecular weight, usually about 100 to 200 Daltons. Similarly, additives to tubes (e.g., anticoagulants such as heparin) may influence spectral patterns. A minimum sample size should be selected and samples should be aliquoted to minimum sizes shortly after collection to avoid repeated freeze-thaw cycles. As demonstrated in Figure 6, peak amplitudes may decline upon several freeze-thaw cycles. The conditions between the collection of samples and storage of specimens should be standardized. It also is important to have conditions of storage consistent; for example, if cases are to be collected in the next two years, one does not want to use controls from an archival serum collection stored for 10 years or more at −70°C. It is critical that samples be stored at best at −70°C or colder. Storing samples at −20°C or warmer, even in a non-self defrost freezer, may result in degredation of proteins as measured by spectral changes (Figure 7). We are aware of MALDI-TOF-MS data that indicate spectral peaks do not change upon storage at −70°C or colder over a 4 year period.


the need for review and understanding of SELDI/MALDI mass spectroscopy data prior to analysis.

Grizzle WE, Semmes OJ, Bigbee W, Zhu L, Malik G, Oelschlager DK, Manne B, Manne U - Cancer Inform (2005)

Figure 7 demonstrates that storage of aliquots of a sample at −20°C (non-self defrost) for more than 6 months results in changes in peak amplitudes (A) and peak amplitude ratios (B vs C). Such changes were not noted on storage of an aliquot from the same original specimen for 10 months at −80°C.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2657646&req=5

f7-cin-01-86: Figure 7 demonstrates that storage of aliquots of a sample at −20°C (non-self defrost) for more than 6 months results in changes in peak amplitudes (A) and peak amplitude ratios (B vs C). Such changes were not noted on storage of an aliquot from the same original specimen for 10 months at −80°C.
Mentions: Once the type of sample is chosen, the sampling conditions need to be standardized. The choice of sample collection and storage containers may influence spectral results. While glass sample collection tubes may activate specific proteins, plastic collection and storage containers may contaminate specimens with plastic components. Because plastics usually are poly-molecular forms (e.g., polyvinyl chloride), plastic contaminants may present as repeating spectral peaks, each separated by a standard molecular weight, usually about 100 to 200 Daltons. Similarly, additives to tubes (e.g., anticoagulants such as heparin) may influence spectral patterns. A minimum sample size should be selected and samples should be aliquoted to minimum sizes shortly after collection to avoid repeated freeze-thaw cycles. As demonstrated in Figure 6, peak amplitudes may decline upon several freeze-thaw cycles. The conditions between the collection of samples and storage of specimens should be standardized. It also is important to have conditions of storage consistent; for example, if cases are to be collected in the next two years, one does not want to use controls from an archival serum collection stored for 10 years or more at −70°C. It is critical that samples be stored at best at −70°C or colder. Storing samples at −20°C or warmer, even in a non-self defrost freezer, may result in degredation of proteins as measured by spectral changes (Figure 7). We are aware of MALDI-TOF-MS data that indicate spectral peaks do not change upon storage at −70°C or colder over a 4 year period.

Bottom Line: Also, all current mass spectroscopy systems have relatively low sensitivity compared with immunoassays (e.g., ELISA).Foremost, this low resolution results in difficulties in determining what constitutes a "peak" if a peak matching approach is used in analysis.Finally, the Ciphergen(®) system has some "noise" of the baseline which results from the accumulation of charge in the detector system.

View Article: PubMed Central - PubMed

Affiliation: University of Alabama at Birmingham, Birmingham, AL, USA. grizzle@path.uab.edu

ABSTRACT
Multiple studies have reported that surface enhanced laser desorption/ionization time of flight mass spectroscopy (SELDI-TOF-MS) is useful in the early detection of disease based on the analysis of bodily fluids. Use of any multiplex mass spectroscopy based approach as in the analysis of bodily fluids to detect disease must be analyzed with great care due to the susceptibility of multiplex and mass spectroscopy methods to biases introduced via experimental design, patient samples, and/or methodology. Specific biases include those related to experimental design, patients, samples, protein chips, chip reader and spectral analysis. Contributions to biases based on patients include demographics (e.g., age, race, ethnicity, sex), homeostasis (e.g., fasting, medications, stress, time of sampling), and site of analysis (hospital, clinic, other). Biases in samples include conditions of sampling (type of sample container, time of processing, time to storage), conditions of storage, (time and temperature of storage), and prior sample manipulation (freeze thaw cycles). Also, there are many potential biases in methodology which can be avoided by careful experimental design including ensuring that cases and controls are analyzed randomly. All the above forms of biases affect any system based on analyzing multiple analytes and especially all mass spectroscopy based methods, not just SELDI-TOF-MS. Also, all current mass spectroscopy systems have relatively low sensitivity compared with immunoassays (e.g., ELISA). There are several problems which may be unique to the SELDI-TOF-MS system marketed by Ciphergen(®). Of these, the most important is a relatively low resolution (±0.2%) of the bundled mass spectrometer which may cause problems with analysis of data. Foremost, this low resolution results in difficulties in determining what constitutes a "peak" if a peak matching approach is used in analysis. Also, once peaks are selected, the peaks may represent multiple proteins. In addition, because peaks may vary slightly in location due to instrumental drift, long term identification of the same peaks may prove to be a challenge. Finally, the Ciphergen(®) system has some "noise" of the baseline which results from the accumulation of charge in the detector system. Thus, we must be very aware of the factors that may affect the use of proteomics in the early detection of disease, in determining aggressive subsets of cancers, in risk assessment and in monitoring the effectiveness of novel therapies.

No MeSH data available.


Related in: MedlinePlus