Reproducibility in Protein Profiling by MALDI-TOF Mass Spectrometry

Albrethsen, Jakob

doi:10.1373/clinchem.2006.082644

Cited by 181 publications

(143 citation statements)

References 38 publications

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“…Acceptable average coefficients of variation of 10 and 17% were obtained for intra-and inter-assay variability, respectively. This is consistent with previously reported studies using SELDI-TOF (Semmes et al, 2005;Albrethsen, 2007).…”

Section: Resultssupporting

confidence: 94%

Serum protein signature may improve detection of ductal carcinoma in situ of the breast

et al. 2009

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Ductal carcinoma in situ (DCIS) of the breast is part of a spectrum of preinvasive lesions that originate within normal breast tissue and progress to invasive breast cancer. The detection of DCIS is important for the reduction of mortality from breast cancer, but the diagnosis of preinvasive breast tumors is hampered by the lack of an adequate detection method. To identify the changes in protein expression during the initial stage of tumorigenesis and to identify the presence of new DCIS markers, we analysed serum from 60 patients with breast cancer and 60 normal controls using mass spectrometry. A 23-protein index was generated that correctly distinguishes the DCIS and control groups with sensitivities and specificities in excess of 80% in two independent cohorts. Two candidate peptides were purified and identified as platelet factor 4 (PF-4) and complement C3a desArg anaphylatoxin (C3a desArg ) using liquid chromatography-tandem mass spectrometry (LC-MS/MS). In an independent serum set of 165 patients, PF-4 and C3a desArg were significantly upregulated in DCIS compared with non-cancerous controls, as validated using western blot and enzyme-linked immunosorbent assay. We conclude that our serum protein-based test, used in conjunction with image-based screening practices, could improve the sensitivity and specificity of breast cancer detection.

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Section: Resultssupporting

confidence: 94%

Serum protein signature may improve detection of ductal carcinoma in situ of the breast

et al. 2009

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“…Albrethsen [17] has reviewed the critical issue of reproducibility in protein profiling and has discussed approaches to improve the analytical performance of MALDI protein profiling including automated sample processing, pre-fractionation, immunocapture, pre-structured target surfaces, standardized matrix (co)crystallization, internal standard peptides, quality-control samples, replicate measurements, and improved algorithms for normalization and peak detection. Protein profiling can be combined with techniques like LC-MALDI and other fractionation approaches to help accommodate the large dynamic range of protein abundances in biological fluids such as serum, plasma and urine.…”

Section: Quantitative Relationshipsmentioning

confidence: 99%

Quantitative matrix-assisted laser desorption/ionization mass spectrometry

Duncan¹,

Röder²,

Hunsucker³

2008

Briefings in Functional Genomics and Proteomics

195

162

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This review summarizes the essential characteristics of matrix-assisted laser desorption/ionization (MALDI) timeof-flight mass spectrometry (TOF MS), especially as they relate to its applications in quantitative analysis. Approaches to quantification by MALDI-TOF MS are presented and published applications are critically reviewed.Keywords: quantification; quantitative analysis; MALDI; mass spectrometry; biomarkers OVERVIEWSince its inception in 1987 [1], matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF MS) has been applied for the analysis of a wide range of biomolecules. Initial applications were almost exclusively for the qualitative analysis of biopolymers because MALDI-TOF MS provided a fast and accurate approach to molecular mass and purity information: Is my material the right mass and is it free from contaminants? Because of the speed of analysis, ease of use, relative low equipment cost, ease of data interpretation and limited potential for cross-contamination between samples/users, MALDI-TOF MS systems were considered walk-up instruments where investigators run their own samples and determine, within minutes, whether they were on the right track with their work.There were, however, two specific areas of application where MALDI-TOF MS was initially viewed as impractical: i.e. the analysis of low mass analytes and quantitative applications. Low mass analysis is complicated by the vast molar excess of the matrix that can swamp any analyte-specific signal in the low m/z region of the spectrum. Quantitative analysis was viewed as implausible because crystallization does not yield a uniform distribution of the analyte and matrix across the target surface and this gives rise to regions where the analyte signal is especially intense relative to other locations on the target surface. MALDI MS was therefore viewed as inherently irreproducible because, for a given amount of analyte loaded onto the target, the measured ion intensity varies.Subsequently, it has been shown that both these perceived limitations can be overcome and quantification can be routine, both for low and high mass analytes. Now, an extensive list of published applications includes quantification of amino acids, lipids, natural products, drugs, polymers, herbicides, metabolites, toxins, oligonucleotides, carbohydrates, peptides and proteins. (Selected applications from these areas are discussed at the end of this review.) Here, we focus on the quantitative applications of MALDI and illustrate applications relating to both low and high-molecular mass analytes. We also discuss the strategies for applying MALDI to relative and absolute quantification. While MALDI is most commonly combined with TOF analysers, other analyser options are possible and applications employing these are also presented. Our aim is not to provide an exhaustive catalogue of published applications, but to discuss the general principles and to illustrate the

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“…A major challenge remains in the development of robust assay platforms and standardised protocols that are required before immunoproteomics-based assays can be implemented in the clinic. Particularly, MS-based approaches necessitate further preanalytical and analytical evaluation before their application in diagnostic medicine [91]. Currently, no single immunoproteomics technology seems optimal for both biomarker discovery and clinical application (Table 1).…”

Section: Perspectivesmentioning

confidence: 99%

Immunoproteomics: From biomarker discovery to diagnostic applications

Tjalsma

Schaeps

Swinkels

2008

Proteomics Clinical Apps

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Circulating antibodies reflect a molecular imprint of antigens that are related to autoimmune diseases, cancer or infection. Importantly, serum antibodies are useful clinical markers as they carry diagnostic information from all around the human body. Moreover, the amplification cascade governed by the humoral immune system causes a surplus of circulating antibodies after appearance of the corresponding (low abundance) antigen. In combination with the fact that antibodies are highly stable compared to many other serum proteins, they seem ideal to be implemented in clinical diagnostic assays for the detection of antigen-associated diseases. This review summarises advances in immunoproteomics with respect to technologies for biomarker discovery, with special emphasis on recently developed gel-free MS-based approaches, and looks forward to potential immunoproteomic applications in diagnostic medicine.

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Reproducibility in Protein Profiling by MALDI-TOF Mass Spectrometry

Cited by 181 publications

References 38 publications

Serum protein signature may improve detection of ductal carcinoma in situ of the breast

Serum protein signature may improve detection of ductal carcinoma in situ of the breast

Quantitative matrix-assisted laser desorption/ionization mass spectrometry

Immunoproteomics: From biomarker discovery to diagnostic applications

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