A new method to analyze matrix‐assisted laser desorption/ionization time‐of‐flight peptide profiling mass spectra

Dekker, Lennard J. M.; Dalebout, Johannes C.; Siccama, Ivar; Jenster, Guido; Smitt, Peter A. Sillevis; Luider, Theo M.

doi:10.1002/rcm.1864

Cited by 38 publications

(47 citation statements)

References 10 publications

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“…Lately MALDI-TOF MS has become a popular method for quantitative analysis of biomolecules (oligonucleotides, proteins, glycoproteins, etc.) originating from various sample types (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22) or even for imaging tissue sections (13)(14)(15)(16)(17)(18)(23)(24)(25)(26). At the same time, several studies discuss the non-quantitative nature of MALDI-TOF MS (7, 8, 13, 19, 22, 26 -30).…”

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confidence: 99%

Investigating the Quantitative Nature of MALDI-TOF MS

Szaéjli

Feheér

Medzihradszky

2008

Molecular & Cellular Proteomics

138

116

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MALDI-TOF MS has been applied by several groups to relative quantitative measurements. At the same time, the non-quantitative character of this method has been widely reported. We conducted experiments to test the reliability of this technique for quantitation using the statistical method of inverse confidence limit calculation for the first time in this context. The relationship between relative intensities of known amounts of standard peptides and their concentration ratios was investigated. We found that the concentration ratios determined by relative intensity measurements were highly inaccurate and strongly influenced by the molecular milieu of the sample analyzed. Thus, we emphasize the necessity of using the sample itself for calibration. We also performed experiments using an isotope-labeled derivative of the analyte as an internal standard for calibration line generation. As expected, the use of such standard led to a dramatic increase in precision and a less pronounced improvement in accuracy. We recommend performing a similar statistical analysis as a demonstration of reliability for every system where MALDI-TOF MS is used for quantitative measurements. Molecular & Cellular Proteomics 7: 2410 -2418, 2008.MALDI-TOF MS is a widely used analytical technique because of its excellent sensitivity, relatively high speed, and simplicity. As a consequence of producing mostly singly charged ions (1, 2) MALDI is especially suitable for mixture analysis. It is commonly used in proteomic studies (3) frequently without any prefractionation (4) as well as in the analysis of other biomolecules. Lately MALDI-TOF MS has become a popular method for quantitative analysis of biomolecules (oligonucleotides, proteins, glycoproteins, etc.) originating from various sample types (5-22) or even for imaging tissue sections (13)(14)(15)(16)(17)(18)(23)(24)(25)(26). At the same time, several studies discuss the non-quantitative nature of MALDI-TOF MS (7, 8, 13, 19, 22, 26 -30). The main problem of MALDI is its poor reproducibility (sample to sample and shot to shot), which makes most quantitative measurements quite difficult at best (19,27,31). This is especially true for complex samples. The presence of so-called hot spots or sweet spots is the main cause of the poor reproducibility and is therefore a factor strongly increasing measurement times and complicating automated measurements. Furthermore this phenomenon is one of the major factors hampering the use of MALDI MS for spatially resolved imaging (27). The reasons for sweet spot formation are not completely understood. It could be caused by variation in the amount and the crystallization of the matrix, the latter being a function of local analyte concentration. Dependence of signal intensities on the orientation of the matrix-analyte crystals relative to the spectrometer axis is also possible (27). The extent of hot spot formation depends strongly on the matrix used. For example, preparations with ␣-cyano-4-hydroxycinnamic acid (CHCA) 1 deliver relatively homogenous samples (...

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confidence: 99%

Investigating the Quantitative Nature of MALDI-TOF MS

Szaéjli

Feheér

Medzihradszky

2008

Molecular & Cellular Proteomics

138

116

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“…15 However, it is not considered a suitable quantitative technique because of non-uniform distribution of analytes during matrix co-crystallization. 10 2,5-DHB is a preferred matrix for glycan analysis, but due to the large crystal formation during the common dried-droplet sample preparation, point-to-point signal reproducibility is the worst among other matrices such as 4-hydroxy-3-methoxycinnamic acid (ferulic aicd, FA); sinapinic acid (SA); 3,4-dhydroxycinnamic acid (CA); 3-hydroxypicolinic acid (3-HPA); 2-(4-hydroxyphenylazo) benzoic acid (HABA); α-cyano-4-hydroxycinnamic acid (CHCA).…”

Section: Resultsmentioning

confidence: 99%

Development of a Matrix-prespotted Plate for Enhancing the Reproducibility of Serum Glycan Analysis by MALDI-TOF-MS

Ha¹,

In²,

Maeng³

et al. 2011

Mass Spectrometry Letters

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Matrix Assisted Laser Desorption/Ionization-Time-of-Flight mass spectrometry (MALDI-TOF-MS) is the most widely used MS technique for glycan analysis. However, the poor point-to-point and sample-to-sample reproducibility becomes a limit in glycan biomarker research. A prespotted MALDI plate which overcomes the large crystal formation of 2,5-dihydroxybenzoic acid (DHB) has been developed and applied for glycan analysis. A homogeneous matrix coated surface without a crystal structure was formed on a hydrophilic/ hydrophobic patterned surface using a piezoelectric device. The reproducible MALDI-TOF-MS data have been presented using MALDI imaging of beer glycan as well as serum glycan eluted from 10% and 20% ACN elution fractions. The glycan profile from the serum glycan by MALDI-TOF-MS with a DHB prespotted plate was highly conserved for 10 different spectra and the coefficient of variations of significant ion peaks of MALDI data varies from 3.59 to 19.95.

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“…After alignment and quality control, the number of good quality spectra per sample was counted, and samples with fewer than seven good quality spectra were discarded. The number of seven spectra is based on an earlier reproducibility study (13). At this threshold, the remaining number of cases per patient group was 41 in group I, 46 in group II, and 43 in group III (Table II).…”

Section: Resultsmentioning

confidence: 99%

“…Second, we did not include the height of the peaks in the model because quantitative measurements of peak heights with both the MALDI and SELDI methods are poorly reproducible (28). In addition, we have carefully determined before analysis the number of replicates per sample that provided the optimal reproducibility (13). The number of replicates that we used (18) was much higher than in other studies.…”

Section: Resultsmentioning

confidence: 99%

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MALDI-TOF Mass Spectrometry Analysis of Cerebrospinal Fluid Tryptic Peptide Profiles to Diagnose Leptomeningeal Metastases in Patients with Breast Cancer

Dekker

Boogerd

Stockhammer

et al. 2005

Molecular & Cellular Proteomics

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Leptomeningeal metastasis (LM) is a devastating complication that occurs in 5% of patients with breast cancer. Early diagnosis and initiation of treatment are essential to prevent neurological deterioration. However, early diagnosis of LM remains challenging because 25% of cerebrospinal fluid (CSF) samples produce false-negative results at first cytological examination. We developed a new, MS-based method to investigate the protein expression patterns present in the CSF from patients with breast cancer with and without LM. CSF samples from 106 patients with active breast cancer (54 with LM and 52 without LM) and 45 control subjects were digested with trypsin. The resulting peptides were measured by MALDI-TOF MS. Then, the mass spectra were analyzed and compared between patient groups using newly developed bioinformatics tools. A total of 895 possible peak positions was detected, and 164 of these peaks discriminated between the patient groups (Kruskal-Wallis, p < 0.01). The discriminatory masses were clustered, and a classifier was built to distinguish patients with breast cancer with and without LM. After bootstrap validation, the classifier had a maximum accuracy of 77% with a sensitivity of 79% and a specificity of 76%. Direct MALDI-TOF analysis of tryptic digests of CSF gives reproducible peptide profiles that can assist in diagnosing LM in patients with breast cancer. The same method can be used to develop diagnostic assays for other neurological disorders. One of the tumors most frequently associated with LM is breast cancer. During the course of the disease, ϳ5% of patients with metastatic breast cancer will develop symptoms caused by LM. This debilitating complication's response to therapy depends upon early treatment. However, diagnosis of LM remains challenging because 25% of samples tested are false negative at the first cytological examination of the CSF, probably because of sampling error (1).Protein expression profiling of body fluids from patients with cancer has recently become a valuable tool for obtaining information on the state of protein circuits inside tumor cells and outside the cells at the host-tumor interface (2, 3). In serum and CSF, low molecular weight proteins and peptides that are related to this altered microenvironmental "cancerous" state can be detected.We studied the differential tryptic peptide profiles in the CSF from patients with breast cancer with and without LM and in CSF from control subjects. Studying CSF has several advantages over studying serum. First, tumor cells in LM patients are located in the CSF and in the leptomeninges that are surrounded by CSF. Before their transport into serum, tumor-related proteins will therefore first be shed into the CSF. Second, the normal protein concentration of CSF is 100-to 400-fold lower than in serum (4). This results in a significant over-representation of LM-related proteins in CSF compared From the ‡Laboratory of Neuro-oncology, Department of Neurology, Dr Molewaterplein 40, 3015 GD, and § §Department

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A new method to analyze matrix‐assisted laser desorption/ionization time‐of‐flight peptide profiling mass spectra

Cited by 38 publications

References 10 publications

Investigating the Quantitative Nature of MALDI-TOF MS

Investigating the Quantitative Nature of MALDI-TOF MS

Development of a Matrix-prespotted Plate for Enhancing the Reproducibility of Serum Glycan Analysis by MALDI-TOF-MS

MALDI-TOF Mass Spectrometry Analysis of Cerebrospinal Fluid Tryptic Peptide Profiles to Diagnose Leptomeningeal Metastases in Patients with Breast Cancer

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