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

In protein and peptide mass spectrometry in which profiling of peaks is involved, their masses and intensities are important characteristics. Because of the relative low reproducibility of peak intensities associated with complex samples in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), it is difficult to accurately assess the number of peaks and their intensities. In this study we evaluate these two characteristics for tryptic digests of cerebrospinal fluid. We observed that the reproducibility of peak intensities was relatively poor (CV ¼ 42%) and that additional normalization or spiking did not lead to a large improvement (CV ¼ 30%). Moreover, at least seven mass spectra per sample were required to obtain a reliable peak list. An improvement of the sensitivity (i.e., eventually more peaks are detected) is observed if more replicates per sample are measured. We conclude that the reproducibility and sensitivity of peptide profiling can be significantly improved by a combination of measuring at least seven spectra per sample with a dichotomous scoring of the intensities. This approach will aid the analysis of large numbers of mass spectra of patient samples in a reproducible way for the detection and validation of candidate biomarkers. Copyright # 2005 John Wiley & Sons, Ltd.Mass spectrometry is extensively used in biomarker research. This has resulted in the development of methods for the analysis and comparison of large numbers of mass spectra. We describe here a new method for the analysis of tryptic peptide measurements for cerebro-spinal fluid (CSF) using matrixassisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) that addresses the problem of the low reproducibility of intensities. The standard method of using peak intensities was compared with a new approach that uses peak frequencies. To this end, the reproducibilities of peak intensities and of peak frequencies were determined.The MALDI-TOFMS technique is characterized by a relatively high mass accuracy and precision. In contrast, the reproducibility of measured intensities is relatively low in MALDI-TOF and SELDI-TOFMS (surface-enhanced laser desorption/ionization time-of-flight), compared to MS with electrospray ionization. For SELDI-TOFMS, the coefficient of variance (CV) for the peak intensities has been reported to be in the range 10-30%.1-4 The relatively low reproducibility of peak intensities is caused by ion suppression, variation in the amount of matrix, and variation in the crystallization of the matrix as a function of the analyte concentration or ratio. Crystallization depends on a number of factors including contamination of the analyte and the ratio of matrix and analyte. 5,6 If the intensities of peaks in the MALDI-TOF mass spectra of complex samples of peptides or proteins are to be used for analysis, it is essential that the reproducibility of these intensities be determined and used in the analysis. Indeed, more and more publications appear that describe peptid...

Protein profiling in blood serum by fractionation and MS analysis has been applied in mice to assess its applicability as a fast, economical alternative to current DNA and RNA analyses for diagnosis of neuromuscular disorders. Mass spectra of peptides and proteins were generated using serum from dystrophin-deficient mdx and control mice by WCX ClinProt bead fractionation, followed by MALDI-MS. Double cross-validatory linear discriminant and logistic regression data analysis methods were compared with a new Bayesian logistic regression method. These were evaluated on their ability to discriminate between healthy and dystrophic samples, and to identify the discriminatory peaks in the mass spectra. All three approaches classified the spectra with comparable misclassification rates (between 18.4 and 20.6%), with much overlap between the differential peaks identified between the methods. The differential peak pattern from the Bayesian method was sparser and easier to interpret than from the other two methods, without compromising classifying strength. One of the two main differentiating peaks at m/z 3908 was identified as an N-terminal peptide of coagulation Factor XIIIa, previously identified in human serum. This work underlines the translational aspect of serum protein profiling in mice and supports a further study with serum from patients with neuromuscular disorders.

Appropriate methods for the analysis of microdissected solid tumour tissues by matrix-assisted laser desorption/ionisation-time of flight-mass spectrometry (MALDI-TOF MS) are not yet well established. Optimisation of sample preparation was performed first on undissected tissue slices, representing approximately 200 000 cells, which were solubilised either in urea containing buffer, trifluoroethanol/NH4HCO3, 0.1% sodium dodecyl sulphate (SDS) or in 0.1% RapiGest solution, then trypsin digested and analysed by MALDI-TOF MS. Solubilisation in 0.1% SDS resulted in detection of the highest number of sample specific peak signals. Interestingly, there was little overlap in detectable peaks using the different buffers, implying that they can be used complementarily to each other. Additionally, we fractionated tryptic digests on a monolithic high-performance liquid chromatography column. Fractionation of tryptic digest from whole tissue sections resulted in a four-fold increase in the total number of peaks detected. To prove this principle, we used 0.1% SDS to generate peptide patterns from 2000 microdissected tumour and stromal cells from five different breast carcinoma tumours. The tumour and stroma specific peaks could be detected upon comparison of the peptide profiles. Identification of differentially expressed peaks by MALDI-TOF/TOF MS was performed on fractionated tryptic digests derived from a whole tissue slice. In conclusion, we describe a method that is suitable for direct peptide profiling on small amounts of microdissected cells obtained from breast cancer tissues.