Mass spectrometry meets chip technology: A new proteomic tool in cancer research?

Eggeling, Ferdinand von; Junker, Kerstin; Fiedler, Wolfgang; Wollscheid, Volker; Dürst, Matthias; Claussen, Uwe; Ernst, Günther

doi:10.1002/1522-2683(200108)22:14<2898::aid-elps2898>3.0.co;2-a

Cited by 126 publications

(57 citation statements)

References 18 publications

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“…A simplification of this type of method may be the use of Ciphergen's ProteinChip™ Array technology which utilizes the surface enhanced laser desorption/ ionization (SELDI) process to integrate protein capture, purification, characterization and quantitative protein interaction assays on a single biochip based platform [4]. Briefly, ProteinChip™ Arrays contain multiple spots derivatized with chemical or biological "docking sites" which are used for the selective capture of proteins and peptides from complex mixtures.…”

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confidence: 99%

Use of ProteinChip™ array surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) to identify thymosin β-4, a differentially secreted protein from lymphoblastoid cell lines

Diamond¹,

Zhang

Gaiger

et al. 2003

J. Am. Soc. Mass Spectrom.

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The identification of proteins differentially expressed between cancer and normal cells is vital for the development of cancer diagnostics, therapeutics and vaccines. Using a ProteinChip Biomarker System (Ciphergen Biosystems, Fremont, CA) which combines ProteinChip™ technology with time-of-flight mass spectrometry, we have developed a simple method to screen and identify differentially secreted proteins from tumor cell lines. Mass spectra of the range of proteins secreted from normal B-cells were generated along with those secreted from Epstein-Barr virus transformed B-cells. A mass peak at m/z ϭ 4972.1 that was highly over-represented in the transformed B-cell line was chosen for identification and purified by reversed phase chromatography with concomitant monitoring of fractions by SELDI-TOF MS. The resulting purified protein was digested with trypsin and the peptide masses derived from the SELDI-TOF spectrum were used to search the public databases for protein identification. Fragment matching of the resulting peptides identified the protein as thymosin ␤-4. Using LC-electrospray ionization MS/MS, the identity of this protein was confirmed. Thymosin ␤-4 is a known marker in LCLs establishing the utility of this method to discover and identify proteins differentially expressed between cancers and their matched normal counterparts. (J Am Soc Mass Spectrom 2003, 14, 760 -765)

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confidence: 99%

Use of ProteinChip™ array surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) to identify thymosin β-4, a differentially secreted protein from lymphoblastoid cell lines

Diamond¹,

Zhang

Gaiger

et al. 2003

J. Am. Soc. Mass Spectrom.

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“…[9][10][11][12][13][15][16][17][18][19][20][21]25 The most interesting discovery of the study was the finding that a SELDI-derived peak (m/z 4,462) was as effective at discriminating cancer from benign serum as the tumor markers CEA or CA19.9, while combining these three serum markers marginally improved classification. Classification could be further improved with data generated from a panel of peaks, suggesting analysis of proteomic profiles, rather than individual proteins, may yield improved diagnostic ability.…”

Section: Discussionmentioning

confidence: 99%

“…[9][10][11][12][13][15][16][17][18][19][20][21]25 A potential source of error in the tissue group not present in the serum study may be sampling error. The high desmoplastic nature of CCs means the sampled tissue may miss the malignant portion of the tumor and may mainly consist of stroma rather than cholangiocytes proper.…”

Section: Discussionmentioning

confidence: 99%

“…Proteomic profiling of serum has been used with a number of other malignancies to discover potential biomarkers. 7,8 In particular, affinity-based arrays-such as the protein chips analyzed via surface-enhanced laser desorption/ionization time-offlight mass spectrometry (SELDI-TOF MS) used in this study-have been used to successfully identify malignant patterns in serum from ovarian, [9][10][11] pancreatic, [12][13][14] head and neck, 15,16 prostate, 17 transitional cell, 18 renal cell, 19,20 and breast 21 cancers. TOF-MS separates ions derived from proteins or protein fragments that are differentially detected according to their mass-to-charge ratio.…”

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confidence: 99%

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Proteomic profiling of cholangiocarcinoma: Diagnostic potential of SELDI-TOF MS in malignant bile duct stricture

et al. 2006

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Proteomic techniques promise to improve the diagnosis of cholangiocarcinoma (CC) in both tissue and serum as histological diagnosis and existing serum markers exhibit poor sensitivities. We explored the use of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) to identify potential protein biomarkers of CC. Twenty-two resected CC samples were compared with adjacent noninvolved bile duct tissue. Serum from patients with CC (n ‫؍‬ 20) was compared with patients with benign disease (n ‫؍‬ 20), and healthy volunteers (n ‫؍‬ 25). Samples were analyzed on hydrophobic protein chips via SELDI-TOF MS, and classification models were developed using logistic regression and cross-validation analysis. Univariate analysis revealed 14 individual peaks differentially expressed between CC and bile duct tissue, 4 peaks between CC and benign disease, and 12 peaks between CC and sera of healthy volunteers. The 4,462 mass-to-charge serum peak had superior discriminatory ability to carbohydrate antigen 19.9 (CA19.9) and carcinoembryonic antigen ( C holangiocarcinoma (CC) is a rare but devastating neoplasm that accounts for 3% of all gastrointestinal cancers and 15% of all primary liver cancers worldwide. 1 Five thousand new cases are diagnosed on average per year in the United States, and the incidence is rising. 2 Northeast Thailand sees the highest incidence, with 96 cases per 100,000. 1 Surgical resection is the only current chance of cure, with no proven adjunctive therapy; however, this approach has a mortality rate of 5% to 10%. 3 Even with margin-free resection, 5-year survival figures only reach 20% to 40%. 3,4 Unresectable disease is usually fatal within 6 months to 1 year, and over one third of patients present at a stage too late for resection. 3 This confirms the need for earlier and more accurate diagnostic processes.At present, diagnosis of CC relies on imaging of the biliary tree with computed tomography or ultrasonography in the presence of high clinical suspicion. Tissue diagnostic confirmation is possible for intrahepatic tumors but is very difficult in more distal and more common (2/3 of cases) extrahepatic cases. These frequently present as a stricture of the common bile duct, which can be further characterized by means of endoscopic retrograde cholangio-pancreatography. 5

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“…This association between exposure to asbestos and excess death from lung cancer was documented in a study on former workers of a plant in Tyler, TX that used amosite to manufacture pipe insulation material (11). In this study, we performed surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF MS) (12,13) on the stored plasma samples of lung cancer patients and disease-free controls from the Tyler, TX cohort to identify lung cancer-specific biomarkers. The availability of serial samples from the same cancer patients, collected from an extended period of time prior to patients' death, allowed us to search for potential early detection markers for lung cancer.…”

Section: Introductionmentioning

confidence: 99%

Plasma proteomic profiling: Search for lung cancer diagnostic and early detection markers

Ali

Xiao²,

Malone³

et al. 2006

Oncol Rep

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Abstract. Environmental and occupational exposure to asbestos is among the established risk factors for lung cancer, the leading cause of cancer-related deaths in the United States. This link between exposure to asbestos and the excessive death rate from lung cancer was evident in a study of former workers of an asbestos pipe insulation manufacturing plant in Tyler, TX. We performed comparative proteomic profiling of plasma samples that were collected from nine patients within 12 months before death and their age-, raceand exposure-matched disease-free controls on strong anion exchange chips using surface-enhanced laser desorption ionization time-of-flight mass spectrometry. A distancedependent K-nearest neighbor (KNN) classification algorithm identified spectral features of m/z values 7558.9 and 15103.0 that were able to distinguish lung cancer patients from disease-free individuals with high sensitivity and specificity. The high correlation between the intensities of these two peaks (r=0.987) strongly suggests that they are the doubly and singly charged ions of the same protein product. Examination of these proteomic markers in the plasma samples of subjects from >5 years before death from lung cancer suggested that they are related to the early development of lung cancer. Validation of these biomarkers would have significant implications for the early detection of lung cancer and better management of high-risk patients.

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Mass spectrometry meets chip technology: A new proteomic tool in cancer research?

Cited by 126 publications

References 18 publications

Use of ProteinChip™ array surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) to identify thymosin β-4, a differentially secreted protein from lymphoblastoid cell lines

Use of ProteinChip™ array surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) to identify thymosin β-4, a differentially secreted protein from lymphoblastoid cell lines

Proteomic profiling of cholangiocarcinoma: Diagnostic potential of SELDI-TOF MS in malignant bile duct stricture

Plasma proteomic profiling: Search for lung cancer diagnostic and early detection markers

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