1
|
Coffinier Y, Nguyen N, Drobecq H, Melnyk O, Thomy V, Boukherroub R. Affinity surface-assisted laser desorption/ionization mass spectrometry for peptide enrichment. Analyst 2012; 137:5527-32. [DOI: 10.1039/c2an35803d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
2
|
Suzuki S, Yamayoshi Y, Nishimuta A, Tanigawara Y. S100A10 protein expression is associated with oxaliplatin sensitivity in human colorectal cancer cells. Proteome Sci 2011; 9:76. [PMID: 22206547 PMCID: PMC3317844 DOI: 10.1186/1477-5956-9-76] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 12/30/2011] [Indexed: 12/27/2022] Open
Abstract
Background Individual responses to oxaliplatin (L-OHP)-based chemotherapy remain unpredictable. The objective of our study was to find candidate protein markers for tumor sensitivity to L-OHP from intracellular proteins of human colorectal cancer (CRC) cell lines. We performed expression difference mapping (EDM) analysis of whole cell lysates from 11 human CRC cell lines with different sensitivities to L-OHP by using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), and identified a candidate protein by liquid chromatography/mass spectrometry ion trap time-of-flight (LCMS-IT-TOF). Results Of the qualified mass peaks obtained by EDM analysis, 41 proteins were differentially expressed in 11 human colorectal cancer cell lines. Among these proteins, the peak intensity of 11.1 kDa protein was strongly correlated with the L-OHP sensitivity (50% inhibitory concentrations) (P < 0.001, R2 = 0.80). We identified this protein as Protein S100-A10 (S100A10) by MS/MS ion search using LCMS-IT-TOF. We verified its differential expression and the correlation between S100A10 protein expression levels in drug-untreated CRC cells and their L-OHP sensitivities by Western blot analyses. In addition, S100A10 protein expression levels were not correlated with sensitivity to 5-fluorouracil, suggesting that S100A10 is more specific to L-OHP than to 5-fluorouracil in CRC cells. S100A10 was detected in cell culture supernatant, suggesting secretion out of cells. Conclusions By proteomic approaches including SELDI technology, we have demonstrated that intracellular S100A10 protein expression levels in drug-untreated CRC cells differ according to cell lines and are significantly correlated with sensitivity of CRC cells to L-OHP exposure. Our findings provide a new clue to searching predictive markers of the response to L-OHP, suggesting that S100A10 is expected to be one of the candidate protein markers.
Collapse
Affiliation(s)
- Sayo Suzuki
- Department of Clinical Pharmacokinetics and Pharmacodynamics, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | | | | | | |
Collapse
|
3
|
Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
Collapse
Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
| | | | | | | |
Collapse
|
4
|
Berrill A, Ho SV, Bracewell DG. Mass spectrometry to describe product and contaminant adsorption properties for bioprocess development. Biotechnol Bioeng 2011; 108:1862-71. [DOI: 10.1002/bit.23115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/21/2011] [Accepted: 02/14/2011] [Indexed: 11/09/2022]
|
5
|
Antonsson B, De Lys P, Dechavanne V, Chevalet L, Boschert U. In vivo processing of CXCL12α/SDF-1α after intravenous and subcutaneous administration to mice. Proteomics 2010; 10:4342-51. [DOI: 10.1002/pmic.201000331] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
6
|
Ding X, Wang L, Ren Y, Zheng W. Differences in mitochondrial proteins in the eutopic endometrium of patients with adenomyosis and endometriosis identified using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry. J Int Med Res 2010; 38:987-93. [PMID: 20819435 DOI: 10.1177/147323001003800325] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Adenomyosis and endometriosis have a similar pathogenesis; indeed, adenomyosis has been considered by some as a variant of endometriosis ('internal endometriosis'). This study aimed to detect differences in mitochondrial proteins in eutopic endometrial samples from women with adenomyosis (n = 13) and endometriosis (n = 24), and from control patients (n = 29) using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) protein chip technology. A total of 82 and 78 mitochondrial protein peaks were found in adenomyosis and endometriosis individuals, respectively. Of these, 14 were common to women with adenomyosis and women with endometriosis, although only one of these (mass-to-charge [m/z] ratio 3499) was significantly different between the adenomyosis and endometriosis groups. It is concluded that, compared with control patients, there are differences in the mitochondrial proteins isolated from the eutopic endometrium of patients with adenomyosis and those with endometriosis. Although the changes in mitochondrial proteins in eutopic endometrium from patients with adenomyosis and endometriosis were largely similar, significant differences were also detected. Further identification of these proteins and elucidation of the differences will help towards the differential diagnosis of adenomyosis and endometriosis and new therapeutic approaches.
Collapse
Affiliation(s)
- X Ding
- Department of Gynaecology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | | | | | | |
Collapse
|
7
|
Deng B, Dong Z, Liu Y, Wang C, Liu J, Wang C, Qu X. Effects of pretreatment protocols on human amniotic fluid protein profiling with SELDI-TOF MS using protein chips and magnetic beads. Clin Chim Acta 2010; 411:1051-7. [PMID: 20361951 DOI: 10.1016/j.cca.2010.03.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2010] [Revised: 03/22/2010] [Accepted: 03/24/2010] [Indexed: 11/25/2022]
Abstract
BACKGROUND There is increasing interest in the use of human amniotic fluid (AF) proteomics with surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) for diagnosing pregnancy-associated abnormalities. A critical parameter of diagnostic biomarkers is the accuracy and reproducibility of protein patterns. We evaluated the effects of common pretreatment protocols on protein patterns generated using SELDI mass spectrometry with two different protein capture strategies (including functional protein chips and functionalized magnetic beads prior to MS analysis) in AF. METHOD Various extrinsic factors involved in processing and storing amniotic fluid, including matrix composition, sample storage time, temperature and freeze-thaw cycles, were analyzed regarding their impact on AF protein patterns using SELDI mass spectrometry with 2 different protein capture strategies. RESULTS Three extrinsic factors (sample storage for 3days at either room temperature or 4 degrees C or freeze-thawing the sample 5 times) significantly decreased the number or intensities of protein peaks detected in AF. Matrix dilutions also changed the spectra of AF, with more peaks and higher intensities observed with 50% alpha-cyano-4-hydroxycinnamic acid (CHCA). Moreover, protein chips captured more proteins or peptides than magnetic beads on SELDI-TOF MS profiling of AF. CONCLUSIONS These results suggest that extrinsic factors must be taken into account for valid data interpretation to ensure good reproducibility of AF profiling by SELDI mass spectrometry.
Collapse
Affiliation(s)
- Biping Deng
- Institute of Basic Medical Sciences, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Jinan, 250012, Shandong, PR China
| | | | | | | | | | | | | |
Collapse
|
8
|
Chakravarti B, Mallik B, Chakravarti DN. Proteomics and systems biology: application in drug discovery and development. Methods Mol Biol 2010; 662:3-28. [PMID: 20824464 DOI: 10.1007/978-1-60761-800-3_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Studies of complex biological systems aimed at understanding their functions at a global level are the goals of systems biology. Proteomics, generally regarded as the comprehensive study of the expression of all the proteins at a particular time in different organs, tissues, and cell types is a key enabling technology for the systems biology approach. Rapid advances in this regard have been made following the success of the human genome project as well as those of various animals and microorganisms. Possibly, one of the most promising outcomes from studies on the human genome and proteome is the identification of potential new drugs for the treatment of different diseases and tailoring the drugs for individualized patient therapy. Following the identification of a new drug candidate, knowledge on organ and system-level responses helps prioritize the drug targets and design clinical trials based on their efficacy and safety. Toxicoproteomics is playing an important role in that respect. In essence, over the past decade, proteomics has played a major role in drug discovery and development. In this review article, we explain systems biology, discuss the current proteomic technologies, and highlight some important applications of proteomics and systems biology approaches in drug discovery and development.
Collapse
Affiliation(s)
- Bulbul Chakravarti
- Department of Biology and Department of Chemistry, York College, City University of New York, New York, CA, USA.
| | | | | |
Collapse
|
9
|
Product and contaminant measurement in bioprocess development by SELDI-MS. Biotechnol Prog 2009; 26:881-7. [DOI: 10.1002/btpr.376] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
10
|
Xu SY, Liu Z, Ma WJ, Sheyhidin I, Zheng ST, Lu XM. New potential biomarkers in the diagnosis of esophageal squamous cell carcinoma. Biomarkers 2009; 14:340-6. [PMID: 19552569 DOI: 10.1080/13547500902903055] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To analyse the alterations of serum proteins in cases of esophageal squamous cell carcinoma (ESCC) in order to screen and validate serum marker patterns for the diagnosis of ESCC in the high-risk populations of Xinjiang, China. METHODS The serum proteomic patterns of 188 cases, including 139 patients with ESCC (54 Uygur, 45 Kazakh and 40 Han subjects) and 49 sex- and age-matched healthy controls, were detected using the SELDI-TOF-MS (surface-enhanced laser desorption/ionization-time of flight-mass spectrometry) technology with the CM10 ProteinChip. Differences in protein peaks between patients with ESCC and controls were analysed using the Biomarker Pattern Software, and a primary diagnosis model of ESCC was developed and validated with SVM (support vector machines). This model was further evaluated by a large-scale blind test. RESULTS Two hundred and eighty-three protein peaks were detected within the molecular range of 0-20 kDa, among which, 140 peaks were significantly different between ESCC cases and controls (p < 0.05). A diagnostic pattern consisting of six protein peaks (m/z 5667, 5709, 5876, 5979, 6043 and 6102) was established with a sensitivity of 97.12% and a specificity of 83.87%. The large-scale blind test generated a sensitivity of 91.43% and a specificity of 88.89%. CONCLUSIONS The differential protein peaks analysed by SELDI-TOF-MS may contain promising serum biomarkers for screening ESCC. The diagnostic model which combined only six protein peaks had a satisfactory discriminatory power. The model should be further evaluated in other populations of ESCC patients and tested against controls. The nature and function of the discriminating proteins have yet to be elucidated.
Collapse
Affiliation(s)
- Shu-Yong Xu
- Medical Research Center, 1st Teaching Hospital, Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | | | | | | | | | | |
Collapse
|
11
|
Rapid screening of purification strategies for the capture of a human recombinant F(ab′)2 expressed in baculovirus-infected cells using a micro-plate approach and SELDI-MS. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:2428-34. [DOI: 10.1016/j.jchromb.2009.04.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 04/20/2009] [Accepted: 04/22/2009] [Indexed: 11/17/2022]
|
12
|
Liu D, Cao L, Yu J, Que R, Jiang W, Zhou Y, Zhu L. Diagnosis of pancreatic adenocarcinoma using protein chip technology. Pancreatology 2008; 9:127-35. [PMID: 19077463 DOI: 10.1159/000178883] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Accepted: 03/21/2008] [Indexed: 12/11/2022]
Abstract
BACKGROUND To develop a serum-specific protein fingerprint which is capable of differentiating samples from patients with pancreatic cancer and those with other pancreatic conditions. METHODS We used SELDI-TOF-MS coupled with CM10 chips and bioinformatics tools to analyze a total of 118 serum samples in this study; 78 serum samples were analyzed to establish the diagnostic models and the other 40 samples were analyzed on the second day as an independent test set. RESULTS The analysis of this independent test set yielded a specificity of 91.6% and a sensitivity of 91.6% for pattern 1, which distinguished pancreatic adenocarcinoma (PC) from healthy individuals and a specificity of 80.0% and a sensitivity of 90.9% for pattern 2, which distinguished PC from chronic pancreatitis. CONCLUSION This study indicated that the SELDI-TOF-MS technique can facilitate the discovery of better serum tumor biomarkers and a combination of specific models is more accurate than a single model in diagnosis of PC.
Collapse
Affiliation(s)
- Daren Liu
- Department of Surgery, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China
| | | | | | | | | | | | | |
Collapse
|
13
|
Ahamed T, Chilamkurthi S, Nfor BK, Verhaert PD, van Dedem GW, van der Wielen LA, Eppink MH, van de Sandt EJ, Ottens M. Selection of pH-related parameters in ion-exchange chromatography using pH-gradient operations. J Chromatogr A 2008; 1194:22-9. [DOI: 10.1016/j.chroma.2007.11.111] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 11/27/2007] [Accepted: 11/30/2007] [Indexed: 10/22/2022]
|
14
|
Brenac Brochier V, Schapman A, Santambien P, Britsch L. Fast purification process optimization using mixed-mode chromatography sorbents in pre-packed mini-columns. J Chromatogr A 2008; 1177:226-33. [PMID: 17904149 DOI: 10.1016/j.chroma.2007.08.086] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Revised: 08/30/2007] [Accepted: 08/31/2007] [Indexed: 10/22/2022]
Abstract
Pre-packed MediaScout MiniChrom columns of 2.5, 5 and 10 mL were investigated for screening three mixed-mode chromatography sorbents (HEA, PPA and MEP HyperCel). Packing performance was of good quality and the three sorbents displayed higher capacity than traditional HIC sorbents in physiological-like conditions. Each sorbent offered a unique selectivity. Bovine beta-lactoglobulin was partially purified after loading milk whey directly on HEA HyperCel sorbent. The combination of small pre-packed columns and SELDI-MS appeared to be a valuable strategy for high-throughput screening of chromatography sorbents and for enabling rapid process development and optimization.
Collapse
|
15
|
Favre-Kontula L, Sattonnet-Roche P, Magnenat E, Proudfoot AEI, Boschert U, Xenarios I, Vilbois F, Antonsson B. Detection and identification of plasma proteins that bind GlialCAM using ProteinChip™ Arrays, SELDI-TOF MS, and nano-LC MS/MS. Proteomics 2008; 8:378-88. [DOI: 10.1002/pmic.200700564] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
16
|
Callesen AK, Christensen RD, Madsen JS, Vach W, Zapico E, Cold S, Jørgensen PE, Mogensen O, Kruse TA, Jensen ON. Reproducibility of serum protein profiling by systematic assessment using solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:291-300. [PMID: 18181248 DOI: 10.1002/rcm.3364] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Protein profiling of human serum by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is potentially a new diagnostic tool for early detection of human diseases, including cancer. Sample preparation is a key issue in MALDI MS and the analysis of complex samples such as serum requires optimized, reproducible methods for handling and deposition of protein samples. Data acquisition in MALDI MS is also a critical issue, since heterogeneity of sample deposits leads to attenuation of ion signals in MALDI MS. In order to improve the robustness and reproducibility of MALDI MS for serum protein profiling we investigated a range of sample preparation techniques and developed a statistical method based on repeated analyses for evaluation of protein-profiling performance of MALDI MS. Two different solid-phase extraction (SPE) methods were investigated, namely custom-made microcolumns and commercially available magnetic beads. Using these two methods, nineteen different sample preparation methods for serum profiling by MALDI MS were systematically tested with regard to matrix selection, stationary phase, selectivity, and reproducibility. Microcolumns were tested with regard to chromatographic properties; reversed phase (C8, C18, SDB-XC), ion-exchange (anion, weak cation, mixed-phase (SDB-RPS)) and magnetic beads were tested with regard to chromatographic properties; reversed phase (C8) or affinity chromatography (Cu-IMAC). The reproducibility of each sample preparation method was determined by enumeration and analysis of protein signals that were detected in at least six out of nine spectra obtained by three triplicate analyses of one serum sample.A candidate for best overall performance as evaluated by the number of peaks generated and the reproducibility of mass spectra was found among the tested methods. Up to 418 reproducible peaks were detected in one cancer serum sample. These protein peaks can be part of a possible diagnostic profile, suggesting that this sample preparation method and data acquisition approach is suitable for large-scale analysis of serum samples for protein profiling.
Collapse
Affiliation(s)
- Anne K Callesen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Schipper RG, Silletti E, Vingerhoeds MH. Saliva as research material: Biochemical, physicochemical and practical aspects. Arch Oral Biol 2007; 52:1114-35. [PMID: 17692813 DOI: 10.1016/j.archoralbio.2007.06.009] [Citation(s) in RCA: 320] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 05/29/2007] [Accepted: 06/23/2007] [Indexed: 12/29/2022]
Abstract
Whole saliva is a complex mixture of proteins and other molecules which originate from several sources. The biochemical and physicochemical properties of saliva contribute to the numerous functions of saliva in, e.g., speech, maintaining oral and general health, and food processing. Interest in saliva has increased in the last few years for its potential to diagnose viral, bacterial and systemic diseases. The use of saliva as research material may pose particular problems due to its inherent variability and instability. This review describes practical aspects of salivary as research material with emphasis on protein biochemistry and physical chemistry.
Collapse
Affiliation(s)
- Raymond G Schipper
- TI Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, The Netherlands.
| | | | | |
Collapse
|
18
|
Harthoorn LF, Schipper RG, Loof A, Vereijken PFG, Van Heerde WL, Dransfield E. Salivary biomarkers associated with perceived satiety and body mass in humans. Proteomics Clin Appl 2007; 1:1637-50. [DOI: 10.1002/prca.200700448] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Indexed: 12/11/2022]
|
19
|
Guerrier L, Lomas L, Boschetti E. A new general approach to purify proteins from complex mixtures. J Chromatogr A 2007; 1156:188-95. [PMID: 17276440 DOI: 10.1016/j.chroma.2007.01.050] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2006] [Revised: 12/26/2006] [Accepted: 01/05/2007] [Indexed: 10/23/2022]
Abstract
The selection of chromatography media and their sequential use represent a major difficulty to isolate a single protein from very crude protein extracts. The process described here consists of two main steps: (i) a rational selection of few media from a relatively large collection and (ii) the definition of the sequence of columns to get the best purity of the target protein. From the first step, one sorbent is selected for its properties to capture the protein to purify, regardless whether other protein impurities are also co-adsorbed; then 5-7 other complementary sorbents are identified to remove impurities but without interacting with the target protein under the same buffering conditions. The second step consists in superimposing sorbents under a cascade manner with the sorbent in charge to capture the target protein located in the last position. Non-adsorbed proteins are eliminated in the flowthrough; other impurities are progressively removed by the sorbent sequence and the target protein is finally desorbed and isolated from the last sorbent using an optimized gradient. All operations are performed with a single adsorption buffer for all columns and all monitoring performed by means of mass spectrometry associated with ProteinChip arrays and polyacrylamide gel electrophoresis. Examples of protein isolation/identification from human serum are described namely thyroxin-binding proteins and transferrin. The first is isolated thanks to a series of dye chromatography media, the second (transferrin) using current chromatographic media. In both cases the target proteins were purified at a level estimated of about 95% and 85%, respectively. Isolated proteins were pure enough for the purpose of formal identification by either peptide fingerprinting or sequencing.
Collapse
Affiliation(s)
- L Guerrier
- Ciphergen Biosystems, 95800 Cergy-Pontoise, France.
| | | | | |
Collapse
|
20
|
Wang JX, Qin P, Liu QL, Yang HY, Fan YZ, Yu JK, Zheng S. Detection and significance of serum protein marker of Hirschsprung disease. Pediatrics 2007; 120:e56-60. [PMID: 17548485 DOI: 10.1542/peds.2006-1364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE The objective of this study was to identify a specific fingerprint chromatogram model of serum proteins for early screening and diagnosis of Hirschsprung disease. METHODS To detect the protein mass spectrograms of 78 serum specimens (42 specimens of Hirschsprung disease, 16 specimens of adhesive ileus including appendicitis and Meckel diverticulum after operation and inflammatory bowel disease, and 20 specimens of normal control subjects), we used surface-enhanced laser desorption/ionization time of flight mass spectrometry technology, combined with bioinformatics methods (support vector machine) to develop and compare protein mass spectrograms from serum samples. RESULTS We identified 3 protein markers, the mass-to-charge ratio of which is positioned at 3221.7, 5639.2, and 6884.2 from the fingerprint chromatogram model of serum protein for early screening and diagnosis of Hirschsprung disease. The markers had 100% sensitivity and specificity. CONCLUSION The fingerprint chromatogram model of serum protein using surface-enhanced laser desorption/ionization time of flight mass spectrometry technology combining support vector machine is a new method of early screening and diagnosis of Hirschsprung disease that is worthy of additional research and application.
Collapse
Affiliation(s)
- Jia-xiang Wang
- Pediatric Surgery Department, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China [corrected]
| | | | | | | | | | | | | |
Collapse
|
21
|
Driemel O, Murzik U, Escher N, Melle C, Bleul A, Dahse R, Reichert T, Ernst G, von Eggeling F. Protein profiling of oral brush biopsies: S100A8 and S100A9 can differentiate between normal, premalignant, and tumor cells. Proteomics Clin Appl 2007; 1:486-93. [DOI: 10.1002/prca.200600669] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Indexed: 11/06/2022]
|
22
|
Schipper R, Loof A, de Groot J, Harthoorn L, Dransfield E, van Heerde W. SELDI-TOF-MS of saliva: Methodology and pre-treatment effects. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 847:45-53. [PMID: 17070117 DOI: 10.1016/j.jchromb.2006.10.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Revised: 09/28/2006] [Accepted: 10/08/2006] [Indexed: 10/24/2022]
Abstract
Interest in saliva as a diagnostic fluid for monitoring general health and for early diagnosis of disease has increased in the last few years. In particular, efforts have focused on the generation of protein maps of saliva using advanced proteomics technology. Surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) is a novel high throughput and extremely sensitive proteomic approach that allows protein expression profiling of large sets of complex biological specimens. In this study, large scale profiling of salivary proteins and peptides, ranging from 2 to 100kDa was demonstrated using SELDI-TOF-MS. Various methodological aspects and pre-analytical variables were analysed with respect to their effects on saliva SELDI-TOF-MS profiling. Results show that chip surface type and sample type (unstimulated versus stimulated) critically affect the amount and composition of detected salivary proteins. Factors that influenced normal saliva protein profiling were matrix composition, sample dilution and binding buffer properties. Delayed processing time experiments show certain new peptides evolving 3h post-saliva donation, and quantitative analyses indicate relative intensity of other proteins and peptides changing with time. The addition of protease inhibitors partly counteracted the destabilization of certain protein/peptide mass spectra over time suggesting that some proteins in saliva are subject to digestion by intrinsic salivary proteases. SELDI-TOF-MS profiles also changed by varying storage time and storage temperature whereas centrifugation speed and freeze-thaw cycles had minimal impact. In conclusion, SELDI-TOF-MS offers a high throughput platform for saliva protein and peptide profiling, however, (pre-)analytical conditions must be taken into account for valid interpretation of the acquired data.
Collapse
Affiliation(s)
- Raymond Schipper
- Wageningen Centre for Food Sciences, P.O. Box 557, 6700 AN Wageningen, The Netherlands.
| | | | | | | | | | | |
Collapse
|
23
|
Wierling PS, Bogumil R, Knieps-Grünhagen E, Hubbuch J. High-throughput screening of packed-bed chromatography coupled with SELDI-TOF MS analysis: monoclonal antibodies versus host cell protein. Biotechnol Bioeng 2007; 98:440-50. [PMID: 17335062 DOI: 10.1002/bit.21399] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A feasibility study to couple high throughput screening of packed bed chromatography with mass spectrometric detection by SELDI-TOF MS is presented. As model system monoclonal antibodies (mAb) versus host cell protein (HCP) from an industrial cultivation was chosen. Packed bed chromatography was screened on a TECAN Evo Freedom 200 station using miniaturized chromatographic columns placed on a specially designed array carrier linked to a commercially available T-Stack module. Gradient elution of the bound proteins was performed by applying a multiple step strategy. When analyzing selected HCP peaks as well as the detected antibody peaks throughout the chromatographic runs a direct correlation between applied and detected components was established. The sensitivity of conventional protein A chromatography was found to be lower than SELDI-TOF MS analysis. During initial screening a shift in the elution pattern for one of the monoclonal antibodies detected with all four resins was identified to be a heterogeneity in the mAb glycosylation pattern. In addition, a detailed differentiation between various HCP fractions through out the chromatographic process using SELDI-TOF analysis let to the detection of HCP components possibly adhering to the mAbs during chromatographic separations.
Collapse
|
24
|
Wang JX, Yu JK, Wang L, Liu QL, Zhang J, Zheng S. Application of serum protein fingerprint in diagnosis of papillary thyroid carcinoma. Proteomics 2006; 6:5344-9. [PMID: 16941571 DOI: 10.1002/pmic.200500833] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To find new biomarkers and establish serum protein fingerprint models for early diagnosis and preoperative staging of papillary thyroid carcinoma, we employed SELDI-TOF-MS and bioinformatics tools. A total of 116 samples were analyzed in this study. The first 80 samples were analyzed by SELDI-TOF-MS and two biomarker patterns were identified. Pattern 1 distinguishes patients with papillary thyroid carcinoma from healthy individuals. Pattern 2 distinguishes papillary thyroid carcinoma from benign thyroid nodes. The remaining 29 samples were analyzed on the second day and served as an independent test set. The analysis of this independent test set yielded a specificity of 80.0% and a sensitivity of 88.9% for pattern 1 and a specificity of 80.0% and a sensitivity of 80.0% for pattern 2. Two additional biomarker patterns were identified to distinguish different stages of the papillary thyroid carcinoma (pattern 3) with an accuracy of 77.1% and different pathological types of thyroid carcinoma (pattern 4) with an accuracy of 88.1%. Taken together, the SELDI-TOF-MS technique combined with bioinformatics approaches can not only facilitate the discovery of better biomarkers for papillary thyroid carcinoma but also provide a useful tool for molecular diagnosis in the future.
Collapse
MESH Headings
- Adenocarcinoma, Follicular/blood
- Adenocarcinoma, Follicular/diagnosis
- Adenocarcinoma, Follicular/pathology
- Blood Proteins/metabolism
- Carcinoma, Medullary/blood
- Carcinoma, Medullary/diagnosis
- Carcinoma, Medullary/pathology
- Carcinoma, Papillary/blood
- Carcinoma, Papillary/diagnosis
- Carcinoma, Papillary/pathology
- Humans
- Neoplasm Proteins/blood
- Neoplasm Staging
- Peptide Mapping/methods
- Protein Array Analysis
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Thyroid Neoplasms/blood
- Thyroid Neoplasms/diagnosis
- Thyroid Neoplasms/pathology
Collapse
Affiliation(s)
- Jia-Xiang Wang
- Department of Surgery, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henang Province, P R China
| | | | | | | | | | | |
Collapse
|
25
|
Mengistu TZ, DeSouza L, Morin S. Probing proteins on functionalized silicon surfaces using matrix-assisted laser desorption/ionization mass spectrometry. J Chromatogr A 2006; 1135:194-202. [PMID: 17054966 DOI: 10.1016/j.chroma.2006.09.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 09/13/2006] [Accepted: 09/18/2006] [Indexed: 11/17/2022]
Abstract
Flat H-terminated Si(111) substrates modified with alkyl monolayers terminated with hydrophobic and hydrophilic functional groups were prepared using known surface functionalization methods and characterized by FTIR, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). The surfaces were then used for the study of non-specific binding of proteins from complex mixtures (using standard mixture of proteins with average molecular weight approximately 6-66 kDa) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Protein adsorption on these surfaces (following on-probe fractionation of the mixture) was found to be dependent on the nature of surface functional groups, and nature and pH of rinsing solutions used. The results obtained in this work demonstrate that simple silicon-based surface modifications can be effective for direct analysis of complex mixtures by MALDI-MS. Preliminary results obtained using similarly functionalized porous silicon substrates proved that such substrates are (due to their increased surface areas) better performing than flat silicon.
Collapse
Affiliation(s)
- Tadesse Z Mengistu
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ont. M3J 1P3, Canada
| | | | | |
Collapse
|
26
|
Bouamrani A, Ternier J, Ratel D, Benabid AL, Issartel JP, Brambilla E, Berger F. Direct-tissue SELDI-TOF mass spectrometry analysis: a new application for clinical proteomics. Clin Chem 2006; 52:2103-6. [PMID: 16990423 DOI: 10.1373/clinchem.2006.070979] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND New molecular profiling technologies can aid in analysis of small pathologic samples obtained by minimally invasive biopsy and may enable the discovery of key biomarkers synergistic with anatomopathologic analysis related to prognosis, therapeutic response, and innovative target validation. Thus proteomic analysis at the histologic level in healthy and pathologic settings is a major issue in the field of clinical proteomics. METHODS We used surface-enhanced laser desorption ionization-time-of-flight mass spectrometry (SELDI-TOF MS) technology with surface chromatographic subproteome enrichment and preservation of the spatial distribution of proteomic patterns to detect discrete modifications of protein expression. We performed in situ proteomic profiling of mouse tissue and samples of human cancer tissue, including brain and lung cancer. RESULTS This approach permitted the discrimination of glioblastomas from oligodendrogliomas and led to the identification of 3 potential markers. CONCLUSION Direct tissue proteomic analysis is an original application of SELDI-TOF MS technology that can expand the use of clinical proteomics as a complement to the anatomopathological diagnosis.
Collapse
Affiliation(s)
- Ali Bouamrani
- INSERM U318, Université de Grenoble, Department of Neurosurgery, Centre Hospitalier Universitaire Grenoble, France
| | | | | | | | | | | | | |
Collapse
|
27
|
Yamayoshi Y, Watanabe T, Tanabe M, Hoshino K, Matsumoto K, Morikawa Y, Shimadzu M, Kitajima M, Tanigawara Y. Novel application of ProteinChip technology exploring acute rejection markers of rat small bowel transplantation. Transplantation 2006; 82:320-6. [PMID: 16906028 DOI: 10.1097/01.tp.0000228909.49640.08] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Because no biomarker that reflects small bowel allograft rejection is available, we applied surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) to develop noninvasive markers required for routine diagnosis. METHODS Heterotopic small bowel transplantation (SBT) was performed in rats, and they were divided into four experimental groups: sham-operated rats (sham), syngeneic transplants (syngeneic), allogeneic transplants (allogeneic), allogeneic transplants received FK506 (allo+FK). Plasma samples were analyzed with SELDI ProteinChip arrays to detect peaks that predominated in the allogeneic model. Possible biomarkers were identified in combination with SELDI retentate chromatography mass spectrometry (RCMS) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The identified protein was further analyzed by immunohistochemistry. RESULTS An increase in the level of a 14.8-kDa protein, identified as lysozyme, was observed specifically in the plasma of the allogeneic group; the levels of this protein remained unchanged in the plasma of the other groups. On the other hand, the levels of a 10.1-kDa and a 13.0-kDa protein, identified as migration inhibitory factor-related proteins (MRP), MRP-8 and MRP-14, respectively, began to increase from an early stage of acute rejection. We also observed that lysozyme-positive macrophages had strongly infiltrated the lamina propria during acute rejection. CONCLUSIONS We identified three plasma proteins-MRP-8, MRP-14, and lysozyme-that increased during small bowel allograft rejection. The identified proteins appeared to be markers for inflammation associated with allograft rejection. This proteomic approach will be useful for the identification of candidate biomarkers.
Collapse
Affiliation(s)
- Yasuko Yamayoshi
- Department of Hospital Pharmacy, School of Medicine, Keio University, Tokyo, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Prahalad AK, Hickey RJ, Huang J, Hoelz DJ, Dobrolecki L, Murthy S, Winata T, Hock JM. Serum proteome profiles identifies parathyroid hormone physiologic response. Proteomics 2006; 6:3482-93. [PMID: 16705755 DOI: 10.1002/pmic.200500929] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Parathyroid hormone (amino acids 1-34) (PTH) regulates bone and calcium homeostasis. The magnitude of the effects of PTH on bone varies in osteoporosis patients. We employed ProteinChip technology to generate protein profiles from sera of mice treated once daily with PTH or vehicle for 3 or 11 days. Data analyses on selected arrays indicated significant increases in serum proteins or peptides in PTH-treated groups, compared to vehicle-controls. The magnitude of change increased with duration of treatment. Anion-exchange fractionation of sera prior to profiling on array surfaces increased the number of proteins detected that were regulated by PTH. The optimized purification conditions developed "on-chip" for subsets of proteins, reflected corresponding behavior with process-compatible chromatographic resins under elution chromatography. We have identified and evaluated subsets of serum proteins regulated by PTH treatment, using a combination of ProteinChip technology, column chromatography, PAGE and LC-MS/MS. Our data demonstrate the feasibility of using a panel of serum proteins to detect PTH responsiveness in humans.
Collapse
Affiliation(s)
- Agasanur K Prahalad
- Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, 46202, USA
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Liang Y, Fang M, Li J, Liu CB, Rudd JA, Kung HF, Yew DTW. Serum proteomic patterns for gastric lesions as revealed by SELDI mass spectrometry. Exp Mol Pathol 2006; 81:176-80. [PMID: 16828742 DOI: 10.1016/j.yexmp.2006.04.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 03/27/2006] [Accepted: 04/13/2006] [Indexed: 01/04/2023]
Abstract
SELDI mass spectrometry was used to investigate protein expression in sera of patients with gastric cancer and gastritis compared to normal volunteers. Differences in peak morphology and intensity were observed in regions of 5910 Da, 5084 Da, 6640 Da and 8691 Da. Patients with gastric cancer exhibited an up-regulation of the 5910 Da peak and a down-regulation of the 8691 Da peak compared to the healthy volunteers; there was also some bi-partitioning and tri-partitioning at the 5084 Da peak. When comparing the sera of these cancer patients with those of gastritis, the former had an up-regulation of the 5910 Da peak and a down-regulation of the 6640 Da peak. This is the first report showing that SELDI sera analysis may be useful in the screening of gastric lesions.
Collapse
Affiliation(s)
- Yong Liang
- Institute of Cell Biology, Medical College of Zhejiang University, Hangzhou, Zhejiang, China
| | | | | | | | | | | | | |
Collapse
|
30
|
Brenac V, Mouz N, Schapman A, Ravault V. Expression optimization and purification process development of an engineered soluble recombinant mouse linker of activation of T cells using surface enhanced laser desorption/ionization-mass spectrometry. Protein Expr Purif 2006; 47:533-41. [PMID: 16600631 DOI: 10.1016/j.pep.2006.02.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 01/31/2006] [Accepted: 02/13/2006] [Indexed: 11/28/2022]
Abstract
Protein purification development is the bottleneck of recombinant protein production therefore there is a need to shorten process development and monitoring. Surface enhanced laser desorption/ionization-mass spectrometry (SELDI-MS) was evaluated to optimize the expression and to develop the purification of a recombinant mouse protein: a transmembrane adaptor involved in T cell receptor signaling named "linker for activation of T cells" (LAT). The protein was expressed as a soluble form (S-LAT) in three strains of Escherichia coli: BL21 (DE3), Rosetta (DE3), and BL21 (DE3) pLys S. The expression of S-LAT was monitored on immobilized metal affinity chromatography (IMAC) ProteinChip arrays. The highest level of expression was found in Rosetta (DE3) with a C-terminal construct after induction at 37 degrees C. The purification scheme was elucidated using SELDI-MS: S-LAT was efficiently captured on an IMAC ProteinChip array saturated with nickel ions (Ni(2+)) and then fractionated on a Q ProteinChip array. These conditions were directly transferred to IMAC-Ni(2+) HyperCel and Q Ceramic HyperD F chromatography sorbents. After these two purification steps, S-LAT was estimated to be more than 80% pure, confirming a very good match between array and sorbent. Finally, a peptide mapping was performed on a hydrophobic array after in gel trypsin digest, verifying that the purified protein was the mouse LAT. This is the first report of a protocol for the production and purification of S-LAT. The selection of the best expression and purification strategy along with the identification were enabled in 5 days with less than 5 mL of soluble fraction of crude culture samples.
Collapse
|
31
|
Williams D, Zhu P, Bowden P, Stacey C, McDonell M, Kowalski P, Kowalski JM, Evans K, Diamandis EP, Michael Siu KW, Marshall J. Comparison of methods to examine the endogenous peptides of fetal calf serum. Clin Proteomics 2006. [DOI: 10.1385/cp:2:1:67] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
|
32
|
Escher N, Spies-Weisshart B, Kaatz M, Melle C, Bleul A, Driesch D, Wollina U, von Eggeling F. Identification of HNP3 as a tumour marker in CD4+ and CD4− lymphocytes of patients with cutaneous T-cell lymphoma. Eur J Cancer 2006; 42:249-55. [PMID: 16338134 DOI: 10.1016/j.ejca.2005.07.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Revised: 07/10/2005] [Accepted: 07/10/2005] [Indexed: 11/16/2022]
Abstract
Cutaneous T-cell lymphomas (CTCL) are characterized by malignant proliferation of skin homing T-cells. Although prognosis is generally good, reliable markers are needed to identify patients at risk for a more aggressive course. ProteinChip (SELDI) technology was used as a tool for the discovery of protein patterns in lymphocytes from patients with CTCL (n=25) and unaffected controls (n=25). Lymphocytes were separated in CD4+ and CD4- fractions by magnetic cell sorting (MACS). Each whole protein extract was analysed by ProteinChip technology. The resulting protein profiles were submitted for bioinformatic analysis including a clustering algorithm, a rule extraction, a rating and a rule-base construction step. For the generated combined rule base for the CD4- cell fraction, both the sensitivity and specificity for the prediction of CTCL reached 96%, while for the CD4+ fraction they were 92% and 84%, respectively, for sensitivity and specificity. The most significant peak at 3489Da could be identified as HNP3, an alpha-defensin, by immunocapturing. These results open up both the possibility for the use of this protein signature, especially HNP3, to more effectively monitor and screen CTCL, and the avenue to identify the other relevant peaks for a better understanding of the development of this tumour.
Collapse
Affiliation(s)
- Niko Escher
- Core Unit Chip Application, Institute of Human Genetics and Anthropology, Friedrich-Schiller-University, 07740 Jena, Germany
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Rawel HM, Rohn S, Kroll J, Schweigert FJ. Surface enhanced laser desorptions ionization-time of flight-mass spectrometry analysis in complex food and biological systems. Mol Nutr Food Res 2005; 49:1104-11. [PMID: 16270379 DOI: 10.1002/mnfr.200500047] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Harshadrai M Rawel
- Department of Physiology and Pathophysiology, Institute of Nutritional Science, University of Potsdam, D-14469 Potsdam, Germany.
| | | | | | | |
Collapse
|
34
|
Bensch M, Schulze Wierling P, von Lieres E, Hubbuch J. High Throughput Screening of Chromatographic Phases for Rapid Process Development. Chem Eng Technol 2005. [DOI: 10.1002/ceat.200500153] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
35
|
Vorderwülbecke S, Cleverley S, Weinberger SR, Wiesner A. Protein quantification by the SELDI-TOF-MS–based ProteinChip® System. Nat Methods 2005. [DOI: 10.1038/nmeth0505-393] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
36
|
Brenac V, Ravault V, Santambien P, Boschetti E. Capture of a monoclonal antibody and prediction of separation conditions using a synthetic multimodal ligand attached on chips and beads. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 818:61-6. [PMID: 15722045 DOI: 10.1016/j.jchromb.2004.09.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Accepted: 09/17/2004] [Indexed: 11/23/2022]
Abstract
A synthetic ligand called 2-mercapto-5-benzimidazolesulfonic acid has been successfully used for the specific chromatographic capture of antibodies from a cell culture supernatant. Adsorption occurred at physiological ionic strength and pH range between 5.0 and 6.0, with some binding capacity variations within this pH range: antibody uptake increased when the pH decreased. With very dilute feedstocks, as was the case with the cell culture supernatant under investigation, it was found that the pH had to be slightly lowered to get a good antibody sorption capacity. To optimize separation conditions, a preliminary study was made using ProteinChip Arrays that displayed the same chemical functionalities as the resin. Arrays were analyzed using SELDI-MS. By this mean, it was possible to cross-over simultaneously different pH conditions at the adsorption and the desorption steps. Best conditions were implemented for preparative separation using regular lab-scale columns. At pH 5.2, antibody adsorption was not complete, while at pH 5.0 the antibody was entirely captured. pH 9 was selected at elution, rather than pH 8.0 or 10.0, and resulted in a complete desorption of antibodies from the column. Benefits of the prediction of separation conditions of antibodies on MBI beads using SELDI-MS were a significant reduction in analysis time and in sample volume. This was possible because the separation of IgG on the chip surface did mimic very well the separation on beads.
Collapse
Affiliation(s)
- Virginie Brenac
- BioSepra, Process Proteomics, Division of Ciphergen Biosystems Inc., 48 Avenue des Genottes, BP 38347 Cergy Saint Christophe, 95804 Cergy Pontoise Cedex, France.
| | | | | | | |
Collapse
|
37
|
Plasma Protein Profiling for Diagnosis of Pancreatic Cancer Reveals the Presence of Host Response Proteins. Clin Cancer Res 2005. [DOI: 10.1158/1078-0432.1110.11.3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Plasma protein profiling using separations coupled to matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) has great potential in translational research; it can be used for biomarker discovery and contribute to disease diagnosis and therapy. Previously reported biomarker searches have been done solely by MS protein profiling followed by bioinformatics analysis of the data. To add to current methods, we tested an alternative strategy for plasma protein profiling using pancreatic cancer as the model. First, offline solid-phase extraction is done with 96-well plates to fractionate and partially purify the proteins. Then, multiple profiling and identification experiments can be conducted on the same protein fractions because only 5% of the fractions are used for MALDI MS profiling. After MALDI MS analysis, the mass spectra are normalized and subjected to a peak detection algorithm. Over three sets of mass spectra acquired using different instrument variables, ∼400 unique ion signals were detected. Classification schemes employing as many as eight individual peaks were developed using a training set with 123 members (82 cancer patients) and a blinded validation set with 125 members (57 cancer patients). The sensitivity of the study was 88%, but the specificity was significantly lower, 75%. The reason for the low specificity becomes apparent upon protein identification of the ion signals used for the classification. The identifications reveal only common serum proteins and components of the acute phase response, including serum amyloid A, α-1-antitrypsin, α-1-antichymotrypsin, and inter-α-trypsin inhibitor.
Collapse
|
38
|
Mengistu TZ, DeSouza L, Morin S. Functionalized porous silicon surfaces as MALDI-MS substrates for protein identification studies. Chem Commun (Camb) 2005:5659-61. [PMID: 16292381 DOI: 10.1039/b511457h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Alkyl monolayer modified porous silicon functional surfaces are employed for selective binding of proteins from complex mixtures (through washing of the deposited mixture spot using appropriate buffer) and MALDI-MS is used to detect the components retained on the surface.
Collapse
Affiliation(s)
- Tadesse Z Mengistu
- Department of Chemistry, 4700 Keele Street, Toronto, Ontario M3J1P3, Canada
| | | | | |
Collapse
|
39
|
Callesen AK, Mohammed S, Bunkenborg J, Kruse TA, Cold S, Mogensen O, Christensen RD, Vach W, Jørgensen PE, Jensen ON. Serum protein profiling by miniaturized solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:1578-86. [PMID: 15915448 DOI: 10.1002/rcm.1960] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Serum profiling by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) holds promise as a clinical tool for early diagnosis of cancer and other human diseases. Sample preparation is key to achieving reproducible and well-resolved signals in MALDI-MS; a prerequisite for translation of MALDI-MS based diagnostic methods to clinical applications. We have investigated a number of MALDI matrices and several miniaturized solid-phase extraction (SPE) methods for serum protein concentration and desalting with the aim of generating reproducible, high-quality protein profiles by MALDI-MS. We developed a simple protocol for serum profiling that combines a matrix mixture of 2,5-dihydroxybenzoic acid and alpha-cyano-4-hydroxycinnamic acid with miniaturized SPE and MALDI-MS. Functionalized membrane discs with hydrophobic, ion-exchange or chelating properties allowed reproducible MALDI mass spectra (m/z 1000-12,000) to be obtained from serum. In a proof-of-principle application, SPE with chelating material and MALDI-MS identified protein peaks in serum that had been previously reported for distinguishing a person diagnosed with breast cancer from a control. These preliminary results indicate that this simple SPE/MALDI-MS method for serum profiling provides a versatile and scalable platform for clinical proteomics.
Collapse
Affiliation(s)
- Anne K Callesen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Seibert V, Wiesner A, Buschmann T, Meuer J. Surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI TOF-MS) and ProteinChip technology in proteomics research. Pathol Res Pract 2004; 200:83-94. [PMID: 15237917 DOI: 10.1016/j.prp.2004.01.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this review article, we describe some of the studies that have been performed using the surface-enhanced laser desorption ionization (SELDI) time-of-flight mass spectrometry and ProteinChip technology over the past few years, and highlight both their findings as well as limitations. Proteomic applications, such as target or marker identification and target validation or toxicology, will be addressed. We will also provide an examination of SELDI technology and go into the question of where possible future research may lead us.
Collapse
Affiliation(s)
- Volker Seibert
- EUROPROTEOME AG, Neuendorfstrasse 24b, 16761 Hennigsdorf, Germany.
| | | | | | | |
Collapse
|
41
|
Melle C, Ernst G, Schimmel B, Bleul A, Koscielny S, Wiesner A, Bogumil R, Möller U, Osterloh D, Halbhuber KJ, von Eggeling F. A Technical Triade for Proteomic Identification and Characterization of Cancer Biomarkers. Cancer Res 2004; 64:4099-104. [PMID: 15205318 DOI: 10.1158/0008-5472.can-03-3807] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biomarkers are needed to elucidate the biological background and to improve the detection of cancer. Therefore, we have analyzed laser-microdissected cryostat sections from head and neck tumors and adjacent mucosa on ProteinChip arrays. Two differentially expressed proteins (P = 3.34 x 10(-5) and 4.6 x 10(-5)) were isolated by two-dimensional gel electrophoresis and identified as S100A8 (calgranulin A) and S100A9 (calgranulin B) by in-gel proteolytic digestion, peptide mapping, tandem mass spectrometry analysis, and immunodepletion assay. The relevance of these single marker proteins was evaluated by immunohistochemistry. Positive tissue areas were reanalyzed on ProteinChip arrays to confirm the identity of these proteins. As a control, a peak with low P was identified as calgizzarin (S100A11) and characterized in the same way. This technical triade of tissue microdissection, ProteinChip technology, and immunohistochemistry opens up the possibility to find, identify, and characterize tumor relevant biomarkers, which will allow the movement toward the clonal heterogeneity of malignant tumors. Taking this approach, proteins were identified that might be responsible for invasion and metastasis.
Collapse
Affiliation(s)
- Christian Melle
- Core Unit Chip Application, Institute of Human Genetics and Anthropology, Friedrich-Schiller-University, Jena, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Marshall J, Jankowski A, Furesz S, Kireeva I, Barker L, Dombrovsky M, Zhu W, Jacks K, Ingratta L, Bruin J, Kristensen E, Zhang R, Stanton E, Takahashi M, Jackowski G. Human Serum Proteins Preseparated by Electrophoresis or Chromatography Followed by Tandem Mass Spectrometry. J Proteome Res 2004; 3:364-82. [PMID: 15253417 DOI: 10.1021/pr034039p] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrophoretic and chromatographic sample preparations were compared and together detected the presence of some 600 types of protein products in human serum. Proteins from crude serum preseparated by ionic electrophoresis, chromatography, or a combination of both were analyzed. Proteins were digested with trypsin or chymotrypsin. Naturally occurring peptides were also collected by reversed-phase chromatography. The resulting peptides were identified by tandem mass spectrometry. The peptides were either desorbed by a laser from a metal chip into a quadrupole-time-of-flight mass spectrometer or ionized as an electro-spray from reversed-phase chromatography via a metal needle under voltage into an ion-trap mass spectrometer. All of the commonly known proteins associated with serum were detected, and the two mass spectrometers agreed on the identity of abundant serum proteins. Preseparation of serum proteins prior to digestion markedly enhanced the capacity to detect un-common proteins from blood. Electrophoretic- and chromatography-based experiments were found to be complementary. Many novel cellular proteins not previously associated with serum were recorded.
Collapse
Affiliation(s)
- John Marshall
- SYNX PHARMA, 1 Marmac Drive, Toronto, Ontario, Canada M9W 1E7.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Approaches to Devise Antibody Purification Processes by Chromatography. Antibodies (Basel) 2004. [DOI: 10.1007/978-1-4419-8877-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
|
44
|
Tang N, Tornatore P, Weinberger SR. Current developments in SELDI affinity technology. MASS SPECTROMETRY REVIEWS 2004; 23:34-44. [PMID: 14625891 DOI: 10.1002/mas.10066] [Citation(s) in RCA: 310] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The overall history and recent advancements in Surface-Enhanced Laser Desorption/Ionization (SELDI) affinity technology is reviewed. A detailed account of SELDI technology, utilizing Immobilized-Metal Affinity surfaces, pseudo-specific chromatographic surfaces, and biospecific interactive surfaces, is presented with particular emphasis placed upon examination of fundamental characteristics as well as specific applications for each. Finally, a detailed review of the specific use of such affinity surfaces in fundamental aspects of clinical, process, and research proteomics activity is presented.
Collapse
Affiliation(s)
- Ning Tang
- Ciphergen Biosystems, 6611 Dumbarton Circle, Fremont, California 94555, USA
| | | | | |
Collapse
|
45
|
Shiwa M, Nishimura Y, Wakatabe R, Fukawa A, Arikuni H, Ota H, Kato Y, Yamori T. Rapid discovery and identification of a tissue-specific tumor biomarker from 39 human cancer cell lines using the SELDI ProteinChip platform. Biochem Biophys Res Commun 2003; 309:18-25. [PMID: 12943657 DOI: 10.1016/s0006-291x(03)01520-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Useful biomarkers are needed for early detection of cancers. To demonstrate the potential diagnostic usefulness of a new proteomic technology, we performed Expression Difference Mapping analysis on 39 cancer cell lines from 9 different tissues using ProteinChip technology. A protein biomarker candidate of 12kDa was found in colon cancer cells. We then optimized the purification conditions for this biomarker by utilizing Retentate Chromatography mass spectrometry (RC-MS). The optimized purification conditions developed "on-chip" were directly transferred to conventional chromatography to purify the biomarker, which was identified as prothymosin-alpha by ProteinChip time-of-flight mass spectrometry (TOF MS) and ProteinChip-Tandem MS systems. The relative expression level of prothymosin-alpha between colon cancer cells and normal colon mucosal cells was evaluated on the same ProteinChip platform. Prothymosin-alpha expression in colon cancer cells was clearly higher than in normal colon cells. These results indicate that prothymosin-alpha could be a potential biomarker for colon cancer, and that the ProteinChip platform could perform the whole process of biomarker discovery from screening to evaluation of the identified marker.
Collapse
Affiliation(s)
- Mieko Shiwa
- Yokohama Laboratory, Ciphergen Biosystems K.K., Yokohama Business Park East Tower 14F, 134 Godo-cho, Hodogaya-ku, Yokohama, Kanagawa, Japan
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Melle C, Ernst G, Schimmel B, Bleul A, Koscielny S, Wiesner A, Bogumil R, Moller U, Osterloh D, Halbhuber KJ, von Eggeling F. Biomarker discovery and identification in laser microdissected head and neck squamous cell carcinoma with ProteinChip technology, two-dimensional gel electrophoresis, tandem mass spectrometry, and immunohistochemistry. Mol Cell Proteomics 2003; 2:443-52. [PMID: 12824440 DOI: 10.1074/mcp.m300033-mcp200] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Head and neck cancer is a frequent malignancy with a complex, and up to now not clear etiology. Therefore, despite of improvements in diagnosis and therapy, the survival rate with head and neck squamous-cell carcinomas is poor. For a better understanding of the molecular mechanisms behind the process of tumorigenesis and tumor progression, we have analyzed changes of protein expression between microdissected normal pharyngeal epithelium and tumor tissue by ProteinChip technology. For this, cryostat sections from head and neck tumors (n = 57) and adjacent mucosa (n = 44) were laser-microdissected and analyzed on ProteinChip arrays. The derived mass spectrometry profiles exhibited numerous statistical differences. One peak significantly higher expressed in the tumor (p = 0.000029) was isolated by two-dimensional gel electrophoresis and identified as annexin V by in-gel proteolytic digestion, peptide mapping, tandem mass spectrometry analysis, and immuno-deplete assay. The relevance of this single marker protein was further evaluated by immunohistochemistry. Annexin-positive tissue areas were re-analyzed on ProteinChip arrays to confirm the identity of this protein. In this study, we could show that biomarker in head and neck cancer can be found, identified, and assessed by combination of ProteinChip technology, two-dimensional gel electrophoresis, and immunohistochemistry. In our experience, however, such studies only make sense if a relatively pure microdissected tumor tissue is used. Only then minute changes in protein expression between normal pharyngeal epithelium and tumor tissue can be detected, and it will become possible to educe a tumor-associated protein pattern that might be used as a marker for tumorigenesis and progression.
Collapse
Affiliation(s)
- Christian Melle
- Core Unit Chip Application (CUCA), Institute of Human Genetics and Anthropology, Friedrich-Schiller-University, 07740 Jena, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Shiloach J, Santambien P, Trinh L, Schapman A, Boschetti E. Endostatin capture from Pichia pastoris culture in a fluidized bed. From on-chip process optimization to application. J Chromatogr B Analyt Technol Biomed Life Sci 2003; 790:327-36. [PMID: 12767341 DOI: 10.1016/s1570-0232(03)00097-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the characteristics of the methylothrophic yeast Pichia pastoris is its ability to grow to a very high cell density. Biomass concentrations of 300-400 g wet mass/l are common. It is therefore obvious that the recovery processes of extracellular proteins from this microorganism should take into account the effect of high biomass content. Separation by filtration and/or centrifugation is possible but these steps are cumbersome and can affect the protein recovery. The use of fluidized beds is attractive proteins capture option since it eliminates the biomass while capturing the desired protein. Zirconia-based resins possess unique properties which make them appropriate for processing high biomass concentrations in an expanded bed mode. The beads are particularly heavy (density is 3.2 g/ml) and small (75 microm) and therefore can accommodate high fluidization velocity and high mass transport. Specific operating conditions for effective capture of expressed protein have to be determined. This determination is generally time consuming and requires relatively large amount of feedstock for the lab trials. To avoid multiple chromatographic trials in columns, optimal conditions of adsorption and elution were determined by ProteinChip technology coupled with mass spectrometry. This technology involves flat chip surfaces functionalized as chromatographic beads where it is possible to adsorb and desorb proteins. Four different functional groups (strong anion-exchange, weak cation-exchange, hydrophobic and metal chelate) were tested and the retained proteins were analyzed directly by mass spectrometry. The weak cation-exchange group was chosen for further work. The Zirconia-based weak cation-exchange sorbent (CM HyperZ) was evaluated for binding capacity in a packed column and then for capturing endostatin from crude feed stock. Based on the previously determined conditions; 45 l of culture containing approximately 15 kg of biomass (wet mass) and 3 g endostatin were applied on an expanded bed at a flow-rate of 535 cm/h, yielding 80% of the endostatin and removing approximately 80% of foreign proteins.
Collapse
|
48
|
Abstract
An insight into protein mechanisms involved in disease is critical to the discovery and design of new therapeutic tools. Direct protein analysis provides a method for studying the proteome of a tissue irrespective of an in-depth knowledge of its transcriptome. The development of a human central nervous system (CNS) proteome database ultimately will serve to accelerate the development of specific diagnostic and prognostic markers, neuropsychiatric disease markers, and the corresponding therapeutic tools. It may also reduce the uncertainties in in silico gene predictions by direct open reading frame verification and the ambiguities that experimental models of disease may provide. Advances in gel independent proteomic analyses by solid phase isotope tagging provide greater scope for the characterization of previously elusive membrane proteins; approximately half of all drug targets are key CNS membrane proteins. These advances hold great promise for improvements in the understanding, diagnosis, and therapy of central nervous system disorders.
Collapse
|
49
|
Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:588-595. [PMID: 12794882 DOI: 10.1002/jms.408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
|
50
|
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003. [PMCID: PMC2448450 DOI: 10.1002/cfg.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|