Abstract
There is an urgent need for accurate biomarkers of disease. The low-molecular weight proteome of blood serum or other biological fluids may be an ideal source of such biomarkers, although its analysis requires high-throughput strategies to enrich and quantify peptides and small proteins with biomarker potential. Herein, serum samples from cancer cases and controls are compared using a workflow of robotic reversed-phase extraction and clean-up, followed by automated MALDI MS spectral acquisition and analysis of the low-molecular weight peptidome. The aim of the presented methodology is to facilitate the discovery of candidate serum biomarkers of cancer using MALDI MS profiling, although the method is applicable to any comparative proteomic analysis of any biofluid.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsNotes
- 1.
RPC18 Dynabeads are paramagnetic, non-porous particles modified with hydrophobic C18 reversed phase chromatographic material. Other manufacturers and chromatographic materials can be used (e.g. C8 reversed phase, weak cation exchange, Cu2+-IMAC), but we have found that the RPC18 Dynabeads gave good yields in terms of the numbers and intensities of the peaks detected.
- 2.
- 3.
Software versions higher (newer) than stated should also be adequate.
- 4.
Other instrumentation and modes of operation can be used for peptide identification.
- 5.
Blood collection requires informed consent from donors and studies require ethical approval from the relevant Committees on the Ethics of Human Research. Blood should be taken by a trained phlebotomist. Time of venepuncture should be recorded along with other subject/patient information relevant to the study, such as clinico-pathological features, treatment details, demographic data and any routine clinical assay results. Ideally, controls should be matched as closely as possible to cases. Ensure all samples are handled and processed identically (see Timms et al. 2010 for further information).
- 6.
Other robotic liquid-handling platforms can be employed, although the protocol would need to be adjusted for other platforms. For example, a CyBi™-Disk liquid handling robot (CyBio AG, Jena, Germany) with pre-packed C4 and C18 ZipTips (Millipore, Watford, UK) was used successfully in previous work (Tiss et al. 2007).
- 7.
Note that drying at relative humidity below ~30–40% has been reported to be detrimental for MALDI MS (Tiss et al. 2007). Thus, ensure that the relative humidity is ≥35–40%.
- 8.
The Ultraflex II MALDI-TOF/TOF mass spectrometer is equipped with a 337 nm nitrogen laser, a gridless ion source, delayed-extraction (DE), a high-resolution timed ion selector and a 2 GHz digitizer. Other MALDI-TOF platforms can be used (see Footnote 2).
- 9.
See Footnote 2 in Sect. 3.1.3.
- 10.
Multi-marker model building and testing can be performed with the ClinProTools software. As before, other (classification) software can be used.
- 11.
See Footnote 4 in Sect. 3.1.4.
- 12.
If the identity of the peak of interest is still ambiguous, it may be necessary to carry out fractionation of the scaled-up extract. For a detailed protocol, refer to (Tiss et al. 2010).
References
Baggerly KA, Morris JS, Coombes KR (2004) Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics 20(5):777–785
Baggerly KA, Morris JS, Edmonson SR, Coombes KR (2005) Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J Natl Cancer Inst 97(4):307–309
Banks RE, Stanley AJ, Cairns DA, Barrett JH, Clarke P, Thompson D, Selby PJ (2005) Influences of blood sample processing on low-molecular-weight proteome identified by surface-enhanced laser desorption/ionization mass spectrometry. Clin Chem 51(9):1637–1649
Conraux L, Pech C, Guerraoui H, Loyaux D, Ferrara P, Guillemot JC, Meininger V, Pradat PF, Salachas F, Bruneteau G, Le Forestier N, Lacomblez L (2013) Plasma peptide biomarker discovery for amyotrophic lateral sclerosis by MALDI-TOF mass spectrometry profiling. PLoS One 8(11), e79733. doi:10.1371/journal.pone.0079733
Davis MT, Auger PL, Patterson SD (2010) Cancer biomarker discovery via low molecular weight serum profiling–are we following circular paths? Clin Chem 56(2):244–247. doi:10.1373/clinchem.2009.127951
Diamandis EP (2004a) Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems. J Natl Cancer Inst 96(5):353–356
Diamandis EP (2004b) Mass spectrometry as a diagnostic and a cancer biomarker discovery tool: opportunities and potential limitations. Mol Cell Proteomics 3(4):367–378
Diamandis EP (2006) Serum proteomic profiling by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for cancer diagnosis: next steps. Cancer Res 66(11):5540–5541
Geho DH, Liotta LA, Petricoin EF, Zhao W, Araujo RP (2006) The amplified peptidome: the new treasure chest of candidate biomarkers. Curr Opin Chem Biol 10(1):50–55. doi:10.1016/j.cbpa.2006.01.008
Hortin GL (2006) The MALDI-TOF mass spectrometric view of the plasma proteome and peptidome. Clin Chem 52(7):1223–1237
Karsan A, Eigl BJ, Flibotte S, Gelmon K, Switzer P, Hassell P, Harrison D, Law J, Hayes M, Stillwell M, Xiao Z, Conrads TP, Veenstra T (2005) Analytical and preanalytical biases in serum proteomic pattern analysis for breast cancer diagnosis. Clin Chem 51(8):1525–1528
Li L, Li J, Jin H, Shang L, Li B, Wei F, Liu Q (2012) Detection of Leishmania donovani infection using magnetic beads-based serum peptide profiling by MALDI-TOF MS in mice model. Parasitol Res 110(3):1287–1290. doi:10.1007/s00436-011-2604-0
Liotta LA, Petricoin EF (2006) Serum peptidome for cancer detection: spinning biologic trash into diagnostic gold. J Clin Invest 116(1):26–30. doi:10.1172/JCI27467
Lu J, Huang Y, Wang Y, Li Y, Zhang Y, Wu J, Zhao F, Meng S, Yu X, Ma Q, Song M, Chang N, Bittles AH, Wang W (2012) Profiling plasma peptides for the identification of potential ageing biomarkers in Chinese Han adults. PLoS One 7(7), e39726. doi:10.1371/journal.pone.0039726
Petricoin EF, Belluco C, Araujo RP, Liotta LA (2006) The blood peptidome: a higher dimension of information content for cancer biomarker discovery. Nat Rev Cancer 6(12):961–967. nrc2011[pii]. doi:10.1038/nrc2011
Pietrowska M, Marczak L, Polanska J, Behrendt K, Nowicka E, Walaszczyk A, Chmura A, Deja R, Stobiecki M, Polanski A, Tarnawski R, Widlak P (2009) Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer. J Transl Med 7:60. doi:10.1186/1479-5876-7-60
Sandanayake NS, Camuzeaux S, Sinclair J, Blyuss O, Andreola F, Chapman MH, Webster GJ, Smith RC, Timms JF, Pereira SP (2014) Identification of potential serum peptide biomarkers of biliary tract cancer using MALDI MS profiling. BMC Clin Pathol 14(1):7. doi:10.1186/1472-6890-14-7
Taguchi F, Solomon B, Gregorc V, Roder H, Gray R, Kasahara K, Nishio M, Brahmer J, Spreafico A, Ludovini V, Massion PP, Dziadziuszko R, Schiller J, Grigorieva J, Tsypin M, Hunsucker SW, Caprioli R, Duncan MW, Hirsch FR, Bunn PA Jr, Carbone DP (2007) Mass spectrometry to classify non-small-cell lung cancer patients for clinical outcome after treatment with epidermal growth factor receptor tyrosine kinase inhibitors: a multicohort cross-institutional study. J Natl Cancer Inst 99(11):838–846. doi:10.1093/jnci/djk195
Terracciano R, Preiano M, Palladino GP, Carpagnano GE, Barbaro MP, Pelaia G, Savino R, Maselli R (2011) Peptidome profiling of induced sputum by mesoporous silica beads and MALDI-TOF MS for non-invasive biomarker discovery of chronic inflammatory lung diseases. Proteomics 11(16):3402–3414. doi:10.1002/pmic.201000828
Teunissen CE, Koel-Simmelink MJ, Pham TV, Knol JC, Khalil M, Trentini A, Killestein J, Nielsen J, Vrenken H, Popescu V, Dijkstra CD, Jimenez CR (2011) Identification of biomarkers for diagnosis and progression of MS by MALDI-TOF mass spectrometry. Mult Scler 17(7):838–850. doi:10.1177/1352458511399614
Timms JF, Arslan-Low E, Gentry-Maharaj A, Luo Z, T'Jampens D, Podust VN, Ford J, Fung ET, Gammerman A, Jacobs I, Menon U (2007) Preanalytic influence of sample handling on SELDI-TOF serum protein profiles. Clin Chem 53(4):645–656
Timms JF, Cramer R, Camuzeaux S, Tiss A, Smith C, Burford B, Nouretdinov I, Devetyarov D, Gentry-Maharaj A, Ford J, Luo Z, Gammerman A, Menon U, Jacobs I (2010) Peptides generated ex vivo from serum proteins by tumor-specific exopeptidases are not useful biomarkers in ovarian cancer. Clin Chem 56(2):262–271
Timms JF, Menon U, Devetyarov D, Tiss A, Camuzeaux S, McCurrie K, Nouretdinov I, Burford B, Smith C, Gentry-Maharaj A, Hallett R, Ford J, Luo Z, Vovk V, Gammerman A, Cramer R, Jacobs I (2011) Early detection of ovarian cancer in samples pre-diagnosis using CA125 and MALDI-MS peaks. Cancer Genomics Proteomics 8(6):289–305
Tiss A, Smith C, Camuzeaux S, Kabir M, Gayther S, Menon U, Waterfield M, Timms JF, Jacobs I, Cramer R (2007) Serum peptide profiling using MALDI mass spectrometry: avoiding the pitfalls of coated magnetic beads using well-established ZipTip technology. Proteomics 7(Suppl 1):77–89
Tiss A, Smith C, Menon U, Jacobs I, Timms JF, Cramer R (2010) A well-characterised peak identification list of MALDI MS profile peaks for human blood serum. Proteomics 10(18):3388–3392
Vafadar-Isfahani B, Laversin SA, Ahmad M, Ball G, Coveney C, Lemetre C, Kathleen Miles A, van Schalkwyk G, Rees R, Matharoo-Ball B (2010) Serum biomarkers which correlate with failure to respond to immunotherapy and tumor progression in a murine colorectal cancer model. Proteomics Clin Appl 4(8-9):682–696. doi:10.1002/prca.200900218
Villanueva J, Lawlor K, Toledo-Crow R, Tempst P (2006a) Automated serum peptide profiling. Nat Protoc 1(2):880–891
Villanueva J, Martorella AJ, Lawlor K, Philip J, Fleisher M, Robbins RJ, Tempst P (2006b) Serum peptidome patterns that distinguish metastatic thyroid carcinoma from cancer-free controls are unbiased by gender and age. Mol Cell Proteomics 5(10):1840–1852
Villanueva J, Shaffer DR, Philip J, Chaparro CA, Erdjument-Bromage H, Olshen AB, Fleisher M, Lilja H, Brogi E, Boyd J, Sanchez-Carbayo M, Holland EC, Cordon-Cardo C, Scher HI, Tempst P (2006c) Differential exoprotease activities confer tumor-specific serum peptidome patterns. J Clin Invest 116(1):271–284
Xiao D, Meng FL, He LH, Gu YX, Zhang JZ (2011) Analysis of the urinary peptidome associated with Helicobacter pylori infection. World J Gastroenterol 17(5):618–624. doi:10.3748/wjg.v17.i5.618
Acknowledgements
This work was funded by MRC grant G0301107 and was supported by the National Institute for Health Research University College London Hospitals Biomedical Research Centre.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Camuzeaux, S., Timms, J.F. (2016). Disease Profiling by MALDI MS Analysis of Biofluids. In: Cramer, R. (eds) Advances in MALDI and Laser-Induced Soft Ionization Mass Spectrometry. Springer, Cham. https://doi.org/10.1007/978-3-319-04819-2_10
Download citation
DOI: https://doi.org/10.1007/978-3-319-04819-2_10
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-04818-5
Online ISBN: 978-3-319-04819-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)