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Targeted proteomics of solid cancers: from quantification of known biomarkers towards reading the digital proteome maps

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  • Boja E, Rivers R, Kinsinger C, et al. Restructuring proteomics through verification. Biomark. Med 2010;4(6):799-803
  • Krisp C, Randall SA, McKay M, Molloy MP. Towards clinical application of selected reaction monitoring for plasma protein biomarker studies. Proteomics Clin. Appl 2012;6:42-59
  • Faktor J, Dvorakova M, Maryas M, et al. Identification and characterization of pro-metastatic targets, pathway and molecular complexes using a toolbox of proteomic technologies. Klin Onkol 2012;25(2):70-7
  • Kawamura T, Nomura M, Tojo H, et al. Proteomic analysis of laser-microdissected paraffin-embedded tissues: (1) Stage-related protein candidates upon non-metastatic lung adenocarcinoma. J Proteomics 2010;73(6):1089-99
  • Shaheed S, Rustogi N, Scally A, et al. Identification of stage specific breast markers using quantitative proteomics. J Proteome Res 2013;12:5696-708
  • DeSouza LV, Krakovska O, Darfler MM, et al.mTRAQ-based quantification of potential endometrial carcinoma biomarkers from archived formalin-fixed paraffin-embedded tissues. Proteomics 2010;10:3108-16
  • Sprung RW, Martinez MA, Carpenter KL, et al. Precision of multiple reaction monitoring mass spectrometry analysis of formalin-fixed, paraffin-embedded tissue. J Proteome Res 2012;11:3498-505
  • Takadate T, Onogawa T, Fukuda T, et al. Novel prognostic protein markers of resectable pancreatic cancer identified by coupled shotgun and targeted proteomics using formalin-fixed paraffin embedded tissues. Int J Cancer 2013;132(6):1368-82
  • Wisniewski JR, Ostasiewitz P, Mann M. High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J Proteome Res 2011;10:3040-9
  • Hembrough T, Thyparambil S, Liao WL, et al. Application of selected reaction monitoring for multiplex quantification of clinically validated biomarkers in formalin-fixed, paraffin-embedded tumor tissue. J Mol Diagn 2013;15(4):454-65
  • Riley CP, Zhang X, Nakshatri H, et al. A large consistent plasma proteomics data set from prospectively collected breast cancer patient and healthy volunteer samples. J Transl Med 2011
  • Selevsek N, Matondo M, Sanchez Carbayo M, et al. Systematic quantification of peptides-proteins in urine using selected reaction monitoring. Proteomics 2011;11:1135-47
  • Cohen A, Wang E, Chrisholm KA, et al. A mass spectrometry-based plasma protein panel targeting the tumor microenvironment in patients with breast cancer. J Proteomics 2013;81:135-47
  • Murphy JP, Pinto DM. Targeted proteomic analysis of glycolysis in cancer cells. J Proteome Res 2010;10:607-313
  • Kennedy JJ, Abatiello SE, Kim K, et al. Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Nat Methods 2014;11(2):149-55
  • Drabovich AP, Pavlou MP, Dimitromanolakis A, et al. Quantitative analysis of energy metabolic pathways in MCF-7 breast cancer cells by selected reaction proteomics. Mol Cell Proteomics 2012;11(8):422-34
  • Moody SE, Sarkisian CJ, Than KT, et al. Conditional activation of Neu in the mammary epithelium of transgenic mice results in reversible pulmonary. Cancer Cell 2002;2(6):451-61
  • Whiteaker JR, Zhang H, Zhao L, et al. Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res 2007;6:3962-75
  • Rangiah K, Tippornwong M, Sangar V, et al. Differential secreted proteome approach in murine model for candidate biomarker discovery in colon cancer. J Proteome Res 2009;8(11):5153-64
  • Ivancic MM, Huttlin EL, Chen X, et al. Candidate serum biomarkers for early intestinal cancer using 15N metabolic labeling and quantitative proteomics in the ApcMin/+ mouse. J Proteome Res 2013;12:4152-66
  • Beer LA, Wang H, Tang HY, et al. Identification of multiple novel protein biomarkers shed by human serous ovarian tumors into the blood of immunocompromised mice and verified in patient sera. PLoS One 2013
  • Tang HY, Beer LA, Chang-Wong T, et al. A xenograft mouse model coupled with in-depth plasma proteome analysis facilitates identification of novel serum biomarkers for human ovarian cancer. J Proteome Res 2012;11:678-91
  • Ebhardt HA, Root A, Sander C, Aebersold R. Application of targeted proteomics in system biology. Proteomics 2015
  • Liu Y, Hüttenhain R, Collins B, Aebersold R. Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Rev Mol Diag 2013;13(8):811-25
  • Chambers AG, Percy AJ, Simon R, Borchers CH. MRM for the verification of cancer biomarker proteins: recent application to human plasma and serum. Expert Rev. Proteomics 2014;11(2):137-48
  • Picotti P, Aebersold R. Selected reaction based-proteomics: workflows, potential, pitfalls and future direction. Nat Methods 2012;9(6):555-66
  • Fortin T, Salvador A, Charrier JP, et al. Multiple reaction monitoring cubed for protein quantification at the low nanogram/milliliter level in nondepleted human serum. Anal Chem 2009;81(22):9343-52
  • Sajic T, Liu Y, Aebersold R. Using data-dependent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications. Proteomics Clin. Appl 2015;9(3-4):307-21
  • Gillet LC, Navarro P, Tate S, et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 2012
  • Schubert O, Gillet LC, Collins BC, et al. Building high-quality spectral libraries for targeted analysis of SWATH MS data. Nat Protoc 2015;10(3):426-41
  • Panchaud A, Scherl A, Shaffer SA, et al. Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal Chem 2009;81(15):6481-8
  • Nicolson J, Scherl A, Way L, et al. A systems wide mass spectrometric based linear motif screen to identify dominant in-vivo interacting proteins for the ubiquitin ligase MDM2. Cell Signal 2014;26(6):1243-57
  • Liu Y, Hüttenhain R, Surinova S, et al. Quantitative measurement of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics 2013;13:1247-56
  • Escher C, Reiter L, MacLean B, et al. Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics 2012;12(8):1111-21
  • Hennrich ML, Gavin AC. Quantitative mass spectrometry of posttranslational modifications: keys to confidence. Sci Signal 2015
  • Ramirez-Correa GA, Martinez-Fernando MI, Zhang P, Murphy AM. Targeted proteomics of myofilament phosphorylation and other protein posttranslational modifications. Proteomics Clin Appl 2014;8(7-8):543-53
  • Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 2008
  • MacLean B, Tomazela DM, Shulman N, et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiment. Bioinformatics 2010;26(7):966-8
  • Chang CY, Picotti P, Hüttenhain R, et al. Protein significance analysis in selected reaction monitoring (SRM) measurements. Mol Cell Proteomics 2012
  • Röst HL, Rosenberger G, Navarro P, et al. OpenSWATH enables automated, targeted analysis of data independent acquisition MS data. Nat Biotechnol 2014;23(3):219-223
  • Tsou CC, Avtonomov D, Larsen B, et al. DIA-umpire: comprehensive computational framework for data-dependent acquisition proteomics. Nat Methods 2015;12(3):258-64
  • Choi M, Chang CY, Clough T, et al. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics 2014;30(17):2524-6
  • Lin D, Alborn WE, Slebos RJC, et al. Comparison of protein immunoprecipitation-multiple reaction monitoring with ELISA for assay of biomarker candidates in plasma. J Proteome Res 2013;12:5996-6003
  • Makawita S, Diamandis EP. The bottleneck in the cancer biomarker pipeline and protein quantification through mass spectrometry-based approaches: current strategies for candidate verification. Clin. Chemistry 2010;56(2):212-22
  • Anderson NL, Anderson NG, Haines LR, et al. Mass spectrometric quantification of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J Proteome Res 2004;3(2):235-44
  • Whiteaker JR, Zhao L, Zhang HY, et al. Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers. Anal Biochem 2007;362:44-54
  • Shi T, Fillmore TL, Sun X, et al. Antibody-free, targeted mass spectrometric approach for quantification of proteins at low picograms per milliliter levels in human plasma/serum. Proc Natl Acad Sci USA 2012;109(38):15395-400
  • Shi T, Sun X, Gao Y, et al. Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion. J Proteome Res 2013;12:3353-61
  • Shi T, Gao Y, Quek SI, et al. A highly sensitive targeted mass spectrometric assay for quantification of ARG2 protein in human urine and serum. J Proteome Res 2014;13(9):875-82
  • He J, Sun X, Shi T, et al. Antibody-independent targeted quantification of TMPRSS2-ERG fusion protein products in prostate cancer. Mol Oncol 2014;8(7):1169-80
  • He J, Schepmoes AA, Shi T, et al. Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods. J Transl Med 2015
  • Maryas J, Faktor J, Dvorakova M, et al. Proteomics investigation of cancer metastasis: Functional and clinical consequences and methodological challenges. Proteomics 2014;0:1-15
  • Muraoka S, Kume H, Watanabe S, et al. Strategy for SRM-based verification of biomarker candidates discovered by iTRAQ method in limited breast cancer tissue samples. J Proteome Res 2012;11:4201-4210
  • Yang T, Chen F, Xu F, et al. A liquid chromatography-tandem mass spectrometry-based targeted proteomics assay for monitoring P-glycoprotein levels in human breast tissue. Clin Chim Acta 2014;436:283-9
  • Sjöström M, Ossola R, Breslin T, et al. A combined shotgun and targeted mass spectrometry strategy for breast cancer biomarker discovery. J Proteome Res 2015
  • van der Broek I, Sparidans RW, Schellens JHM, Beijnen JH. Quantitative assay for six potential breast cancer biomarker peptides in human serum by liquid chromatography coupled to tandem mass spectrometry. J Chromatography B 2010;878(5-6):590-602
  • Such-Sanmartín G, Bache N, Callesen AK, et al. Targeted mass spectrometry analysis of the proteins IGF1, IGF2, IBP2, IBP3 and A2GL by blood protein precipitation. J Proteomics 2015;113:29-37
  • Murphy JP, Pinto DM. Temporal proteomic analysis of IGF-1R signaling in MCF-7 breast adenocarcinoma cells. Proteomics 2010;10:1847-60
  • Neve RM, Chin K, Fridlyand J, et al. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 2010;10(6):515-27
  • Leong S, McKay MJ, Christopherson RI, Baxter RC. Biomarkers of breast cancer apoptosis induced by chemotherapy and TRAIL. J Proteome Res 2012;11:1240-50
  • Biarc J, Gonzalo P, Mikaelian I, et al. Combination of a discovery LC-MS/MS analysis and label-free quantification for the characterization of an epithelial-mesenchymal transition signature. J Proteomics 2014;110:183-94
  • Ishiba T, Nagahara M, Nakagawa T, et al. Periostin suppression induces decorin secretion leading to reduced breast cancer cell motility. Sci. Rep 2014
  • Held JM, Schilling B. D`Souza AK, et al. Label-free quantitation and mapping of the ErbB2 tumor receptor by multiple protease digestion with data-dependent (MS1) and data-independent (MS2) acquisition. Int J Proteomics 2013
  • Hengel SM, Murray E, Langdon S, et al. Data-independent proteomic screen identifies novel tamoxifen agonist that mediates drug resistence. J Proteome Res 2011;10(10):4567-78
  • Domanski D, Murphy LC, Borchers CH. Assay development for the determination of phosphorylation stoichiometry using multiple reaction monitoring methods with and without phosphate treatment: application to breast cancer signaling pathways. Anal Chem 2010;82:5610-20
  • Held JM, Britton DJ, Scott GK, et al. Ligand binding promotes CDK-dependent phosphorylation of ER-alpha on hinge serine 294 but inhibits phosphorylation of serine 305. Mol Cancer Res 2012;10(8):1120-32
  • Krautkramer KA, Reiter L, Denu JM, Dowell JA. Quantification of SAHA-dependent changes in histone modifications using data-independent acquisition mass spectrometry. J Proteome Res 2015;14(8):3252-62
  • Jemal A, Siegel R, Ward E, et al. Cancer statistics, 2008. CA Cancer J Clin 2008;58(2):71-96
  • Etzioni R, Urban N, Ramsey S, et al. The case for early detection. Nat Rev Cancer 2003;3(4):243-52
  • Yin HR, Zhang L, Xie LQ, et al. Hyperplex-MRM: a hybrid multiple reaction monitoring method using mTRAQ/iTRAQ labeling for multiplex absolute quantification of human colorectal cancer biomarker. J Proteome Res 2013;12:3912-19
  • Ang CS, Nice EC. Targeted in-gel MRM: a hypothesis driven approach for colorectal cancer biomarker discovery in human feces. J Proteome Res 2010;9:4346-55
  • Ang CS, Rothacker J, Patsiouras H, et al. Use of multiple reaction monitoring for multiplex analysis of colorectal cancer-associated proteins in human feces. Electrophoresis 2011;32:1926-38
  • Bröker ME, Lalmahomed ZS, Roest HP, et al. Collagen peptides in urine: a new promising biomarker for the detection of colorectal liver metastases. PLoS One 2013
  • Ahn YH, Lee JY, Lee JY, et al. Quantitative analysis of an aberrant glycoforms of TIMP1 from colon cancer serum by L-PHA-enrichment and SISCAPA with MRM mass spectrometry. J Proteome Res 2009;8:4216-24
  • Chen Y, Gruidl M, Remily-Wood E, et al. Quantification of β-catenin signaling components in colon cancer cell lines, tissue sections, and microdissected tumor cells using reaction monitoring mass spectrometry. J Proteome Res 2010;9(8):4215-27
  • Martínez-Aguilar J, Molloy MP. Label-free selected reaction monitoring enables multiplexed quantification of S100 protein isoforms in cancer cells. J Proteome Res 2013;12:3679-88
  • Ahn YH, Kim YS, Ji ES, et al. Comparative quantification of aberrant glycoforms by lectin-based glycoprotein enrichment coupled with multiple-reaction monitoring mass spectrometry. Anal Chem 2010;82:4441-7
  • Barry MJ. Screening for prostate cancer – The controversy that refuses to die. N. Eng. J. Med 2009;360(13):1351-4
  • Wolf AMD, Wender RC, Etzioni RB, et al. American cancer society guideline for the early detection of prostate cancer: update 2010. CA Cancer J Clin 2010;60:70-98
  • Li Y, Tian Y, Rezai T, et al. Simultaneous analysis of glycosylated and sialylated prostate-specific antigen revealing differential distribution of glycosylated prostate-specific antigen isoforms in prostate cancer tissues. Anal Chem 2011;83:240-5
  • Liu Y, Chen J, Sethi A, et al. Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Mol Cell Proteomics 2014;13(7):1753-68
  • Liu T, Hossain M, Schepmoes AA, et al. Analysis of serum total and free PSA using immunoaffinity coupled to SRM: Correlation with clinical immunoassay tests. J Proteomics 2012;75(15):4747-57
  • Chen YT, Tuan LP, Chen HW, et al. Quantitative analysis of prostate specific antigen isoforms using immunoprecipitation and stable isotope labeling mass spectrometry. Anal Chem 2015;87:545-53
  • Vérvári Á, Sjödin K, Rezeli M, et al. Identification of a novel proteoform of prostate specific antigen (SNL-L132I) in clinical samples by multiple reaction monitoring. Mol Cell Proteomics 2013;12(10):2761-73
  • Rafalko A, Dai S, Hancock WS, et al. Development of a Chip/Chip/SRM platform using digital chip isoelectric focusing and LC-Chip mass spectrometry for enrichment and quantification of low abundance protein biomarkers in human plasma. J Proteome Res 2012;11(2):808-17
  • Shi T, Fillmore TL, Gao Y, et al. Long-gradient separations coupled with selected reaction monitoring for highly sensitive, large scale targeted protein quantification in a single analysis. Anal Chem 2013;85:9196-203
  • Geisler C, Gaisa NT, Pfister D, et al. Identification and validation of potential new biomarkers for prostate cancer diagnosis and prognosis using 2D-DIGE and MS. Biomed. Res. Int 2015
  • Yocum AK, Khan AP, Zhao R, Chinnaiyan AM. Development of selected reaction monitoring-MS methodology to measure peptide biomarkers in prostate cancer. Proteomics 2010;10:3506-14
  • Jacobs I, Bast RCJr. The CA 125 tumour-associated antigen: a review of a literature. Hum Reprod 1989;4(1):1-12
  • Haslene-Hox H, Oveland E, Woie K, et al. Increased WD-repeat containing protein 1 in interstitial fluid from ovarian carcinomas shown by comparative proteomic analysis of malignant and healthy gynecological tissue. Biochim Biophys Acta 2013;1834(11):2347-59
  • Hüttenhain R, Soste M, Selevsek N, et al. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci Transl Med 2012
  • Tang HY, Beer LA, Tanyi JL, et al. Protein isoform-specific validation defines multiple chloride intracellular channel and tropomyosin isoforms as serological biomarkers for ovarian cancer. J Proteomics 2013;89:165-78
  • Drabovich AP, Diamandis EP, et al. Combinatorial peptide libraries facilitate development of multiple reaction monitoring assays for low-abundance proteins. J Proteome Res 2010;9:1236-45
  • Elschenbroisch S, Ignatchenko V, Clarke B, et al. In-depth proteomics of ovarian ascites: Combining shotgun proteomics and selected reaction monitoring mass spectrometry. J Proteome Res 2011;10:2286-99
  • Kimura A, Arakawa N, Hirano H. Mass spectrometric analysis of the phosphorylation levels of the SWI/SNF chromatin remodeling/tumor suppressor proteins ARID1A and Bgr1 in ovarian clear cell adenocarcinoma cell lines. J Proteome Res 2014;13:4959-69
  • Kim JW, Nie B, Sahm H, et al. Targeted quantitative analysis of superoxide dismutase 1 in cisplatin-sensitive and cisplatin-resistant human ovarian cancer cells. J Chromatogr B Analyt Technol Biomed Life Sci 2010;878(7-8):700-4
  • Haslehurst AM, Koti M, Dharsee M, et al. EMT transcription factors snail and slug directly contribute to cisplatin resistance in ovarian cancer. BMC Cancer 2012
  • Monge M, Doll A, Colas E, et al. Subtractive proteomic approach to the endometrial carcinoma invasion front. J Proteome Res 2009;8:4676-84
  • Yasa C, Takmaz O, Dural O, Akhan SE. The value of tumor markers in endometrial carcinoma: Review of literature. Journal of Cancer Therapy 2013;4:699-970
  • DeSouza LV, Grigull J, Ghanny S, et al. Endometrial carcinoma biomarker discovery and verification using differentially tagged clinical samples with multidimensional liquid chromatography and tandem mass spectrometry. Mol Cell Proteomics 2007;6(7):1170-82
  • DeSouza LV, Taylor AM, Li W, et al. Multiple reaction monitoring of mTRAQ labeled peptides enables absolute quantification of endogenous levels of potential cancer marker in cancerous and normal endometrial tissues. J Proteome Res 2008;7:3525-34
  • DeSouza LV, Romaschin AD, Colgan TJ, Siu KWM. Absolute quantification of potential cancer markers in clinical tissue homogenates using multiple reaction monitoring on a hybrid triple quadrupole/linear ion trap tandem mass spectrometer. Anal Chem 2009;81(9):3462-70
  • Turtoi A, Musmeci D, Wang Y, et al. Identification of novel accessible proteins bearing diagnostic and therapeutic potential in human pancreatic ductal adenocarcinoma. J Proteome Res 2011;10:4302-13
  • Kawahara T, Hotta N, Ozawa Y, et al. Quantitative proteomic profiling identifies DPYSL3 as pancreatic ductal adenocarcinoma-associated molecule that regulates cell adhesion and migration by stabilization of focal adhesion complex. PLoS One 2013
  • Luga C, Seicean A, Iancu C, et al. Proteomic identification of potential prognostic biomarkers in resectable pancreatic ductal adenocarcinoma. Proteomics 2014;14(7-8):945-55
  • Wehr AY, Hwang WT, Blair IA, Yu KH. Relative quantification of serum protein from pancreatic ductal adenocarcinoma patients by stable isotope dilution liquid chromatography-mass spectrometry. J Proteome Res 2012;11:1749-58
  • Yoneyama T, Ohtsuki S, Ono M, et al. Quantitative targeted absolute proteomics-based large-scale quantification of proline-hydroxylated α-fibrinogen in plasma for pancreatic cancer diagnosis. J Proteome Res 2013;12:753-62
  • Nie S, Yin H, Tan Z, et al. Quantitative analysis of single amino acid variant peptides associated with pancreatic cancer in serum by an isobaric labeling quantitative method. J Proteome Res 2014;13:6058-66
  • Halvey PJ, Ferrone CR, Liebler DC. GeLC-MRM quantification of mutant KRAS oncoprotein in complex biological samples. J Proteome Res 2012;11:3908-13
  • Wang B, Chen D, Chen Y, et al. Metabolomic profiles discriminate hepatocellular carcinoma from liver cirrhosis by ultraperformance liquid chromatography-mass spectrometry. J Proteome Res 2012;11(2):1217-27
  • Kim H, Kim K, Ju SY, et al. Development of biomarkers for screening hepatocellular carcinoma using global data mining and multiple reaction monitoring. PLoS One 2013
  • Kim H, Kim K, Jin J, et al. Measurement of glycosylated alpha-fetoprotein improves diagnostic power over native form in hepatocellular carcinoma. PLoS One 2014
  • Zhao Y, Jia W, Sun W, et al. Combination of improved 18O-incorporation and multiple reaction monitoring: A universal strategy for absolute quantitative verification of serum candidate biomarkers of liver cancer. J Proteome Res 2010;9:3319-27
  • Mustafa MG, Petersen JR, Ju H, et al. Biomarker discovery for early detection of hepatocellular carcinoma in hepatitis C-infected patients. Mol Cell Proteomics 2013;12(12):3640-52
  • Brouillette CG, Anantharamaiah GM, Engler JA, Borhani DW. Structural models of human apolipoprotein A-I: a critical analysis and review. Biochim Biophys Acta 2001;1531:4-46
  • Tsai TH, Song E, Zhu R, et al. LC-MS/MS based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma. Proteomics 2015
  • Sanda M, Pompach P, Brnakova Z, et al. Quantitative liquid chromatography-mass spectrometry-multiple reaction monitoring (LC-MS-MRM) analysis of site-specific glycoforms of haptoglobin in liver disease. Mol Cell Proteomics 2013;12(5):1294-305
  • Ahn YH, Shin PM, Ji ES, et al. A lectin-coupled, multiple reaction monitoring based quantitative analysis of human plasma glycoproteins by mass spectrometry. Anal Bioanal Chem 2012;402:2101-12
  • Ahn YH, Shin PM, Oh NR, et al. A lectin-coupled, targeted proteomic mass spectrometry (MRM MS) platform for identification of multiple liver cancer biomarkers in human plasma. J Proteomics 2012;75:5507-15
  • Ahn YH, Shin PM, Kim YS, et al. Quantitative analysis of aberrant protein glycosylation in liver cancer plasma by ALL-enrichment and MRM mass spectrometry. Analyst 2013;138(21):6454-62
  • Lee JY, Kim JY, Park GW, et al. Targeted mass spectrometric approach for biomarker discovery and validation with nonglycosylated tryptic peptides from N-linked glycoproteins in human plasma. Mol Cell Proteomics 2011
  • Lee JY, Kim JY, Cheon MH, et al. MRM validation of targeted nonglycosylated peptides from N-glycoprotein biomarkers using direct trypsin digestion of undepleted human plasma. J Proteomics 2014;98:206-17
  • Kim JY, Oh D, Kim SK, et al. Isotope-coded carbamidomethylation for quantification of N-glycoproteins with online microbore hollow fiber enzyme reactor-nanoflow liquid chromatography-tandem mass spectrometry. Anal Chem 2014;86:7650-7
  • Yang L, Zhang J, Zhang S, et al. Quantitative evaluation of aldo-keto reductase expression in hepatocellular carcinoma (HCC) cell lines. Genomics Proteomics Bioinformatics 2013;11(3):230-40
  • Bharti A, Ma PC, Salgia R. Biomarker discovery in lung cancer – promises and challenges of clinical proteomics. Mass Spectrom. Rev 2007;26(3):451-66
  • Nishimura T, Nomura M, Tojo H, et al. Proteomic analysis of laser-microdissected paraffin-embedded tissues: (2) Stage-related protein candidates upon non-metastatic lung adenocarcinoma. J Proteomics 2010;73(6):1100-10
  • Zhang H, Liu Q, Zimmerman LJ, et al. Methods for peptide and protein quantitation by liquid chromatography-multiple reaction monitoring mass spectrometry. Mol Cell Proteomics 2011
  • Hembrough T, Thyparambil S, Liao WL, et al. Selected reaction monitoring (SRM) analysis of epidermal growth factor receptor (EGFR) in formalin fixed tumor tissues. Clin Proteomics 2012
  • Torsetnes SB, Levernæs MS, Broughton MN, et al. Multiplexing determination of small cell lung cancer biomarkers and their isovariants in serum by immunocapture LC-MS/MS. Anal Chem 2014;86:6983-92
  • Toyama A, Nakagawa H, Matsuda K, et al. Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer. Proteome Sci 2011
  • Liu Y, Luo X, Hu H, et al. Interactive proteomics and tissue microarray profiling indicate the association between overexpressed serum proteins and non-small cell lung cancer. PLoS One 2012
  • Sung HJ, Jeon SA, Ahn JM, et al. Large-scale isotype-specific quantification of Serum amyloid A 1/2 by multiple reaction monitoring in crude sera. J Proteomics 2012;75(7):2170-80
  • Zeng X, Hood BL, Zhao T, et al. Lung cancer serum biomarker discovery using label free LC-MS/MS. J Thorac Oncol 2011;6(4):725-34
  • Park J, Yang JS, Jung G, et al. Subunit-specific mass spectrometry method identifies haptoglobin subunit alpha as a diagnostic marker in non-small cell lung cancer. J Proteomics 2013;94:302-10
  • Li XJ, Hayward C, Fong PY, et al. A blood-based classifier for the molecular characterization of pulmonary nodules. Sci Transl Med 2013
  • Kim YJ, Sertamo K, Pierrard MA, et al. Verification of the biomarker candidates for non-small-cell lung cancer using a targeted proteomics approach. J Proteome Res 2015;14:1412-19
  • Zhang F, Lin H, Gu A, et al. SWATH- and iTRAQ-based quantitative proteomic analyses reveal an overexpression and biological relevance of CD109 in advanced NSCLC. J Proteomics 2014;102:125-36
  • Zhang G, Fang B, Liu RZ, et al. Mass spectrometry mapping of epidermal growth factor receptor phosphorylation related to oncogenic mutations and tyrosine kinase inhibitor sensitivity. J Proteome Res 2011;10(1):305-19
  • Assiddiq BF, Tan KY, Toy W, et al. EGFR S1166 phosphorylation induced by a combination of EGF and gefinitib has a potentially negative impact on lung cancer cell growth. J Proteome Res 2012;11:4110-19
  • Kim JS, Lee Y, Lee MY, et al. Multiple reaction monitoring of multiple low abundance transcription factors in whole lung cancer cell lysates. J Proteome Res 2013;12:2582-96
  • Fang B, Hoffman MA, Mirza AS, et al. Evaluating kinase ATP uptake and tyrosine phosphorylation using multiplexed quantification of chemically labeled and post-translationally modified peptides. Methods 2015
  • Köhler CU, Martin L, Bonberg N, et al. Automated quantification of FISH signals in urinary cell enabled the assessment of chromosomal aberration patterns characteristic for bladder cancer. Biochem Biophys Res Commun 2014
  • Chen YT, Chen HW, Domanski D, et al. Multiplexed quantification of 63 proteins in human urine by multiple reaction monitoring-based mass spectrometry for discovery of potential bladder cancer biomarkers. J Proteomics 2012;72(12):3529-45
  • Canesin G, Gonzalez-Peramato P, Palou J, et al. Galectin-3 expression is associated with bladder cancer progression and clinical outcome. Tumour Biol 2010;31(4):277-85
  • Osman I, Bajorin DF, Sun TT, et al. Novel blood biomarkers of human urinary bladder cancer. Clin Cancer Res 2006;12:3374-80
  • Kageyama S, Isono T, Matsuda S, et al. Urinary calreticulin in the diagnosis of bladder urothelial carcinoma. Int J Urol 2009;16(5):481-6
  • Abbatiello SE, Schilling B, Mani DR, et al. Large-scale inter-laboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma. Mol Cell Proteomics 2015
  • Cottingham K. Clinical proteomics: are we there yet? Anal Chem 2003;75(21):472A-6A
  • Peterson AC, Russell JD, Bailey DJ, et al. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol Cell Proteomics 2012;11(11):1475-88
  • Gallien S, Duriez E, Crone C, et al. Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol Cell Proteomics 2012;11(12):1709-23
  • Lesur A, Domon B. Advances in high-resolution accurate mass spectrometry application to targeted proteomics. Proteomics 2015;15(5-6):880-90

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