Immunocapture strategies in translational proteomics

Expert Review of Proteomics

Volumn 13, Issue 1, 2016, Pages 83-98

  Fredolini, Claudia ^a   Byström, Sanna ^a   Pin, Elisa ^a   Edfors, Fredrik ^a   Tamburro, Davide ^b   Iglesias, Maria Jesus ^a   Häggmark, Anna ^a   Hong, Mun Gwan ^a   Uhlen, Mathias ^a   Nilsson, Peter ^a   Schwenk, Jochen M ^a  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Antibodies; Immunocapture; Mass spectrometry; Protein enrichment; Sandwich assays; SRM

Indexed keywords

ANTIBODY; PROTEOME; REAGENT; PROTEIN BINDING;

ANTIBODY AFFINITY; DATA ANALYSIS; ENZYME LINKED IMMUNOSORBENT ASSAY; EXPERIMENTAL DESIGN; HUMAN; IMMUNOASSAY; IMMUNOCAPTURE; IMMUNOHISTOCHEMISTRY; MASS SPECTROMETRY; NONHUMAN; PROTEIN MICROARRAY; PROTEOMICS; REVIEW; TRANSLATIONAL RESEARCH; VALIDATION PROCESS; ANIMAL; CHEMISTRY; IMMUNOPRECIPITATION; ISOLATION AND PURIFICATION; LIMIT OF DETECTION; PROCEDURES;

ANIMALS; ANTIBODIES; HUMANS; IMMUNOPRECIPITATION; LIMIT OF DETECTION; MASS SPECTROMETRY; PROTEIN BINDING; PROTEOME; PROTEOMICS; TRANSLATIONAL MEDICAL RESEARCH;

EID: 84946595130     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.2016.1111141     Document Type: Review

References (168)

1. Davies DR, Padlan EA, Sheriff S. Antibody-antigen complexes. Annu Rev Biochem. 1990;59:439-473.
2. Kozak KR, Wang J, Lye M, et al. Micro-volume wall-less immunoassays using patterned planar plates. Lab Chip. 2013;13(7):1342-1350.
3. Leslie D, Lipsky P, Notkins AL. Autoantibodies as predictors of disease. J Clin Invest. 2001;108(10):1417-1422.
4. Ayoglu B, Häggmark A, Neiman M, et al. Systematic antibody and antigenbased proteomic profiling with microarrays. Expert Rev Mol Diagn. 2011;11(2):219-234.
5. Caron M, Choquet-Kastylevsky G, Joubert-Caron R. Cancer immunomics using autoantibody signatures for biomarker discovery. Mol Cell Proteomics. 2007;6(7):1115-1122.
6. Tan HT, Low J, Lim SG, et al. Serum autoantibodies as biomarkers for early cancer detection. FEBS J. 2009;276(23):6880-6904.
7. Duraiyan J, Govindarajan R, Kaliyappan K, et al. Applications of immunohistochemistry. J Pharm Bioallied Sci. 2012;4(Suppl 2):S307-309.
8. Camp RL, Chung GG, Rimm DL. Automated subcellular localization and quantification of protein expression in tissue microarrays. Nat Med. 2002;8(11):1323-1327.
9. Anderson NL. The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clin Chem. 2010;56(2):177-185.
10. Brown M, Wittwer C. Flow cytometry: principles and clinical applications in hematology. Clin Chem. 2000;46((8 Pt 2):1221-1229.
11. Berrade L, Garcia AE, Camarero JA. Protein microarrays: novel developments and applications. Pharm Res. 2011;28(7):1480-1499.
12. Mueller C, Liotta LA, Espina V. Reverse phase protein microarrays advance to use in clinical trials. Mol Oncol. 2010;4(6):461-481.
13. Hagan S, Tomlinson A. Tear fluid biomarker profiling: a review of multiplex bead analysis. Ocul Surf. 2013;11(4):219-235.
14. Nelson BP. Multiplexed antibody arrays for the discovery and validation of glycosylated protein biomarkers. Bioanalysis. 2009;1(8):1431-1444.
15. Sarah S, Sandra M, Harald S. Up-todate applications of microarrays and their way to commercialization. Microarrays. 2015;4:196-213.
16. Kumar V, Barnidge DR, Chen LS, et al. Quantification of serum 1-84 parathyroid hormone in patients with hyperparathyroidism by immunocapture in situ digestion liquid chromatography-tandem mass spectrometry. Clin Chem. 2010;56(2):306-313.
17. Becker JO, Hoofnagle AN. Replacing immunoassays with tryptic digestionpeptide immunoaffinity enrichment and LC-MS/MS. Bioanalysis. 2012;4(3):281-290.
18. Berglund L, Björling E, Oksvold P, et al. A genecentric Human Protein Atlas for expression profiles based on antibodies. Mol Cell Proteomics. 2008;7(10):2019-2027.
19. Egelhofer TA, Minoda A, Klugman S, et al. An assessment of histone-modification antibody quality. Nat Struct Mol Biol. 2011;18(1):91-93.
20. About antibodypedia. Antibodypedia. 2015 [Internet; 2015 Oct. 16]. Available from: http://www.antibody pedia.com/.
21. Björling E, Uhlén M. Antibodypedia, a portal for sharing antibody and antigen validation data. Mol Cell Proteomics. 2008;7(10):2028-2037.
22. Resources antibodies-online GmbH [Internet]. 2015 [cited 2015 Oct. 16]. Available from: http://www.antibo dies-online.com/.
23. Linscott's Directory of immunological and biological reagents [Internet]. 2015 [cited 2015 Oct. 16]. Available from: http://www.linscottsdirectory. com/.
24. Use biocompare to explore, learn, decide. The buyer's guide for life scientists [Internet]. 2015 [cited 2015 Oct. 16]. Available from: http://www.biocompare.com/.
25. About the antibody registry [Internet]. Antibody registry [cited 2015 Oct. 16]. Available from: www.antibodyregistry.org.
26. National Cancer Institute [Internet]. Antibody portal [cited 2015 Oct. 16]. 2015. Available from: http://antibo dies.cancer.gov/.
27. National Cancer Institute [Internet]. 2015. Assay portal [cited 2015 Oct. 16]. Available from: https://assays.can cer.gov.
28. Pauly F, Smedby KE, Jerkeman M, et al. Identification of B-cell lymphoma subsets by plasma protein profiling using recombinant antibody microarrays. Leuk Res. 2014;38(6):682-690.
29. Sandström A, Andersson R, Segersvärd R, et al. Serum proteome profiling of pancreatitis using recombinant antibody microarrays reveals disease-associated biomarker signatures. Proteomics Clin Appl. 2012;6(9-10):486-496.
30. Carlsson A, Wuttge DM, Ingvarsson J, et al. Serum protein profiling of systemic lupus erythematosus and systemic sclerosis using recombinant antibody microarrays. Mol Cell Proteomics. 2011;10(5):M110.005033.
31. Whiteaker JR, Zhao L, Frisch C, et al. High-affinity recombinant antibody fragments (Fabs) can be applied in peptide enrichment immuno-MRM assays. J Proteome Res. 2014;13(4):2187-2196.
32. Li Y, He J, Xia C, et al. Ultrasensitive electrochemical immunosensor based on orderly oriented conductive wires for the detection of human monocyte chemotactic protein-1 in serum. Biosens Bioelectron. 2015;70:392-397.
33. Sattlecker M, Kiddle SJ, Newhouse S, et al. Alzheimer's disease biomarker discovery using SOMAscan multiplexed protein technology. Alzheimers Dement. 2014;10(6):724-734.
34. Hathout Y, Brody E, Clemens PR, et al. Large-scale serum protein biomarker discovery in Duchenne muscular dystrophy. Proc Natl Acad Sci USA. 2015;112(23):7153-7158.
35. Groll N, Emele F, Poetz O, et al. Towards multiplexed protein-protein interaction analysis using protein tagspecific nanobodies. J Proteomics. 2015;127:289-299.
36. Muyldermans S. Nanobodies: natural single-domain antibodies. Annu Rev Biochem. 2013;82:775-797.
37. Zahnd C, Wyler E, Schwenk JM, et al. A designed ankyrin repeat protein evolved to picomolar affinity to Her2. J Mol Biol. 2007;369(4):1015-1028.
38. Renberg B, Nordin J, Merca A, et al. Affibody molecules in protein capture microarrays: evaluation of multidomain ligands and different detection formats. J Proteome Res. 2007;6(1):171-179.
39. Wilhelm M, Schlegl J, Hahne H, et al. Mass-spectrometry-based draft of the human proteome. Nature. 2014;509(7502):582-587.
40. Farrah T, Deutsch EW, Hoopmann MR, et al. The state of the human proteome in 2012 as viewed through PeptideAtlas. J Proteome Res. 2013;12(1):162-171.
41. Bausch-Fluck D, Hofmann A, Bock T, et al. A mass spectrometric-derived cell surface protein atlas. PLoS One. 2015;10(3):e0121314.
42. Uhlén M, Fagerberg L, Hallström BM, et al. Proteomics. Tissue-based map of the human proteome. Science. 2015;347(6220):1260419.
43. Introduction [Internet]. The Human Protein Atlas [cited 2015 Oct. 16]. Available from: http://www.proteina tlas.org.
44. Häggmark A, Mikus M, Mohsenchian A, et al. Plasma profiling reveals three proteins associated to amyotrophic lateral sclerosis. Ann Clin Transl Neurol. 2014;1(8):544-553.
45. About Human Proteome Map [Internet]. Human Proteome Map. 2015 [cited 2015 Oct. 16]. Available from: http://www.humanproteome map.org.
46. Welcome to ProteomicsDB [Internet]! ProteomicsDB. 2015 [cited 2015 Oct. 16]. Available from: http://www.pro teomicsdb.org/.
47. Overview [Internet]. Human Proteome Project (HPP) [cited 2015 Oct. 16]. 2015. Available from: http://www.thehpp. org.
48. Vizcaíno JA, Deutsch EW, Wang R, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. 2014;32(3):223-226.
49. Reisinger F, Del-Toro N, Ternent T, et al. Introducing the PRIDE Archive RESTful web services. Nucleic Acids Res. 2015;43(W1):W599-604.
50. Chandra H, Reddy PJ, Srivastava S. Protein microarrays and novel detection platforms. Expert Rev Proteomics. 2011;8(1):61-79.
51. Schwenk JM, Gry M, Rimini R, et al. Antibody suspension bead arrays within serum proteomics. J Proteome Res. 2008;7(8):3168-3179.
52. Fredriksson S, Gullberg M, Jarvius J, et al. Protein detection using proximity-dependent DNA ligation assays. Nat Biotechnol. 2002;20(5):473-477.
53. Leng SX, McElhaney JE, Walston JD, et al. ELISA and multiplex technologies for cytokine measurement in inflammation and aging research. J Gerontol A Biol Sci Med Sci. 2008;63(8):879-884.
54. Gold L, Ayers D, Bertino J, et al. Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS One. 2010;5(12):e15004.
55. Holford TR, Davis F, Higson SP. Recent trends in antibody based sensors. Biosens Bioelectron. 2012;34(1):12-24.
56. Kadimisetty K, Malla S, Sardesai NP, et al. Automated multiplexed ECL immunoarrays for cancer biomarker proteins. Anal Chem. 2015;87(8):4472-4478.
57. Lin YH, Peng PY. Semiconductor sensor embedded microfluidic chip for protein biomarker detection using a bead-based immunoassay combined with deoxyribonucleic acid strand labeling. Anal Chim Acta. 2015;869:34-42.
58. Sharma A, Hong S, Singh R, et al. Single-walled carbon nanotube based transparent immunosensor for detection of a prostate cancer biomarker osteopontin. Anal Chim Acta. 2015;869:68-73.
59. Souada M, Piro B, Reisberg S, et al. Label-free electrochemical detection of prostate-specific antigen based on nucleic acid aptamer. Biosens Bioelectron. 2015;68:49-54.
60. Zhu Q, Chai Y, Zhuo Y, et al. Ultrasensitive simultaneous detection of four biomarkers based on hybridization chain reaction and biotin-streptavidin signal amplification strategy. Biosens Bioelectron. 2015;68:42-48.
61. Han KN, Li CA, Seong GH. Microfluidic chips for immunoassays. Annu Rev Anal Chem (Palo Alto Calif). 2013;6:119-141.
62. Sourial S, Marcusson-Ståhl M, Cederbrant K. Meso scale discovery and luminex comparative analysis of calbindin D28K. J Biomed Biotechnol. 2009;2009:187426.
63. Tighe P, Negm O, Todd I, et al. Utility, reliability and reproducibility of immunoassay multiplex kits. Methods. 2013;61(1):23-29.
64. Hsu HY, Wittemann S, Joos TO. Miniaturized parallelized sandwich immunoassays. Methods Mol Biol. 2008;428:247-261.
65. Rivnak AJ, Rissin DM, Kan CW, et al. A fully-automated, six-plex single molecule immunoassay for measuring cytokines in blood. J Immunol Methods. 2015;424:20-27.
66. Applications [Internet]. ProteinSimple [cited 2015 Oct. 16]. 2015. Available from: http://www.proteinsimple.com/ella.
67. Pavlou MP, Diamandis EP, Blasutig IM. The long journey of cancer biomarkers from the bench to the clinic. Clin Chem. 2013;59(1):147-157.
68. Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol. 2006;24(8):971-983.
69. Prassas I, Brinc D, Farkona S, et al. False biomarker discovery due to reactivity of a commercial ELISA for CUZD1 with cancer antigen CA125. Clin Chem. 2014;60(2):381-388.
70. Feng Z, Prentice R, Srivastava S. Research issues and strategies for genomic and proteomic biomarker discovery and validation: a statistical perspective. Pharmacogenomics. 2004;5(6):709-719.
71. Schottenfeld D. Epidemiology: an introduction. Am J Epidemiol. 2002;156(2):188-190.
72. Qundos U, Hong MG, Tybring G, et al. Profiling post-centrifugation delay of serum and plasma with antibody bead arrays. J Proteomics. 2013;95:46-54.
73. Ayache S, Panelli M, Marincola FM, et al. Effects of storage time and exogenous protease inhibitors on plasma protein levels. Am J Clin Pathol. 2006;126(2):174-184.
74. Qundos U, Drobin K, Mattsson C, et al. Affinity proteomics discovers decreased levels of AMFR in plasma from osteoporosis patients. Proteomics Clin Appl. 2015. DOI:10.1002/prca.201400167. [Epub ahead of print].
75. Bystrom S, Ayoglu B, Haggmark A, et al. Affinity proteomic profiling of plasma, cerebrospinal fluid, and brain tissue within multiple sclerosis. J Proteome Res. 2014;13(11):4607-4619.
76. Neiman M, Hedberg JJ, Dönnes PR, et al. Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment. J Proteome Res. 2011;10(11):4925-4934.
77. Bachmann J, Burté F, Pramana S, et al. Affinity proteomics reveals elevated muscle proteins in plasma of children with cerebral malaria. PLoS Pathog. 2014;10(4):e1004038.
78. Ayoglu B, Chaouch A, Lochmuller H, et al. Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies. EMBO Mol Med. 2014;6(7):918-936.
79. Hye A, Riddoch-Contreras J, Baird AL, et al. Plasma proteins predict conversion to dementia from prodromal disease. Alzheimers Dement. 2014;10(6):799-807.e792.
80. Qundos U, Johannesson H, Fredolini C, et al. Analysis of plasma from prostate cancer patients links decreased carnosine dipeptidase 1 levels to lymph node metastasis. Transl Proteom. 2014;2:14-24
81. Grote T, Siwak DR, Fritsche HA, et al. Validation of reverse phase protein array for practical screening of potential biomarkers in serum and plasma: accurate detection of CA19-9 levels in pancreatic cancer. Proteomics. 2008;8(15):3051-3060.
82. Janzi M, Odling J, Pan-Hammarstrom Q, et al. Serum microarrays for large scale screening of protein levels. Mol Cell Proteomics. 2005;4(12):1942-1947.
83. Janzi M, Sjoberg R, Wan J, et al. Screening for C3 deficiency in newborns using microarrays. PLoS One. 2009;4(4):e5321.
84. Longo C, Gambara G, Espina V, et al. A novel biomarker harvesting nanotechnology identifies Bak as a candidate melanoma biomarker in serum. Exp Dermatol. 2011;20(1):29-34.
85. Pla-Roca M, Leulmi RF, Tourekhanova S, et al. Antibody colocalization microarray: a scalable technology for multiplex protein analysis in complex samples. Mol Cell Proteomics. 2012;11(4):M111-011460.
86. Ardizzoni A, Capuccini B, Baschieri MC, et al. A protein microarray immunoassay for the serological evaluation of the antibody response in vertically transmitted infections. Eur J Clin Microbiol Infect Dis. 2009;28(9):1067-1075.
87. D'Angelo S, Mignone F, Deantonio C, et al. Profiling celiac disease antibody repertoire. Clin Immunology. 2013;148(1):99-109.
88. Ayoglu B, Haggmark A, Khademi M, et al. Autoantibody profiling in multiple sclerosis using arrays of human protein fragments. Mol Cell Proteomics. 2013;12(9):2657-2672.
89. Horn S, Lueking A, Murphy D, et al. Profiling humoral autoimmune repertoire of dilated cardiomyopathy (DCM) patients and development of a disease-associated protein chip. Proteomics. 2006;6(2):605-613.
90. Oláh Z, Kálmán J, Tóth ME, et al. Proteomic analysis of cerebrospinal fluid in Alzheimer's disease: wanted dead or alive. J Alzheimers Dis. 2015;44(4):1303-1312.
91. Häggmark A, Byström S, Ayoglu B, et al. Antibody-based profiling of cerebrospinal fluid within multiple sclerosis. Proteomics. 2013;13(15):2256-2267.
92. Fine DH, Markowitz K, Furgang D, et al. Macrophage inflammatory protein-1 alpha: a salivary biomarker of bone loss in a longitudinal cohort study of children at risk for aggressive periodontal disease? J Periodontol. 2009;80(1):106-113.
93. Liotta LA, Kohn EC. The microenvironment of the tumour-host interface. Nature. 2001;411(6835):375-379.
94. Charboneau L, Paweletz CP, Liotta LA. Laser capture microdissection. Curr Protoc Cell Biol. 2001; Chapter 2:Unit 2.5.
95. Baldelli E, Haura EB, Crinò L, et al. Impact of upfront cellular enrichment by laser capture microdissection on protein and phosphoprotein drug target signaling activation measurements in human lung cancer: implications for personalized medicine. Proteomics Clin Appl. 2015;9(9-10):928-937.
96. Wulfkuhle JD, Aquino JA, Calvert VS, et al. Signal pathway profiling of ovarian cancer from human tissue specimens using reverse-phase protein microarrays. Proteomics. 2003;3(11):2085-2090.
97. Kornblau SM, Qutub A, Yao H, et al. Proteomic profiling identifies distinct protein patterns in acute myelogenous leukemia CD34+CD38-stem-like cells. PLoS One. 2013;8(10):e78453.
98. Paweletz CP, Charboneau L, Bichsel VE, et al. Reverse phase protein microarrays which capture disease progression show activation of prosurvival pathways at the cancer invasion front. Oncogene. 2001;20(16):1981-1989.
99. Berg D, Wolff C, Langer R, et al. Discovery of new molecular subtypes in oesophageal adenocarcinoma. PLoS One. 2011;6(9):e23985.
100. Malinowsky K, Wolff C, Berg D, et al. uPA and PAI-1-related signaling pathways differ between primary breast cancers and lymph node metastases. Transl Oncol. 2012;5(2):98-104.
101. Sheehan KM, Calvert VS, Kay EW, et al. Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol Cell Proteomics. 2005;4(4):346-355.
102. Pierobon M, Calvert V, Belluco C, et al. Multiplexed cell signaling analysis of metastatic and nonmetastatic colorectal cancer reveals COX2-EGFR signaling activation as a potential prognostic pathway biomarker. Clin Colorectal Cancer. 2009;8(2):110-117.
103. Chiechi A, Novello C, Magagnoli G, et al. Elevated TNFR1 and serotonin in bone metastasis are correlated with poor survival following bone metastasis diagnosis for both carcinoma and sarcoma primary tumors. Clin Cancer Res. 2013;19(9):2473-2485.
104. Petricoin EF, Bichsel VE, Calvert VS, et al. Mapping molecular networks using proteomics: a vision for patienttailored combination therapy. J Clin Oncol. 2005;23(15):3614-3621.
105. Quintás-Cardama A, Zhang N, Qiu YH, et al. Loss of TRIM62 expression is an independent adverse prognostic factor in acute myeloid leukemia. Clin Lymphoma Myeloma Leuk. 2015;15(2):115-127.e115.
106. Zeng Z, Shi YX, Tsao T, et al. Targeting of mTORC1/2 by the mTOR kinase inhibitor PP242 induces apoptosis in AML cells under conditions mimicking the bone marrow microenvironment. Blood. 2012;120(13):2679-2689.
107. Charboneau L, Tory H, Scott H, et al. Utility of reverse phase protein arrays: applications to signalling pathways and human body arrays. Brief Funct Genomic Proteomic. 2002;1(3):305-315.
108. Cremona M, Espina V, Caccia D, et al. Stratification of clear cell renal cell carcinoma by signaling pathway analysis. Expert Rev Proteomics. 2014;11(2):237-249.
109. Sereni MI, Baldelli E, Gambara G, et al. Functional characterization of epithelial ovarian cancer histotypes by drug target based protein signaling activation mapping: implications for personalized cancer therapy. Proteomics. 2015;15(2-3):365-373.
110. Paweletz CP, Charboneau L, Liotta LA. Overview of metastasis assays. Curr Protoc Cell Biol. 2001 Chapter 19: Unit 19.11.
111. Konopleva MY, Walter RB, Faderl SH, et al. Preclinical and early clinical evaluation of the oral AKT inhibitor, MK-2206, for the treatment of acute myelogenous leukemia. Clin Cancer Res. 2014;20(8):2226-2235.
112. Pilot study using molecular profiling to find potential targets and select treatments for patients with metastatic breast cancer [Internet]. [cited 2015 Oct. 16]. ClinicalTrials.gov. Available from: https://www.clinicaltrials.gov.
113. Alix-Panabières C, Pantel K. Challenges in circulating tumour cell research. Nat Rev Cancer. 2014;14(9):623-631.
114. Miller MC, Doyle GV, Terstappen LW. Significance of circulating tumor cells detected by the CellSearch system in patients with metastatic breast colorectal and prostate cancer. J Oncol. 2010;2010:617421.
115. Hong B, Zu Y. Detecting circulating tumor cells: current challenges and new trends. Theranostics. 2013;3(6):377-394.
116. Kirby BJ, Jodari M, Loftus MS, et al. Functional characterization of circulating tumor cells with a prostate-cancer-specific microfluidic device. PLoS One. 2012;7(4):e35976.
117. Thege FI, Lannin TB, Saha TN, et al. Microfluidic immunocapture of circulating pancreatic cells using parallel EpCAM and MUC1 capture: characterization, optimization and downstream analysis. Lab Chip. 2014;14(10):1775-1784.
118. Baker M. Reproducibility crisis: blame it on the antibodies. Nature. 2015;521(7552):274-276.
119. Di Palma S, Zoumaro-Djayoon A, Peng M, et al. Finding the same needles in the haystack? A comparison of phosphotyrosine peptides enriched by immuno-affinity precipitation and metal-based affinity chromatography. J Proteomics. 2013;91:331-337.
120. Whiteaker JR, Zhao L, Yan P, et al. Peptide immunoaffinity enrichment and targeted mass spectrometry enables multiplex, quantitative pharmacodynamic studies of phospho-signaling. Mol Cell Proteomics. 2015;14(8):2261-2273.
121. Thaysen-Andersen M, Thøgersen IB, Lademann U, et al. Investigating the biomarker potential of glycoproteins using comparative glycoprofiling - application to tissue inhibitor of metalloproteinases-1. Biochim Biophys Acta. 2008;1784(3):455-463.
122. Wu Z, Na CH, Tan H, et al. Global ubiquitination analysis by SILAC in mammalian cells. Methods Mol Biol. 2014;1188:149-160.
123. Meistermann H, Gao J, Golling S, et al. A novel immuno-competitive capture mass spectrometry strategy for protein-protein interaction profiling reveals that LATS kinases regulate HCV replication through NS5A phosphorylation. Mol Cell Proteomics. 2014;13(11):3040-3048.
124. Mellacheruvu D, Wright Z, Couzens AL, et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods. 2013;10(8):730-736.
125. Keilhauer EC, Hein MY, Mann M. Accurate protein complex retrieval by affinity enrichment mass spectrometry (AE-MS) rather than affinity purification mass spectrometry (AP-MS). Mol Cell Proteomics. 2015;14(1):120-135.
126. Malovannaya A, Lanz RB, Jung SY, et al. Analysis of the human endogenous coregulator complexome. Cell. 2011;145(5):787-799.
127. Korwar AM, Vannuruswamy G, Jagadeeshaprasad MG, et al. Development of diagnostic fragment ion library for glycated peptides of human serum albumin: targeted quantification in prediabetic, diabetic and microalbuminuria plasma by PRM, SWATH and MSE. Mol Cell Proteomics. 2015;14(8):2150-2159.
128. Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods. 2012;9(6):555-566.
129. Method of the Year 2012. Nat Meth. 2013;10(1):1-1.
130. Addona TA, Abbatiello SE, Schilling B, et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol. 2009;27(7):633-641.
131. Abbatiello SE, Schilling B, Mani DR, et al. Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma. Mol Cell Proteomics. 2015;14(9):2357-2374.
132. Lange V, Picotti P, Domon B, et al. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol. 2008;4:222.
133. Mani DR, Abbatiello SE, Carr SA. Statistical characterization of multiplereaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics. BMC Bioinformatics. 2012;13(Suppl 16):S9.
134. Kito K, Ito T. Mass spectrometrybased approaches toward absolute quantitative proteomics. Curr Genomics. 2008;9(4):263-274.
135. Anderson NL, Anderson NG, Haines LR, et al. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J Proteome Res. 2004;3(2):235-244.
136. Kuhn E, Whiteaker JR, Mani DR, et al. Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol Cell Proteomics. 2012;11(6):M111.013854.
137. Whiteaker JR, Zhao L, Anderson L, et al. An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers. Mol Cell Proteomics. 2010;9(1):184-196.
138. Whiteaker JR, Zhao L, Abbatiello SE, et al. Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry. Mol Cell Proteomics. 2011;10(4):M110.005645.
139. Kuhn E, Addona T, Keshishian H, et al. Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin Chem. 2009;55(6):1108-1117.
140. Hoofnagle AN, Becker JO, Wener MH, et al. Quantification of thyroglobulin, a low-abundance serum protein, by immunoaffinity peptide enrichment and tandem mass spectrometry. Clin Chem. 2008;54(11):1796-1804.
141. Ahn YH, Kim KH, Shin PM, et al. Identification of low-abundance cancer biomarker candidate TIMP1 from serum with lectin fractionation and peptide affinity enrichment by ultrahigh-resolution mass spectrometry. Anal Chem. 2012;84(3):1425-1431.
142. Anderson NL, Razavi M, Pearson TW, et al. Precision of heavy-light peptide ratios measured by MALDI-TOF mass spectrometry. J Proteome Res. 2012;11(3):1868-1878.
143. Razavi M, Johnson LD, Lum JJ, et al. Quantification of a proteotypic peptide from protein C inhibitor by liquid chromatography-free SISCAPA-MALDI mass spectrometry: application to identification of recurrence of prostate cancer. Clin Chem. 2013;59(10):1514-1522.
144. Andersson T, Johansson M, Bolmsjö G, et al. Automating MALDI sample plate loading. J Proteome Res. 2007;6(2):894-896.
145. Poetz O, Hoeppe S, Templin MF, et al. Proteome wide screening using peptide affinity capture. Proteomics. 2009;9(6):1518-1523.
146. Furlong MT, Ouyang Z, Wu S, et al. A universal surrogate peptide to enable LC-MS/MS bioanalysis of a diversity of human monoclonal antibody and human Fc-fusion protein drug candidates in pre-clinical animal studies. Biomed Chromatogr. 2012;26(8):1024-1032.
147. Edfors F, Boström T, Forsström B, et al. Immunoproteomics using polyclonal antibodies and stable isotopelabeled affinity-purified recombinant proteins. Mol Cell Proteomics. 2014;13(6):1611-1624.
148. Boström T, Johansson HJ, Lehtiö J, et al. Investigating the applicability of antibodies generated within the human protein atlas as capture agents in immunoenrichment coupled to mass spectrometry. J Proteome Res. 2014;13(10):4424-4435.
149. Lund H, Snilsberg AH, Paus E, et al. Sports drug testing using immuno-MS: clinical study comprising administration of human chorionic gonadotropin to males. Anal Bioanal Chem. 2013;405(5):1569-1576.
150. Lund H, Løvsletten K, Paus E, et al. Immuno-MS based targeted proteomics: highly specific, sensitive, and reproducible human chorionic gonadotropin determination for clinical diagnostics and doping analysis. Anal Chem. 2012;84(18):7926-7932.
151. Torsetnes SB, Nordlund MS, Paus E, et al. Digging deeper into the field of the small cell lung cancer tumor marker ProGRP: a method for differentiation of its isoforms. J Proteome Res. 2013;12(1):412-420.
152. Torsetnes SB, Broughton MN, Paus E, et al. Determining ProGRP and isoforms in lung and thyroid cancer patient samples: comparing an MS method with a routine clinical immunoassay. Anal Bioanal Chem. 2014;406(11):2733-2738.
153. Torsetnes SB, Løvbak SG, Claus C, et al. Immunocapture and LC-MS/MS for selective quantification and differentiation of the isozymes of the biomarker neuron-specific enolase in serum. J Chromatogr B Analyt Technol Biomed Life Sci. 2013;929:125-132.
154. Rosenberger G, Koh CC, Guo T, et al. A repository of assays to quantify 10, 000 human proteins by SWATH-MS. Sci Data. 2014;1:140031.
155. Liu Y, Buil A, Collins BC, et al. Quantitative variability of 342 plasma proteins in a human twin population. Mol Syst Biol. 2015;11(1):786.
156. 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):1753-1768.
157. Neiman M, Fredolini C, Johansson H, et al. Selectivity analysis of single binder assays used in plasma protein profiling. Proteomics. 2013;13(23-24):3406-3410.
158. Marcon E, Jain H, Bhattacharya A, et al. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat Methods. 2015;12(8):725-731.
159. Korbakis D, Brinc D, Schiza C, et al. Immunocapture-selected reaction monitoring screening facilitates the development of ELISA for the measurement of native TEX101 in biological fluids. Mol Cell Proteomics. 2015;14(6):1517-1526.
160. Korbakis D, Prassas I, Brinc D, et al. Delineating monoclonal antibody specificity by mass spectrometry. J Proteomics. 2015;114:115-124.
161. Bendall SC, Simonds EF, Qiu P, et al. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science. 2011;332(6030):687-696.
162. Nair N, Mei HE, Chen SY, et al. Mass cytometry as a platform for the discovery of cellular biomarkers to guide effective rheumatic disease therapy. Arthritis Res Ther. 2015;17(1):127.
163. Gaudillière B, Ganio EA, Tingle M, et al. Implementing mass cytometry at the bedside to study the immunological basis of human diseases: distinctive immune features in patients with a history of term or preterm birth. Cytometry A. 2015;87(9):817-829.
164. Sen N, Mukherjee G, Arvin AM. Single cell mass cytometry reveals remodeling of human T cell phenotypes by varicella zoster virus. Methods. 2015; DOI:10.1016/j. ymeth.2015.07.008. [Epub ahead of print].
165. Hansmann L, Blum L, Ju CH, et al. Mass cytometry analysis shows that a novel memory phenotype B cell is expanded in multiple myeloma. Cancer Immunol Res. 2015;3(6):650-660.
166. Levenson RM, Borowsky AD, Angelo M. Immunohistochemistry and mass spectrometry for highly multiplexed cellular molecular imaging. Lab Invest. 2015;95(4):397-405.
167. Angelo M, Bendall SC, Finck R, et al. Multiplexed ion beam imaging of human breast tumors. Nat Med. 2014;20(4):436-442.
168. Mischak H, Critselis E, Hanash S, et al. Epidemiologic design and analysis for proteomic studies: a primer on-omic technologies. Am J Epidemiol. 2015;181(9):635-647.