-
1
-
-
0035100888
-
Biomarkers Definitions Working Group, Biomarkers and surrogate endpoints: preferred definitions and conceptual framework
-
Biomarkers Definitions Working Group, Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clin. Pharmacol. Ther. 2001, 69, 89-95.
-
(2001)
Clin. Pharmacol. Ther.
, vol.69
, pp. 89-95
-
-
-
2
-
-
67650432879
-
The fundamental flaws of immunoassays and potential solutions using tandem mass spectrometry
-
Hoofnagle, A. N., Wener, M. H., The fundamental flaws of immunoassays and potential solutions using tandem mass spectrometry. J. Immunol. Methods 2009, 347, 3-11.
-
(2009)
J. Immunol. Methods
, vol.347
, pp. 3-11
-
-
Hoofnagle, A.N.1
Wener, M.H.2
-
3
-
-
33845787470
-
Heat-induced antigen retrieval: mechanisms and application to histochemistry
-
Yamashita, S., Heat-induced antigen retrieval: mechanisms and application to histochemistry. Prog. Histochem. Cytochem. 2007, 41, 141-200.
-
(2007)
Prog. Histochem. Cytochem.
, vol.41
, pp. 141-200
-
-
Yamashita, S.1
-
4
-
-
1542469713
-
Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay
-
Cronin, M., Pho, M., Dutta, D., Stephans, J. C. et al., Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am. J. Pathol. 2004, 164, 35-42.
-
(2004)
Am. J. Pathol.
, vol.164
, pp. 35-42
-
-
Cronin, M.1
Pho, M.2
Dutta, D.3
Stephans, J.C.4
-
5
-
-
0035134463
-
Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue
-
Specht, K., Richter, T., Muller, U., Walch, A. et al., Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. Am. J. Pathol. 2001, 158, 419-429.
-
(2001)
Am. J. Pathol.
, vol.158
, pp. 419-429
-
-
Specht, K.1
Richter, T.2
Muller, U.3
Walch, A.4
-
6
-
-
0034189805
-
Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5' nuclease quantitative reverse transcription-polymerase chain reaction
-
Godfrey, T. E., Kim, S. H., Chavira, M., Ruff, D. W. et al., Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5' nuclease quantitative reverse transcription-polymerase chain reaction. J. Mol. Diagn. 2000, 2, 84-91.
-
(2000)
J. Mol. Diagn.
, vol.2
, pp. 84-91
-
-
Godfrey, T.E.1
Kim, S.H.2
Chavira, M.3
Ruff, D.W.4
-
7
-
-
84858994198
-
Setting proteins free: progresses and achievements in proteomics of formalin-fixed, paraffin-embedded tissues
-
Tanca, A., Pagnozzi, D., Addis, M. F., Setting proteins free: progresses and achievements in proteomics of formalin-fixed, paraffin-embedded tissues. Proteomics Clin. Appl. 2012, 6, 7-21.
-
(2012)
Proteomics Clin. Appl.
, vol.6
, pp. 7-21
-
-
Tanca, A.1
Pagnozzi, D.2
Addis, M.F.3
-
8
-
-
84876136632
-
Proteomic studies of formalin-fixed paraffin-embedded tissues
-
Giusti, L., Lucacchini, A., Proteomic studies of formalin-fixed paraffin-embedded tissues. Expert Rev. Proteomics 2013, 10, 165-177.
-
(2013)
Expert Rev. Proteomics
, vol.10
, pp. 165-177
-
-
Giusti, L.1
Lucacchini, A.2
-
9
-
-
84894101339
-
MALDI imaging mass spectrometry and analysis of endogenous peptides
-
Chatterji, B., Pich, A., MALDI imaging mass spectrometry and analysis of endogenous peptides. Expert Rev. Proteomics 2013, 10, 381-388.
-
(2013)
Expert Rev. Proteomics
, vol.10
, pp. 381-388
-
-
Chatterji, B.1
Pich, A.2
-
10
-
-
71849100285
-
Imaging mass spectrometry of gastric carcinoma in formalin-fixed paraffin-embedded tissue microarray
-
Morita, Y., Ikegami, K., Goto-Inoue, N., Hayasaka, T. et al., Imaging mass spectrometry of gastric carcinoma in formalin-fixed paraffin-embedded tissue microarray. Cancer Sci. 2010, 101, 267-273.
-
(2010)
Cancer Sci.
, vol.101
, pp. 267-273
-
-
Morita, Y.1
Ikegami, K.2
Goto-Inoue, N.3
Hayasaka, T.4
-
11
-
-
84873712068
-
Imaging the clear cell renal cell carcinoma proteome
-
Morgan, T. M., Seeley, E. H., Fadare, O., Caprioli, R. M., Clark, P. E., Imaging the clear cell renal cell carcinoma proteome. J. Urol. 2013, 189, 1097-1103.
-
(2013)
J. Urol.
, vol.189
, pp. 1097-1103
-
-
Morgan, T.M.1
Seeley, E.H.2
Fadare, O.3
Caprioli, R.M.4
Clark, P.E.5
-
12
-
-
0022112084
-
Formaldehyde fixation
-
Fox, C. H., Johnson, F. B., Whiting, J., Roller, P. P., Formaldehyde fixation. J. Histochem. Cytochem. 1985, 33, 845-853.
-
(1985)
J. Histochem. Cytochem.
, vol.33
, pp. 845-853
-
-
Fox, C.H.1
Johnson, F.B.2
Whiting, J.3
Roller, P.P.4
-
13
-
-
34447566048
-
'Tissue surrogates' as a model for archival formalin-fixed paraffin-embedded tissues
-
Fowler, C. B., Cunningham, R. E., O'Leary, T. J., Mason, J. T., 'Tissue surrogates' as a model for archival formalin-fixed paraffin-embedded tissues. Lab. Invest. 2007, 87, 836-846.
-
(2007)
Lab. Invest.
, vol.87
, pp. 836-846
-
-
Fowler, C.B.1
Cunningham, R.E.2
O'Leary, T.J.3
Mason, J.T.4
-
14
-
-
0036321629
-
DNA extraction from archival formalin-fixed, paraffin-embedded tissue sections based on the antigen retrieval principle: heating under the influence of pH
-
Shi, S. R., Cote, R. J., Wu, L., Liu, C. et al., DNA extraction from archival formalin-fixed, paraffin-embedded tissue sections based on the antigen retrieval principle: heating under the influence of pH. J. Histochem. Cytochem. 2002, 50, 1005-1011.
-
(2002)
J. Histochem. Cytochem.
, vol.50
, pp. 1005-1011
-
-
Shi, S.R.1
Cote, R.J.2
Wu, L.3
Liu, C.4
-
15
-
-
0030443649
-
Extraction and protein sequencing of immunoglobulin light chain from formalin-fixed cerebrovascular amyloid deposits
-
Layfield, R., Bailey, K., Lowe, J., Allibone, R. et al., Extraction and protein sequencing of immunoglobulin light chain from formalin-fixed cerebrovascular amyloid deposits. J. Pathol. 1996, 180, 455-459.
-
(1996)
J. Pathol.
, vol.180
, pp. 455-459
-
-
Layfield, R.1
Bailey, K.2
Lowe, J.3
Allibone, R.4
-
16
-
-
14444276493
-
Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin-embedded tissue sections
-
Ikeda, K., Monden, T., Kanoh, T., Tsujie, M. et al., Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin-embedded tissue sections. J. Histochem. Cytochem. 1998, 46, 397-403.
-
(1998)
J. Histochem. Cytochem.
, vol.46
, pp. 397-403
-
-
Ikeda, K.1
Monden, T.2
Kanoh, T.3
Tsujie, M.4
-
17
-
-
10644254712
-
Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry
-
Vasilescu, J., Guo, X., Kast, J., Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry. Proteomics 2004, 4, 3845-3854.
-
(2004)
Proteomics
, vol.4
, pp. 3845-3854
-
-
Vasilescu, J.1
Guo, X.2
Kast, J.3
-
18
-
-
28644451439
-
Proteomic analysis of formalin-fixed prostate cancer tissue
-
Hood, B. L., Darfler, M. M., Guiel, T. G., Furusato, B. et al., Proteomic analysis of formalin-fixed prostate cancer tissue. Mol. Cell. Proteomics 2005, 4, 1741-1753.
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 1741-1753
-
-
Hood, B.L.1
Darfler, M.M.2
Guiel, T.G.3
Furusato, B.4
-
19
-
-
29144518633
-
Efficient method for the proteomic analysis of fixed and embedded tissues
-
Palmer-Toy, D. E., Krastins, B., Sarracino, D. A., Nadol, J. B., Jr., Merchant, S. N., Efficient method for the proteomic analysis of fixed and embedded tissues. J. Proteome Res. 2005, 4, 2404-2411.
-
(2005)
J. Proteome Res.
, vol.4
, pp. 2404-2411
-
-
Palmer-Toy, D.E.1
Krastins, B.2
Sarracino, D.A.3
Nadol Jr, J.B.4
Merchant, S.N.5
-
20
-
-
27144511949
-
Liquid Tissue: proteomic profiling of formalin-fixed tissues
-
Prieto, D. A., Hood, B. L., Darfler, M. M., Guiel, T. G. et al., Liquid Tissue: proteomic profiling of formalin-fixed tissues. Biotechniques 2005, 38, 32-35.
-
(2005)
Biotechniques
, vol.38
, pp. 32-35
-
-
Prieto, D.A.1
Hood, B.L.2
Darfler, M.M.3
Guiel, T.G.4
-
21
-
-
27144544744
-
Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS
-
Crockett, D. K., Lin, Z., Vaughn, C. P., Lim, M. S., Elenitoba-Johnson, K. S., Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS. Lab. Invest. 2005, 85, 1405-1415.
-
(2005)
Lab. Invest.
, vol.85
, pp. 1405-1415
-
-
Crockett, D.K.1
Lin, Z.2
Vaughn, C.P.3
Lim, M.S.4
Elenitoba-Johnson, K.S.5
-
22
-
-
78650814932
-
Antigen retrieval immunohistochemistry: review and future prospects in research and diagnosis over two decades
-
Shi, S. R., Shi, Y., Taylor, C. R., Antigen retrieval immunohistochemistry: review and future prospects in research and diagnosis over two decades. J. Histochem. Cytochem. 2011, 59, 13-32.
-
(2011)
J. Histochem. Cytochem.
, vol.59
, pp. 13-32
-
-
Shi, S.R.1
Shi, Y.2
Taylor, C.R.3
-
23
-
-
71049161234
-
Molecular profiling of signalling pathways in formalin-fixed and paraffin-embedded cancer tissues
-
Berg, D., Hipp, S., Malinowsky, K., Bollner, C., Becker, K. F., Molecular profiling of signalling pathways in formalin-fixed and paraffin-embedded cancer tissues. Eur. J. Cancer 2010, 46, 47-55.
-
(2010)
Eur. J. Cancer
, vol.46
, pp. 47-55
-
-
Berg, D.1
Hipp, S.2
Malinowsky, K.3
Bollner, C.4
Becker, K.F.5
-
24
-
-
84880803012
-
Analysis of the formalin-fixed paraffin-embedded tissue proteome: pitfalls, challenges, and future prospectives
-
Maes, E., Broeckx, V., Mertens, I., Sagaert, X. et al., Analysis of the formalin-fixed paraffin-embedded tissue proteome: pitfalls, challenges, and future prospectives. Amino Acids 2013, 45, 205-218.
-
(2013)
Amino Acids
, vol.45
, pp. 205-218
-
-
Maes, E.1
Broeckx, V.2
Mertens, I.3
Sagaert, X.4
-
25
-
-
84859965675
-
Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues
-
Magdeldin, S., Yamamoto, T., Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues. Proteomics 2012, 12, 1045-1058.
-
(2012)
Proteomics
, vol.12
, pp. 1045-1058
-
-
Magdeldin, S.1
Yamamoto, T.2
-
26
-
-
84876313066
-
Complete solubilization of formalin-fixed, paraffin-embedded tissue may improve proteomic studies
-
Shi, S. R., Taylor, C. R., Fowler, C. B., Mason, J. T., Complete solubilization of formalin-fixed, paraffin-embedded tissue may improve proteomic studies. Proteomics Clin. Appl. 2013, 7, 264-272.
-
(2013)
Proteomics Clin. Appl.
, vol.7
, pp. 264-272
-
-
Shi, S.R.1
Taylor, C.R.2
Fowler, C.B.3
Mason, J.T.4
-
27
-
-
84876316245
-
Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue
-
Thompson, S. M., Craven, R. A., Nirmalan, N. J., Harnden, P. et al., Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue. Proteomics Clin. Appl. 2013, 7, 241-251.
-
(2013)
Proteomics Clin. Appl.
, vol.7
, pp. 241-251
-
-
Thompson, S.M.1
Craven, R.A.2
Nirmalan, N.J.3
Harnden, P.4
-
28
-
-
71049141298
-
Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis
-
Sprung, R. W., Jr., Brock, J. W., Tanksley, J. P., Li, M. et al., Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol. Cell. Proteomics 2009, 8, 1988-1998.
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 1988-1998
-
-
Sprung Jr., R.W.1
Brock, J.W.2
Tanksley, J.P.3
Li, M.4
-
29
-
-
79961145364
-
Standardized assessment of the HER2 status in breast cancer by immunohistochemistry
-
Hicks, D. G., Schiffhauer, L., Standardized assessment of the HER2 status in breast cancer by immunohistochemistry. LabMedicine 2011, 42, 459-467.
-
(2011)
LabMedicine
, vol.42
, pp. 459-467
-
-
Hicks, D.G.1
Schiffhauer, L.2
-
30
-
-
83755205824
-
The challenge and importance of standardizing pre-analytical variables in surgical pathology specimens for clinical care and translational research
-
Hicks, D. G., Boyce, B. F., The challenge and importance of standardizing pre-analytical variables in surgical pathology specimens for clinical care and translational research. Biotech. Histochem. 2012, 87, 14-17.
-
(2012)
Biotech. Histochem.
, vol.87
, pp. 14-17
-
-
Hicks, D.G.1
Boyce, B.F.2
-
31
-
-
84876299279
-
Proteomic analysis of formalin-fixed paraffin-embedded renal tissue samples by label-free MS: assessment of overall technical variability and the impact of block age
-
Craven, R. A., Cairns, D. A., Zougman, A., Harnden, P. et al., Proteomic analysis of formalin-fixed paraffin-embedded renal tissue samples by label-free MS: assessment of overall technical variability and the impact of block age. Proteomics Clin. Appl. 2013, 7, 273-282.
-
(2013)
Proteomics Clin. Appl.
, vol.7
, pp. 273-282
-
-
Craven, R.A.1
Cairns, D.A.2
Zougman, A.3
Harnden, P.4
-
32
-
-
79959946214
-
Multiple reaction monitoring assay for pre-eclampsia related calcyclin peptides in formalin fixed paraffin embedded placenta
-
Guzel, C., Ursem, N. T., Dekker, L. J., Derkx, P. et al., Multiple reaction monitoring assay for pre-eclampsia related calcyclin peptides in formalin fixed paraffin embedded placenta. J. Proteome Res. 2011, 10, 3274-3282.
-
(2011)
J. Proteome Res.
, vol.10
, pp. 3274-3282
-
-
Guzel, C.1
Ursem, N.T.2
Dekker, L.J.3
Derkx, P.4
-
33
-
-
34250840587
-
Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens
-
Guo, T., Wang, W., Rudnick, P. A., Song, T. et al., Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. J. Histochem. Cytochem. 2007, 55, 763-772.
-
(2007)
J. Histochem. Cytochem.
, vol.55
, pp. 763-772
-
-
Guo, T.1
Wang, W.2
Rudnick, P.A.3
Song, T.4
-
34
-
-
84870393717
-
Comparability of differential proteomics data generated from paired archival fresh-frozen and formalin-fixed samples by GeLC-MS/MS and spectral counting
-
Tanca, A., Pagnozzi, D., Burrai, G. P., Polinas, M. et al., Comparability of differential proteomics data generated from paired archival fresh-frozen and formalin-fixed samples by GeLC-MS/MS and spectral counting. J. Proteomics 2012, 77, 561-576.
-
(2012)
J. Proteomics
, vol.77
, pp. 561-576
-
-
Tanca, A.1
Pagnozzi, D.2
Burrai, G.P.3
Polinas, M.4
-
35
-
-
84876338400
-
Application of 2D-DIGE to formalin-fixed diseased tissue samples from hospital repositories: results from four case studies
-
Tanca, A., Pisanu, S., Biosa, G., Pagnozzi, D. et al., Application of 2D-DIGE to formalin-fixed diseased tissue samples from hospital repositories: results from four case studies. Proteomics Clin. Appl. 2013, 7, 252-263.
-
(2013)
Proteomics Clin. Appl.
, vol.7
, pp. 252-263
-
-
Tanca, A.1
Pisanu, S.2
Biosa, G.3
Pagnozzi, D.4
-
36
-
-
77954378942
-
Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry
-
Ostasiewicz, P., Zielinska, D. F., Mann, M., Wisniewski, J. R., Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. J. Proteome Res. 2010, 9, 3688-3700.
-
(2010)
J. Proteome Res.
, vol.9
, pp. 3688-3700
-
-
Ostasiewicz, P.1
Zielinska, D.F.2
Mann, M.3
Wisniewski, J.R.4
-
37
-
-
79960350722
-
Protein phosphorylation analysis in archival clinical cancer samples by shotgun and targeted proteomics approaches
-
Gamez-Pozo, A., Sanchez-Navarro, I., Calvo, E., Diaz, E. et al., Protein phosphorylation analysis in archival clinical cancer samples by shotgun and targeted proteomics approaches. Mol. Biosyst. 2011, 7, 2368-2374.
-
(2011)
Mol. Biosyst.
, vol.7
, pp. 2368-2374
-
-
Gamez-Pozo, A.1
Sanchez-Navarro, I.2
Calvo, E.3
Diaz, E.4
-
38
-
-
55049089416
-
A portrait of tissue phosphoprotein stability in the clinical tissue procurement process
-
Espina, V., Edmiston, K. H., Heiby, M., Pierobon, M. et al., A portrait of tissue phosphoprotein stability in the clinical tissue procurement process. Mol. Cell. Proteomics 2008, 7, 1998-2018.
-
(2008)
Mol. Cell. Proteomics
, vol.7
, pp. 1998-2018
-
-
Espina, V.1
Edmiston, K.H.2
Heiby, M.3
Pierobon, M.4
-
39
-
-
84870930884
-
Variability of protein and phosphoprotein levels in clinical tissue specimens during the preanalytical phase
-
Gundisch, S., Hauck, S., Sarioglu, H., Schott, C. et al., Variability of protein and phosphoprotein levels in clinical tissue specimens during the preanalytical phase. J. Proteome Res. 2012, 11, 5748-5762.
-
(2012)
J. Proteome Res.
, vol.11
, pp. 5748-5762
-
-
Gundisch, S.1
Hauck, S.2
Sarioglu, H.3
Schott, C.4
-
40
-
-
84885199044
-
Delayed times to tissue fixation result in unpredictable global phosphoproteome changes
-
Gundisch, S., Grundner-Culemann, K., Wolff, C., Schott, C. et al., Delayed times to tissue fixation result in unpredictable global phosphoproteome changes. J. Proteome Res. 2013, 12, 4424-4434.
-
(2013)
J. Proteome Res.
, vol.12
, pp. 4424-4434
-
-
Gundisch, S.1
Grundner-Culemann, K.2
Wolff, C.3
Schott, C.4
-
41
-
-
0036583926
-
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
-
Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B. et al., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376-386.
-
(2002)
Mol. Cell. Proteomics
, vol.1
, pp. 376-386
-
-
Ong, S.E.1
Blagoev, B.2
Kratchmarova, I.3
Kristensen, D.B.4
-
42
-
-
84865790403
-
Proteome analysis of laser microdissected glomeruli from formalin-fixed paraffin-embedded kidneys of autopsies of diabetic patients: nephronectin is associated with the development of diabetic glomerulosclerosis
-
Nakatani, S., Wei, M., Ishimura, E., Kakehashi, A. et al., Proteome analysis of laser microdissected glomeruli from formalin-fixed paraffin-embedded kidneys of autopsies of diabetic patients: nephronectin is associated with the development of diabetic glomerulosclerosis. Nephrol. Dial. Transplant. 2012, 27, 1889-1897.
-
(2012)
Nephrol. Dial. Transplant.
, vol.27
, pp. 1889-1897
-
-
Nakatani, S.1
Wei, M.2
Ishimura, E.3
Kakehashi, A.4
-
43
-
-
84863231370
-
Proteomic identification of immunoproteasome accumulation in formalin-fixed rodent spinal cords with experimental autoimmune encephalomyelitis
-
Jain, M. R., Li, Q., Liu, T., Rinaggio, J. et al., Proteomic identification of immunoproteasome accumulation in formalin-fixed rodent spinal cords with experimental autoimmune encephalomyelitis. J. Proteome Res. 2012, 11, 1791-1803.
-
(2012)
J. Proteome Res.
, vol.11
, pp. 1791-1803
-
-
Jain, M.R.1
Li, Q.2
Liu, T.3
Rinaggio, J.4
-
44
-
-
84874618870
-
Tools for label-free peptide quantification
-
Nahnsen, S., Bielow, C., Reinert, K., Kohlbacher, O., Tools for label-free peptide quantification. Mol. Cell. Proteomics 2013, 12, 549-556.
-
(2013)
Mol. Cell. Proteomics
, vol.12
, pp. 549-556
-
-
Nahnsen, S.1
Bielow, C.2
Reinert, K.3
Kohlbacher, O.4
-
45
-
-
75349102311
-
Quantitative proteomic analysis of formalin fixed paraffin embedded oral HPV lesions from HIV patients
-
Jain, M. R., Liu, T., Hu, J., Darfler, M. et al., Quantitative proteomic analysis of formalin fixed paraffin embedded oral HPV lesions from HIV patients. Open Proteomics J. 2008, 1, 40-45.
-
(2008)
Open Proteomics J.
, vol.1
, pp. 40-45
-
-
Jain, M.R.1
Liu, T.2
Hu, J.3
Darfler, M.4
-
46
-
-
38649090064
-
False discovery rates and related statistical concepts in mass spectrometry-based proteomics
-
Choi, H., Nesvizhskii, A. I., False discovery rates and related statistical concepts in mass spectrometry-based proteomics. J. Proteome Res. 2008, 7, 47-50.
-
(2008)
J. Proteome Res.
, vol.7
, pp. 47-50
-
-
Choi, H.1
Nesvizhskii, A.I.2
-
47
-
-
79952304665
-
Generic workflow for quality assessment of quantitative label-free LC-MS analysis
-
Sandin, M., Krogh, M., Hansson, K., Levander, F., Generic workflow for quality assessment of quantitative label-free LC-MS analysis. Proteomics 2011, 11, 1114-1124.
-
(2011)
Proteomics
, vol.11
, pp. 1114-1124
-
-
Sandin, M.1
Krogh, M.2
Hansson, K.3
Levander, F.4
-
48
-
-
84878051310
-
Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs
-
Clough, T., Thaminy, S., Ragg, S., Aebersold, R., Vitek, O., Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs. BMC Bioinform. 2012, 13(Suppl 16), 1-17.
-
(2012)
BMC Bioinform.
, vol.13
, Issue.SUPPL. 16
, pp. 1-17
-
-
Clough, T.1
Thaminy, S.2
Ragg, S.3
Aebersold, R.4
Vitek, O.5
-
49
-
-
54049090766
-
Selected reaction monitoring for quantitative proteomics: a tutorial
-
Lange, V., Picotti, P., Domon, B., Aebersold, R., Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 2008, 4, 1-14.
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 1-14
-
-
Lange, V.1
Picotti, P.2
Domon, B.3
Aebersold, R.4
-
50
-
-
84876333265
-
Improved protein extraction and protein identification from archival formalin-fixed paraffin-embedded human aortas
-
Fu, Z., Yan, K., Rosenberg, A., Jin, Z. et al., Improved protein extraction and protein identification from archival formalin-fixed paraffin-embedded human aortas. Proteomics Clin. Appl. 2013, 7, 217-224.
-
(2013)
Proteomics Clin. Appl.
, vol.7
, pp. 217-224
-
-
Fu, Z.1
Yan, K.2
Rosenberg, A.3
Jin, Z.4
-
51
-
-
33846109371
-
Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues
-
Hwang, S. I., Thumar, J., Lundgren, D. H., Rezaul, K. et al., Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene 2007, 26, 65-76.
-
(2007)
Oncogene
, vol.26
, pp. 65-76
-
-
Hwang, S.I.1
Thumar, J.2
Lundgren, D.H.3
Rezaul, K.4
-
52
-
-
84856710193
-
Protein expression signatures for inhibition of epidermal growth factor receptor-mediated signaling
-
Myers, M. V., Manning, H. C., Coffey, R. J., Liebler, D. C., Protein expression signatures for inhibition of epidermal growth factor receptor-mediated signaling. Mol. Cell. Proteomics 2012, 11, M111 015222.
-
(2012)
Mol. Cell. Proteomics
, vol.11
-
-
Myers, M.V.1
Manning, H.C.2
Coffey, R.J.3
Liebler, D.C.4
-
53
-
-
84885869771
-
Selected reaction monitoring (SRM) analysis of epidermal growth factor receptor (EGFR) in formalin fixed tumor tissue
-
Hembrough, T., Thyparambil, S., Liao, W. L., Darfler, M. M. et al., Selected reaction monitoring (SRM) analysis of epidermal growth factor receptor (EGFR) in formalin fixed tumor tissue. Clin. Proteomics 2012, 9, 1-10.
-
(2012)
Clin. Proteomics
, vol.9
, pp. 1-10
-
-
Hembrough, T.1
Thyparambil, S.2
Liao, W.L.3
Darfler, M.M.4
-
54
-
-
84879320040
-
Application of selected reaction monitoring for multiplex quantification of clinically validated biomarkers in formalin-fixed, paraffin-embedded tumor tissue
-
Hembrough, T., Thyparambil, S., Liao, W. L., Darfler, M. M. 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, 454-465.
-
(2013)
J. Mol. Diagn.
, vol.15
, pp. 454-465
-
-
Hembrough, T.1
Thyparambil, S.2
Liao, W.L.3
Darfler, M.M.4
-
55
-
-
77956108790
-
mTRAQ-based quantification of potential endometrial carcinoma biomarkers from archived formalin-fixed paraffin-embedded tissues
-
DeSouza, L. V., Krakovska, O., Darfler, M. M., Krizman, D. B. et al., mTRAQ-based quantification of potential endometrial carcinoma biomarkers from archived formalin-fixed paraffin-embedded tissues. Proteomics 2010, 10, 3108-3116.
-
(2010)
Proteomics
, vol.10
, pp. 3108-3116
-
-
DeSouza, L.V.1
Krakovska, O.2
Darfler, M.M.3
Krizman, D.B.4
-
56
-
-
77950517812
-
Proteomic analysis of laser-microdissected paraffin-embedded tissues: (2) MRM assay for stage-related proteins upon non-metastatic lung adenocarcinoma
-
Nishimura, T., Nomura, M., Tojo, H., Hamasaki, H. et al., Proteomic analysis of laser-microdissected paraffin-embedded tissues: (2) MRM assay for stage-related proteins upon non-metastatic lung adenocarcinoma. J. Proteomics 2010, 73, 1100-1110.
-
(2010)
J. Proteomics
, vol.73
, pp. 1100-1110
-
-
Nishimura, T.1
Nomura, M.2
Tojo, H.3
Hamasaki, H.4
-
57
-
-
84861814883
-
Precision of multiple reaction monitoring mass spectrometry analysis of formalin-fixed, paraffin-embedded tissue
-
Sprung, R. W., Martinez, M. A., Carpenter, K. L., Ham, A. J. et al., Precision of multiple reaction monitoring mass spectrometry analysis of formalin-fixed, paraffin-embedded tissue. J. Proteome Res. 2012, 11, 3498-3505.
-
(2012)
J. Proteome Res.
, vol.11
, pp. 3498-3505
-
-
Sprung, R.W.1
Martinez, M.A.2
Carpenter, K.L.3
Ham, A.J.4
-
58
-
-
0037663202
-
Strategies for the assessment of matrix effect in quantitative bioanalytical methods based on HPLC-MS/MS
-
Matuszewski, B. K., Constanzer, M. L., Chavez-Eng, C. M., Strategies for the assessment of matrix effect in quantitative bioanalytical methods based on HPLC-MS/MS. Anal. Chem. 2003, 75, 3019-3030.
-
(2003)
Anal. Chem.
, vol.75
, pp. 3019-3030
-
-
Matuszewski, B.K.1
Constanzer, M.L.2
Chavez-Eng, C.M.3
-
59
-
-
84881364985
-
Proteomic analysis of nuclei dissected from fixed rat brain tissue using expression microdissection
-
Blackler, A. R., Morgan, N. Y., Gao, B., Olano, L. R. et al., Proteomic analysis of nuclei dissected from fixed rat brain tissue using expression microdissection. Anal. Chem. 2013, 85, 7139-7145.
-
(2013)
Anal. Chem.
, vol.85
, pp. 7139-7145
-
-
Blackler, A.R.1
Morgan, N.Y.2
Gao, B.3
Olano, L.R.4
-
60
-
-
84872952806
-
Novel prognostic protein markers of resectable pancreatic cancer identified by coupled shotgun and targeted proteomics using formalin-fixed paraffin-embedded tissues
-
Takadate, T., Onogawa, T., Fukuda, T., Motoi, F. 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, 1368-1382.
-
(2013)
Int. J. Cancer
, vol.132
, pp. 1368-1382
-
-
Takadate, T.1
Onogawa, T.2
Fukuda, T.3
Motoi, F.4
-
61
-
-
79952300698
-
Evaluation of absolute peptide quantitation strategies using selected reaction monitoring
-
Campbell, J., Rezai, T., Prakash, A., Krastins, B. et al., Evaluation of absolute peptide quantitation strategies using selected reaction monitoring. Proteomics 2011, 11, 1148-1152.
-
(2011)
Proteomics
, vol.11
, pp. 1148-1152
-
-
Campbell, J.1
Rezai, T.2
Prakash, A.3
Krastins, B.4
-
62
-
-
79952540456
-
Selected reaction monitoring applied to proteomics
-
Gallien, S., Duriez, E., Domon, B., Selected reaction monitoring applied to proteomics. J. Mass Spectrom. 2011, 46, 298-312.
-
(2011)
J. Mass Spectrom.
, vol.46
, pp. 298-312
-
-
Gallien, S.1
Duriez, E.2
Domon, B.3
-
63
-
-
84859880168
-
Protein significance analysis in selected reaction monitoring (SRM) measurements
-
Chang, C. Y., Picotti, P., Huttenhain, R., Heinzelmann-Schwarz, V. et al., Protein significance analysis in selected reaction monitoring (SRM) measurements. Mol. Cell. Proteomics 2012, 11, M111 014662.
-
(2012)
Mol. Cell. Proteomics
, vol.11
-
-
Chang, C.Y.1
Picotti, P.2
Huttenhain, R.3
Heinzelmann-Schwarz, V.4
-
64
-
-
84875078031
-
Determination of free desmosine in human plasma and its application in two experimental medicine studies
-
Lamerz, J., Friedlein, A., Soder, N., Cutler, P., Dobeli, H., Determination of free desmosine in human plasma and its application in two experimental medicine studies. Anal. Biochem. 2013, 436, 127-136.
-
(2013)
Anal. Biochem.
, vol.436
, pp. 127-136
-
-
Lamerz, J.1
Friedlein, A.2
Soder, N.3
Cutler, P.4
Dobeli, H.5
-
65
-
-
57249105121
-
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models
-
Rogers, S., Girolami, M., Kolch, W., Waters, K. M. et al., Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. Bioinformatics 2008, 24, 2894-2900.
-
(2008)
Bioinformatics
, vol.24
, pp. 2894-2900
-
-
Rogers, S.1
Girolami, M.2
Kolch, W.3
Waters, K.M.4
-
66
-
-
21844453211
-
New frontiers in proteomics research: a perspective
-
Dhingra, V., Gupta, M., Andacht, T., Fu, Z. F., New frontiers in proteomics research: a perspective. Int. J. Pharm. 2005, 299, 1-18.
-
(2005)
Int. J. Pharm.
, vol.299
, pp. 1-18
-
-
Dhingra, V.1
Gupta, M.2
Andacht, T.3
Fu, Z.F.4
-
67
-
-
0033016717
-
Correlation between protein and mRNA abundance in yeast
-
Gygi, S. P., Rochon, Y., Franza, B. R., Aebersold, R., Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 1999, 19, 1720-1730.
-
(1999)
Mol. Cell. Biol.
, vol.19
, pp. 1720-1730
-
-
Gygi, S.P.1
Rochon, Y.2
Franza, B.R.3
Aebersold, R.4
-
68
-
-
84874625369
-
Proteoform: a single term describing protein complexity
-
Smith, L. M., Kelleher, N. L., Proteoform: a single term describing protein complexity. Nat. Methods 2013, 10, 186-187.
-
(2013)
Nat. Methods
, vol.10
, pp. 186-187
-
-
Smith, L.M.1
Kelleher, N.L.2
-
69
-
-
79551663189
-
Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics
-
Geiger, T., Wisniewski, J. R., Cox, J., Zanivan, S. et al., Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics. Nat. Protoc. 2011, 6, 147-157.
-
(2011)
Nat. Protoc.
, vol.6
, pp. 147-157
-
-
Geiger, T.1
Wisniewski, J.R.2
Cox, J.3
Zanivan, S.4
-
70
-
-
84865791474
-
Peptide production and decay rates affect the quantitative accuracy of protein cleavage isotope dilution mass spectrometry (PC-IDMS)
-
Shuford, C. M., Sederoff, R. R., Chiang, V. L., Muddiman, D. C., Peptide production and decay rates affect the quantitative accuracy of protein cleavage isotope dilution mass spectrometry (PC-IDMS). Mol. Cell. Proteomics 2012, 11, 814-823.
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 814-823
-
-
Shuford, C.M.1
Sederoff, R.R.2
Chiang, V.L.3
Muddiman, D.C.4
-
71
-
-
84865577612
-
Advancing formaldehyde cross-linking towards quantitative proteomic applications
-
Klockenbusch, C., O'Hara, J. E., Kast, J., Advancing formaldehyde cross-linking towards quantitative proteomic applications. Anal. Bioanal. Chem. 2012, 404, 1057-1067.
-
(2012)
Anal. Bioanal. Chem.
, vol.404
, pp. 1057-1067
-
-
Klockenbusch, C.1
O'Hara, J.E.2
Kast, J.3
-
72
-
-
77950518174
-
Proteomic analysis of laser-microdissected paraffin-embedded tissues: (1) stage-related protein candidates upon non-metastatic lung adenocarcinoma
-
Kawamura, T., Nomura, M., Tojo, H., Fujii, K. et al., Proteomic analysis of laser-microdissected paraffin-embedded tissues: (1) stage-related protein candidates upon non-metastatic lung adenocarcinoma. J. Proteomics 2010, 73, 1089-1099.
-
(2010)
J. Proteomics
, vol.73
, pp. 1089-1099
-
-
Kawamura, T.1
Nomura, M.2
Tojo, H.3
Fujii, K.4
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