The plasma peptides of breast versus ovarian cancer.
Breast cancer
Chi Square test and ANOVA
Discovery of variation
Electrospray ionization tandem mass spectrometry
Human EDTA plasma
LC–ESI–MS/MS
Linear quadrupole ion trap
Nano chromatography
Organic extraction
Random and independent sampling
SQL SERVER and R
Journal
Clinical proteomics
ISSN: 1542-6416
Titre abrégé: Clin Proteomics
Pays: England
ID NLM: 101184586
Informations de publication
Date de publication:
2019
2019
Historique:
received:
02
08
2019
accepted:
05
12
2019
entrez:
1
1
2020
pubmed:
1
1
2020
medline:
1
1
2020
Statut:
epublish
Résumé
There is a need to demonstrate a proof of principle that proteomics has the capacity to analyze plasma from breast cancer versus other diseases and controls in a multisite clinical trial design. The peptides or proteins that show a high observation frequency, and/or precursor intensity, specific to breast cancer plasma might be discovered by comparison to other diseases and matched controls. The endogenous tryptic peptides of breast cancer plasma were compared to ovarian cancer, female normal, sepsis, heart attack, Alzheimer's and multiple sclerosis along with the institution-matched normal and control samples collected directly onto ice. Endogenous tryptic peptides were extracted from individual breast cancer and control EDTA plasma samples in a step gradient of acetonitrile, and collected over preparative C18 for LC-ESI-MS/MS with a set of LTQ XL linear quadrupole ion traps working together in parallel to randomly and independently sample clinical populations. The MS/MS spectra were fit to fully tryptic peptides or phosphopeptides within proteins using the X!TANDEM algorithm. The protein observation frequency was counted using the SEQUEST algorithm after selecting the single best charge state and peptide sequence for each MS/MS spectra. The observation frequency was subsequently tested by Chi Square analysis. The log Peptides and/or phosphopeptides of common plasma proteins such as APOE, C4A, C4B, C3, APOA1, APOC2, APOC4, ITIH3 and ITIH4 showed increased observation frequency and/or precursor intensity in breast cancer. Many cellular proteins also showed large changes in frequency by Chi Square (χ There was striking agreement between the breast cancer plasma peptides and proteins discovered by LC-ESI-MS/MS with previous biomarkers from tumors, cells lines or body fluids by genetic or biochemical methods. The results indicate that variation in plasma peptides from breast cancer versus ovarian cancer may be directly discovered by LC-ESI-MS/MS that will be a powerful tool for clinical research. It may be possible to use a battery of sensitive and robust linear quadrupole ion traps for random and independent sampling of plasma from a multisite clinical trial.
Sections du résumé
BACKGROUND
BACKGROUND
There is a need to demonstrate a proof of principle that proteomics has the capacity to analyze plasma from breast cancer versus other diseases and controls in a multisite clinical trial design. The peptides or proteins that show a high observation frequency, and/or precursor intensity, specific to breast cancer plasma might be discovered by comparison to other diseases and matched controls. The endogenous tryptic peptides of breast cancer plasma were compared to ovarian cancer, female normal, sepsis, heart attack, Alzheimer's and multiple sclerosis along with the institution-matched normal and control samples collected directly onto ice.
METHODS
METHODS
Endogenous tryptic peptides were extracted from individual breast cancer and control EDTA plasma samples in a step gradient of acetonitrile, and collected over preparative C18 for LC-ESI-MS/MS with a set of LTQ XL linear quadrupole ion traps working together in parallel to randomly and independently sample clinical populations. The MS/MS spectra were fit to fully tryptic peptides or phosphopeptides within proteins using the X!TANDEM algorithm. The protein observation frequency was counted using the SEQUEST algorithm after selecting the single best charge state and peptide sequence for each MS/MS spectra. The observation frequency was subsequently tested by Chi Square analysis. The log
RESULTS
RESULTS
Peptides and/or phosphopeptides of common plasma proteins such as APOE, C4A, C4B, C3, APOA1, APOC2, APOC4, ITIH3 and ITIH4 showed increased observation frequency and/or precursor intensity in breast cancer. Many cellular proteins also showed large changes in frequency by Chi Square (χ
CONCLUSION
CONCLUSIONS
There was striking agreement between the breast cancer plasma peptides and proteins discovered by LC-ESI-MS/MS with previous biomarkers from tumors, cells lines or body fluids by genetic or biochemical methods. The results indicate that variation in plasma peptides from breast cancer versus ovarian cancer may be directly discovered by LC-ESI-MS/MS that will be a powerful tool for clinical research. It may be possible to use a battery of sensitive and robust linear quadrupole ion traps for random and independent sampling of plasma from a multisite clinical trial.
Identifiants
pubmed: 31889940
doi: 10.1186/s12014-019-9262-0
pii: 9262
pmc: PMC6927194
doi:
Types de publication
Journal Article
Langues
eng
Pagination
43Informations de copyright
© The Author(s) 2019.
Déclaration de conflit d'intérêts
Competing interestsThe authors declare that they have no competing interests.
Références
Cancer Genet. 2014 Mar;207(3):87-93
pubmed: 24674866
J Proteome Res. 2003 Jul-Aug;2(4):361-72
pubmed: 12938926
Clin Proteomics. 2017 Dec 8;14:41
pubmed: 29234243
Int J Clin Exp Pathol. 2015 Dec 01;8(12):16046-54
pubmed: 26884881
J Proteome Res. 2004 May-Jun;3(3):364-82
pubmed: 15253417
Biochem Biophys Res Commun. 2015 Dec 4-11;468(1-2):53-8
pubmed: 26545775
Proteomics. 2019 Apr;19(8):e1800148
pubmed: 30582284
J Cell Sci. 2017 Feb 15;130(4):697-711
pubmed: 28062852
Proteomics. 2004 Apr;4(4):1195-203
pubmed: 15048999
Anal Chem. 1995 Apr 15;67(8):1426-36
pubmed: 7741214
Urology. 2002 May;59(5):784-9
pubmed: 11992929
Anal Biochem. 2011 Feb 15;409(2):189-94
pubmed: 20977879
Mol Cell Oncol. 2018 Apr 11;5(3):e1445941
pubmed: 30250898
Oncotarget. 2016 Jul 5;7(27):42661-42682
pubmed: 26894976
Expert Rev Mol Diagn. 2002 Jul;2(4):312-20
pubmed: 12138495
Mol Cell Proteomics. 2004 Apr;3(4):327-44
pubmed: 14754989
J Clin Invest. 2006 Jan;116(1):271-84
pubmed: 16395409
J Chromatogr B Analyt Technol Biomed Life Sci. 2010 Feb 15;878(5-6):590-602
pubmed: 20116351
J Proteomics. 2010 Apr 18;73(6):1163-75
pubmed: 20170764
PLoS Genet. 2013 Mar;9(3):e1003419
pubmed: 23555315
J Cell Physiol. 2015 Jan;230(1):191-8
pubmed: 24931902
Proteomics. 2004 Jan;4(1):244-56
pubmed: 14730686
J Proteomics. 2009 Nov 2;73(1):103-11
pubmed: 19703602
Clin Cancer Res. 2003 Aug 1;9(8):2904-11
pubmed: 12912935
Proc Natl Acad Sci U S A. 2000 Oct 10;97(21):11451-4
pubmed: 11027344
Anal Biochem. 2011 Apr 15;411(2):241-53
pubmed: 21138726
Pharmacogenomics J. 2013 Oct;13(5):417-22
pubmed: 22664479
Nat Med. 2012 Mar 04;18(4):529-37
pubmed: 22388088
Nat Biotechnol. 2003 Mar;21(3):221-2
pubmed: 12610558
Clin Proteomics. 2018 Dec 21;15:41
pubmed: 30598658
J Biomol Tech. 2005 Dec;16(4):429-40
pubmed: 16522866
J Proteomics. 2010 Apr 18;73(6):1254-69
pubmed: 20211283
J Proteome Res. 2012 Apr 6;11(4):2032-47
pubmed: 22316523
Clin Sci (Lond). 2015 Dec;129(12):1037-45
pubmed: 26405042
Breast Cancer Res. 2014 Apr 15;16(2):R40
pubmed: 24735615
Eur Rev Med Pharmacol Sci. 2015;19(2):241-6
pubmed: 25683937
PLoS One. 2017 Nov 8;12(11):e0187194
pubmed: 29117220
J Proteomics. 2014 May 30;103:121-36
pubmed: 24681409
J Chromatogr A. 2009 Jul 10;1216(28):5377-84
pubmed: 19482289
J Proteomics. 2012 Feb 2;75(4):1303-17
pubmed: 22120120
Sci Rep. 2018 Oct 18;8(1):15399
pubmed: 30337557
J Proteome Res. 2009 Mar;8(3):1143-55
pubmed: 19265436
Ai Zheng. 2008 May;27(5):460-5
pubmed: 18479593
Cell Death Dis. 2019 Mar 8;10(3):228
pubmed: 30850587
Cancer Cell. 2013 Aug 12;24(2):229-41
pubmed: 23871637
J Biol Chem. 2004 Jan 23;279(4):2666-72
pubmed: 14612439
J Proteome Res. 2012 Oct 5;11(10):5034-45
pubmed: 22934887
Anal Biochem. 2016 Nov 15;513:7-20
pubmed: 27510553
Clin Proteomics. 2017 Oct 27;14:35
pubmed: 29093647
Anal Biochem. 2018 May 15;549:188-196
pubmed: 29486203
Clin Proteomics. 2018 Dec 1;15:39
pubmed: 30519149
Oncotarget. 2017 Jan 24;8(4):6775-6786
pubmed: 28036274
Mol Carcinog. 2015 Jul;54(7):577-83
pubmed: 24510587
Medicine (Baltimore). 2018 Dec;97(51):e13551
pubmed: 30572455
Cancer. 2015 Oct 15;121(20):3684-91
pubmed: 26108676
OMICS. 2009 Aug;13(4):291-300
pubmed: 19624269
J Immunol Methods. 2018 Jan;452:12-19
pubmed: 28974366
Nat Biotechnol. 2015 Jul;33(7):743-9
pubmed: 26076430
Proteomics. 2003 Sep;3(9):1667-72
pubmed: 12973722
Biochem Biophys Res Commun. 2006 Dec 1;350(4):890-9
pubmed: 17045569
J Clin Invest. 2015 Apr;125(4):1648-64
pubmed: 25774502
Clin Cancer Res. 2005 Oct 15;11(20):7434-43
pubmed: 16243817
Pharmacogenomics J. 2016 Nov;16(6):525-529
pubmed: 26503812
Clin Chem. 2006 Oct;52(10):1897-905
pubmed: 16916992
Cancer Treat Rev. 2014 Feb;40(1):129-38
pubmed: 23891266
Mass Spectrom Rev. 2011 Sep-Oct;30(5):685-732
pubmed: 24737629
Proteomics. 2010 Sep;10(18):3388-92
pubmed: 20707003
PLoS One. 2017 Oct 10;12(10):e0185565
pubmed: 29016617
J Am Soc Mass Spectrom. 2002 Jun;13(6):659-69
pubmed: 12056566
FEBS Open Bio. 2019 Jul;9(7):1270-1280
pubmed: 31102318
Anal Biochem. 2007 Nov 15;370(2):228-45
pubmed: 17884004
Clin Epigenetics. 2015 May 27;7:57
pubmed: 26052355
Nat Commun. 2018 Aug 28;9(1):3489
pubmed: 30154480
Lancet. 2002 Feb 16;359(9306):572-7
pubmed: 11867112
Cancer Res. 2013 Jul 15;73(14):4488-99
pubmed: 23636126
Mol Cell Biol. 2014 Jul;34(13):2409-17
pubmed: 24752894
Clin Proteomics. 2017 Dec 2;14:39
pubmed: 29213220
Mol Cell Biochem. 2007 Apr;298(1-2):59-68
pubmed: 17119850
Clin Cancer Res. 2016 Jul 1;22(13):3298-309
pubmed: 26861454
Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):E1307-16
pubmed: 25737553
J Biol Chem. 2010 Apr 30;285(18):13966-78
pubmed: 20139422
Cancer Res. 2007 Jul 15;67(14):6657-64
pubmed: 17638875
Exp Dermatol. 2005 May;14(5):336-48
pubmed: 15854127
Mol Cell Proteomics. 2003 Oct;2(10):1096-103
pubmed: 12917320
Mol Cell Proteomics. 2008 Mar;7(3):509-18
pubmed: 17986438
Bioinformatics. 2004 Jun 12;20(9):1466-7
pubmed: 14976030
Biochem Biophys Res Commun. 2009 Jan 16;378(3):433-8
pubmed: 19028452
Breast Cancer Res Treat. 2011 Jan;125(1):55-63
pubmed: 20224928
Biostatistics. 2009 Jul;10(3):481-500
pubmed: 19325168
Clin Proteomics. 2014 Apr 02;11(1):13
pubmed: 24694173
Mol Cell Proteomics. 2006 Oct;5(10):1840-52
pubmed: 16896061
Clin Chem. 2010 Feb;56(2):262-71
pubmed: 20093557
Anal Bioanal Chem. 2010 Feb;396(3):1223-47
pubmed: 20033139
Nature. 2015 Jul 9;523(7559):177-82
pubmed: 26106858
Anal Biochem. 2018 Nov 1;560:39-49
pubmed: 30171831
PLoS One. 2017 Mar 23;12(3):e0174126
pubmed: 28333977
PLoS One. 2016 May 12;11(5):e0155660
pubmed: 27171439
Oncotarget. 2016 Jul 5;7(27):41346-41362
pubmed: 27191656
J Biol Chem. 2014 Nov 7;289(45):31373-81
pubmed: 25258321
Blood. 2009 Oct 8;114(15):3292-8
pubmed: 19654405
Nat Struct Mol Biol. 2010 Oct;17(10):1247-54
pubmed: 20871615
Carcinogenesis. 2014 Jun;35(6):1352-61
pubmed: 24517997
Int J Oncol. 2016 Sep;49(3):1221-9
pubmed: 27500741
J Proteomics. 2016 Oct 4;148:183-93
pubmed: 27498393
J Proteomics. 2011 Dec 21;75(2):450-68
pubmed: 21911091
PLoS One. 2012;7(9):e43721
pubmed: 22957033
Curr Drug Metab. 2018;19(1):55-74
pubmed: 29090664
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Oncogene. 2015 Mar 5;34(10):1300-11
pubmed: 24662836
Expert Opin Investig Drugs. 2010 Apr;19 Suppl 1:S79-89
pubmed: 20374034
Proteomics. 2003 Jul;3(7):1345-64
pubmed: 12872236
Biomaterials. 2000 Aug;21(16):1701-10
pubmed: 10905411
Proteomics. 2012 Nov;12(22):3407-15
pubmed: 22997041
Clin Proteomics. 2014 Jan 29;11(1):3
pubmed: 24476026
Int J Mol Med. 2006 Mar;17(3):457-63
pubmed: 16465392