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Chen ZZ, Dufresne J, Bowden P, Miao M, Marshall JG. Extraction of naturally occurring peptides versus the tryptic digestion of proteins from fetal versus adult bovine serum for LC-ESI-MS/MS. Anal Biochem 2024; 689:115497. [PMID: 38461948 DOI: 10.1016/j.ab.2024.115497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/12/2024]
Abstract
The naturally occurring peptides and digested proteins of fetal versus adult bovine serum were compared by LC-ESI-MS/MS after correction against noise from blank injections and random MS/MS spectra as statistical controls. Serum peptides were extracted by differential precipitation with mixtures of acetonitrile and water. Serum proteins were separated by partition chromatography over quaternary amine resin followed by tryptic digestion. The rigorous X!TANDEM goodness of fit algorithm that has a low error rate as demonstrated by low FDR q-values (q ≤ 0.01) showed qualitative and quantitative agreement with the SEQUEST cross correlation algorithm on 12,052 protein gene symbols. Tryptic digestion provided a quantitative identification of the serum proteins where observation frequency reflected known high abundance. In contrast, the naturally occurring peptides reflected the cleavage of common serum proteins such as C4A, C3, FGB, HPX, A2M but also proteins in lower concentration such as F13A1, IK, collagens and protocadherins. Proteins associated with cellular growth and development such as actins (ACT), ribosomal proteins like Ribosomal protein S6 (RPS6), synthetic enzymes and extracellular matrix factors were enriched in fetal calf serum. In contrast to the large literature from cord blood, IgG light chains were absent from fetal serum as observed by LC-ESI-MS/MS and confirmed by ELISA.
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Affiliation(s)
- Zhuo Zhen Chen
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Jaimie Dufresne
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Peter Bowden
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Ming Miao
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - John G Marshall
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
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Chen ZZ, Johnson L, Trahtemberg U, Baker A, Huq S, Dufresne J, Bowden P, Miao M, Ho JA, Hsu CC, Dos Santos CC, Marshall JG. Mitochondria and cytochrome components released into the plasma of severe COVID-19 and ICU acute respiratory distress syndrome patients. Clin Proteomics 2023; 20:17. [PMID: 37031181 PMCID: PMC10082440 DOI: 10.1186/s12014-023-09394-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 01/20/2023] [Indexed: 04/10/2023] Open
Abstract
INTRODUCTION Proteomic analysis of human plasma by LC-ESI-MS/MS has discovered a limited number of new cellular protein biomarkers that may be confirmed by independent biochemical methods. Analysis of COVID-19 plasma has indicated the re-purposing of known biomarkers that might be used as prognostic markers of COVID-19 infection. However, multiple molecular approaches have previously indicated that the SARS-COV2 infection cycle is linked to the biology of mitochondria and that the response to infections may involve the action of heme containing oxidative enzymes. METHODS Human plasma from COVID-19 and ICU-ARDS was analyzed by classical analytical biochemistry techniques and classical frequency-based statistical approaches to look for prognostic markers of severe COVID-19 lung damage. Plasma proteins from COVID-19 and ICU-ARDS were identified and enumerated versus the controls of normal human plasma (NHP) by LC-ESI-MS/MS. The observation frequency of proteins detected in COVID-19 and ICU-ARDS patients were compared to normal human plasma, alongside random and noise MS/MS spectra controls, using the Chi Square (χ2) distribution. RESULTS PCR showed the presence of MT-ND1 DNA in the plasma of COVID-19, ICU-ARDS, as well as normal human plasma. Mitochondrial proteins such as MRPL, L2HGDH, ATP, CYB, CYTB, CYP, NDUF and others, were increased in COVID-19 and ICU-ARDS plasma. The apparent activity of the cytochrome components were tested alongside NHP by dot blotting on PVDF against a purified cytochrome c standard preparation for H2O2 dependent reaction with luminol as measured by enhanced chemiluminescence (ECL) that showed increased activity in COVID-19 and ICU-ARDS patients. DISCUSSION The results from PCR, LC-ESI-MS/MS of tryptic peptides, and cytochrome ECL assays confirmed that mitochondrial components were present in the plasma, in agreement with the established central role of the mitochondria in SARS-COV-2 biology. The cytochrome activity assay showed that there was the equivalent of at least nanogram amounts of cytochrome(s) in the plasma sample that should be clearly detectable by LC-ESI-MS/MS. The release of the luminol oxidase activity from cells into plasma forms the basis of a simple and rapid test for the severity of cell damage and lung injury in COVID-19 infection and ICU-ARDS.
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Affiliation(s)
- Zhuo Zhen Chen
- Department of Chemistry and Biology, Faculty of Science, Toronto Metropolitan, University, 350 Victoria Street, Toronto, ON, Canada
| | - Lloyd Johnson
- Department of Chemistry and Biology, Faculty of Science, Toronto Metropolitan, University, 350 Victoria Street, Toronto, ON, Canada
| | - Uriel Trahtemberg
- St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Andrew Baker
- St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Saaimatul Huq
- Department of Chemistry and Biology, Faculty of Science, Toronto Metropolitan, University, 350 Victoria Street, Toronto, ON, Canada
| | | | | | | | - Ja-An Ho
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Claudia C Dos Santos
- St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada.
| | - John G Marshall
- Department of Chemistry and Biology, Faculty of Science, Toronto Metropolitan, University, 350 Victoria Street, Toronto, ON, Canada.
- Integrated BioBank of Luxembourg, Luxembourg Institute of Health, 6 R. Nicolas-Ernest Barblé, Luxembourg, Luxembourg.
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Chen ZZ, Bowden P, Dufresne J, Miao M, Marshall JG. LEDGF is a new growth factor in fetal serum. Anal Biochem 2022; 655:114845. [PMID: 35970411 DOI: 10.1016/j.ab.2022.114845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/23/2022] [Accepted: 08/01/2022] [Indexed: 11/26/2022]
Abstract
Fetal serum supports the immortal growth of mammalian cell lines in culture while adult serum leads to the terminal differentiation and death of cells in culture. Many of the proteins in fetal serum that support the indefinite division and growth of cancerous cell lines remain obscure. The peptides and proteins of fetal versus adult serum were analyzed by liquid chromatography, nano electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS). Three batches of fetal serum contained the Alpha Fetoprotein marker while adult serum batches did not. Insulin (INS), and insulin-like growth factor (ILGF), fibroblast growth factor (FGF), epidermal growth factor (EGF) and platelet derived growth factor (PDGF) were increased in fetal serum. New fetal growth factors including MEGF, HDGFRP and PSIP1 and soluble growth receptors such as TNFR, EGFR, NTRK2 and THRA were discovered. Addition of insulin or the homeotic transcription factor PSIP1, also referred to as Lens Epithelium Derived Growth Factor (LEDGF), partially restored the rounded phenotype of rapidly dividing cells but was not as effective as fetal serum. Thus, a new growth factor in fetal serum, LEDGF/PSIP1, was directly observed by tandem mass spectrometry and confirmed by add back experiments to cell culture media alongside insulin.
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Affiliation(s)
- Zhuo Zhen Chen
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Peter Bowden
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Jaimie Dufresne
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Ming Miao
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - John G Marshall
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
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Gecili E, Sivaganesan S, Asar O, Clancy JP, Ziady A, Szczesniak RD. Bayesian regularization for a nonstationary Gaussian linear mixed effects model. Stat Med 2022; 41:681-697. [PMID: 34897771 PMCID: PMC8795479 DOI: 10.1002/sim.9279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/12/2021] [Accepted: 11/20/2021] [Indexed: 11/06/2022]
Abstract
In omics experiments, estimation and variable selection can involve thousands of proteins/genes observed from a relatively small number of subjects. Many regression regularization procedures have been developed for estimation and variable selection in such high-dimensional problems. However, approaches have predominantly focused on linear regression models that ignore correlation arising from long sequences of repeated measurements on the outcome. Our work is motivated by the need to identify proteomic biomarkers that improve the prediction of rapid lung-function decline for individuals with cystic fibrosis (CF) lung disease. We extend four Bayesian penalized regression approaches for a Gaussian linear mixed effects model with nonstationary covariance structure to account for the complicated structure of longitudinal lung function data while simultaneously estimating unknown parameters and selecting important protein isoforms to improve predictive performance. Different types of shrinkage priors are evaluated to induce variable selection in a fully Bayesian framework. The approaches are studied with simulations. We apply the proposed method to real proteomics and lung-function outcome data from our motivating CF study, identifying a set of relevant clinical/demographic predictors and a proteomic biomarker for rapid decline of lung function. We also illustrate the methods on CD4 yeast cell-cycle genomic data, confirming that the proposed method identifies transcription factors that have been highlighted in the literature for their importance as cell cycle transcription factors.
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Affiliation(s)
- Emrah Gecili
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center, OH, USA,Correspondence: Emrah Gecili, Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA.
| | - Siva Sivaganesan
- Division of Statistics and Data Science, Department of Mathematical Sciences, University of Cincinnati, OH, USA
| | - Ozgur Asar
- Department of Biostatistics and Medical Informatics, Acibadem University, Istanbul, Turkey
| | | | - Assem Ziady
- Division of Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, OH, USA
| | - Rhonda D. Szczesniak
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center, OH, USA
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Todorović-Raković N, Milovanović J, Greenman J, Radulovic M. The significance of HOXB7 and IL17RB serum levels in prognosis of hormonally dependent breast cancer: A pilot study. Adv Med Sci 2021; 66:359-365. [PMID: 34304115 DOI: 10.1016/j.advms.2021.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/18/2021] [Accepted: 07/15/2021] [Indexed: 12/01/2022]
Abstract
PURPOSE Improved prognostication of a patient's outcome could allow for personalized treatment decisions in breast cancer. Homeobox B7 (HOXB7) and interleukin 17 receptor B (IL17RB) are proteins reportedly involved in the development of hormonal therapy resistance. Their prognostic value was previously investigated in tumor tissue but recent mass spectrometric detection of HOXB7 and IL17RB proteins in serum has prompted us to perform the first prognostic evaluation of their serum levels. PATIENTS AND METHODS The study included 81 premenopausal breast cancer patients that received adjuvant hormonal therapy. The median follow-up period was 61 months. HOXB7 and IL17RB serum protein levels were measured by quantitative sandwich ELISA and prognostically evaluated by Cox proportional hazards regression analysis. RESULTS HOXB7 protein was detected in 96.3% and IL17RB in 33.3% of serum samples. Higher levels of serum HOXB7 significantly associated with favorable disease outcome by prognosticating distant (by HR = 0.04; P = 0.001) and local recurrence (by HR = 0.03, P = 0.001). The recurrence rates in the HOXB7high and HOXB7low subgroups of patients (cut-off 81.5 pg/mL) were 0% and 17%, respectively. Serum IL17RB levels did not significantly associate with either local or distant events. The multivariate analysis highlighted estrogen receptor, histological grade, nodal status and HOXB7 as independent prognostic parameters. CONCLUSIONS Our findings validate the previous mass-spectrometry data by showing that HOXB7 and IL17RB cellular proteins are detectable in serum by a standard ELISA assay. Furthermore, we show that HOXB7 serum levels are the relevant prognosticator of response to hormonal therapy.
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Affiliation(s)
- Nataša Todorović-Raković
- Department of Experimental Oncology, Institute of Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Jelena Milovanović
- Department of Experimental Oncology, Institute of Oncology and Radiology of Serbia, Belgrade, Serbia.
| | - John Greenman
- Department of Biomedical Sciences, University of Hull, Hull, UK
| | - Marko Radulovic
- Department of Experimental Oncology, Institute of Oncology and Radiology of Serbia, Belgrade, Serbia
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Florentinus-Mefailoski A, Bowden P, Scheltens P, Killestein J, Teunissen C, Marshall JG. The plasma peptides of Alzheimer's disease. Clin Proteomics 2021; 18:17. [PMID: 34182925 PMCID: PMC8240224 DOI: 10.1186/s12014-021-09320-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023] Open
Abstract
Background A practical strategy to discover proteins specific to Alzheimer’s dementia (AD) may be to compare the plasma peptides and proteins from patients with dementia to normal controls and patients with neurological conditions like multiple sclerosis or other diseases. The aim was a proof of principle for a method to discover proteins and/or peptides of plasma that show greater observation frequency and/or precursor intensity in AD. The endogenous tryptic peptides of Alzheimer’s were compared to normals, multiple sclerosis, ovarian cancer, breast cancer, female normal, sepsis, ICU Control, heart attack, along with their institution-matched controls, and normal samples collected directly onto ice. Methods Endogenous tryptic peptides were extracted from blinded, individual AD and control EDTA plasma samples in a step gradient of acetonitrile for random and independent sampling by LC–ESI–MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were fit to fully tryptic peptides within proteins identified using the X!TANDEM algorithm. Observation frequency of the identified proteins was counted using SEQUEST algorithm. The proteins with apparently increased observation frequency in AD versus AD Control were revealed graphically and subsequently tested by Chi Square analysis. The proteins specific to AD plasma by Chi Square with FDR correction were analyzed by the STRING algorithm. The average protein or peptide log10 precursor intensity was compared across disease and control treatments by ANOVA in the R statistical system. Results Peptides and/or phosphopeptides of common plasma proteins such as complement C2, C7, and C1QBP among others showed increased observation frequency by Chi Square and/or precursor intensity in AD. Cellular gene symbols with large Chi Square values (χ2 ≥ 25, p ≤ 0.001) from tryptic peptides included KIF12, DISC1, OR8B12, ZC3H12A, TNF, TBC1D8B, GALNT3, EME2, CD1B, BAG1, CPSF2, MMP15, DNAJC2, PHACTR4, OR8B3, GCK, EXOSC7, HMGA1 and NT5C3A among others. Similarly, increased frequency of tryptic phosphopeptides were observed from MOK, SMIM19, NXNL1, SLC24A2, Nbla10317, AHRR, C10orf90, MAEA, SRSF8, TBATA, TNIK, UBE2G1, PDE4C, PCGF2, KIR3DP1, TJP2, CPNE8, and NGF amongst others. STRING analysis showed an increase in cytoplasmic proteins and proteins associated with alternate splicing, exocytosis of luminal proteins, and proteins involved in the regulation of the cell cycle, mitochondrial functions or metabolism and apoptosis. Increases in mean precursor intensity of peptides from common plasma proteins such as DISC1, EXOSC5, UBE2G1, SMIM19, NXNL1, PANO, EIF4G1, KIR3DP1, MED25, MGRN1, OR8B3, MGC24039, POLR1A, SYTL4, RNF111, IREB2, ANKMY2, SGKL, SLC25A5, CHMP3 among others were associated with AD. Tryptic peptides from the highly conserved C-terminus of DISC1 within the sequence MPGGGPQGAPAAAGGGGVSHRAGSRDCLPPAACFR and ARQCGLDSR showed a higher frequency and highest intensity in AD compared to all other disease and controls. Conclusion Proteins apparently expressed in the brain that were directly related to Alzheimer’s including Nerve Growth Factor (NFG), Sphingomyelin Phosphodiesterase, Disrupted in Schizophrenia 1 (DISC1), the cell death regulator retinitis pigmentosa (NXNl1) that governs the loss of nerve cells in the retina and the cell death regulator ZC3H12A showed much higher observation frequency in AD plasma vs the matched control. There was a striking agreement between the proteins known to be mutated or dis-regulated in the brains of AD patients with the proteins observed in the plasma of AD patients from endogenous peptides including NBN, BAG1, NOX1, PDCD5, SGK3, UBE2G1, SMPD3 neuronal proteins associated with synapse function such as KSYTL4, VTI1B and brain specific proteins such as TBATA. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09320-2.
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Affiliation(s)
- Angelique Florentinus-Mefailoski
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada
| | - Peter Bowden
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada
| | - Philip Scheltens
- Alzheimer Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Joep Killestein
- MS Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Charlotte Teunissen
- Neurochemistry Lab and Biobank, Dept of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - John G Marshall
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada. .,International Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (Formerly CRP Sante Luxembourg), Strassen, Luxembourg.
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Dufresne J, Bowden P, Thavarajah T, Florentinus-Mefailoski A, Chen ZZ, Tucholska M, Norzin T, Ho MT, Phan M, Mohamed N, Ravandi A, Stanton E, Slutsky AS, Dos Santos CC, Romaschin A, Marshall JC, Addison C, Malone S, Heyland D, Scheltens P, Killestein J, Teunissen C, Diamandis EP, Siu KWM, Marshall JG. The plasma peptides of breast versus ovarian cancer. Clin Proteomics 2019; 16:43. [PMID: 31889940 PMCID: PMC6927194 DOI: 10.1186/s12014-019-9262-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
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 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 log10 precursor intensity was compared by ANOVA in the R statistical system. 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 (χ2 > 100, p < 0.0001) in the breast cancer samples such as CPEB1, LTBP4, HIF-1A, IGHE, RAB44, NEFM, C19orf82, SLC35B1, 1D12A, C8orf34, HIF1A, OCLN, EYA1, HLA-DRB1, LARS, PTPDC1, WWC1, ZNF562, PTMA, MGAT1, NDUFA1, NOGOC, OR1E1, OR1E2, CFI, HSA12, GCSH, ELTD1, TBX15, NR2C2, FLJ00045, PDLIM1, GALNT9, ASH2L, PPFIBP1, LRRC4B, SLCO3A1, BHMT2, CS, FAM188B2, LGALS7, SAT2, SFRS8, SLC22A12, WNT9B, SLC2A4, ZNF101, WT1, CCDC47, ERLIN1, SPFH1, EID2, THOC1, DDX47, MREG, PTPRE, EMILIN1, DKFZp779G1236 and MAP3K8 among others. The protein gene symbols with large Chi Square values were significantly enriched in proteins that showed a complex set of previously established functional and structural relationships by STRING analysis. An increase in mean precursor intensity of peptides was observed for QSER1 as well as SLC35B1, IQCJ-SCHIP1, MREG, BHMT2, LGALS7, THOC1, ANXA4, DHDDS, SAT2, PTMA and FYCO1 among others. In contrast, the QSER1 peptide QPKVKAEPPPK was apparently specific to ovarian cancer. Conclusion 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.
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Affiliation(s)
- Jaimie Dufresne
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Pete Bowden
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Thanusi Thavarajah
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Angelique Florentinus-Mefailoski
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Zhuo Zhen Chen
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Monika Tucholska
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Tenzin Norzin
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Margaret Truc Ho
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Morla Phan
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Nargiz Mohamed
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Amir Ravandi
- 2Institute of Cardiovascular Sciences, St. Boniface Hospital Research Center, University of Manitoba, Winnipeg, Canada
| | - Eric Stanton
- 3Division of Cardiology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Arthur S Slutsky
- 4St. Michael's Hospital, Keenan Chair in Medicine, Professor of Medicine, Surgery & Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Claudia C Dos Santos
- 5St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Alexander Romaschin
- 5St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - John C Marshall
- 5St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Christina Addison
- 6Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Shawn Malone
- 6Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Daren Heyland
- 7Clinical Evaluation Research Unit, Kingston General Hospital, Kingston, Canada
| | - Philip Scheltens
- 8Alzheimer Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Joep Killestein
- 9MS Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Charlotte Teunissen
- 10Neurochemistry Lab and Biobank, Dept of Clinical Chemsitry, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | | | - K W M Siu
- 12University of Windsor, Windsor, Canada
| | - John G Marshall
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada.,13International Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (formerly CRP Sante Luxembourg), Strassen, Luxembourg
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Picó C, Serra F, Rodríguez AM, Keijer J, Palou A. Biomarkers of Nutrition and Health: New Tools for New Approaches. Nutrients 2019; 11:E1092. [PMID: 31100942 PMCID: PMC6567133 DOI: 10.3390/nu11051092] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 12/18/2022] Open
Abstract
A main challenge in nutritional studies is the valid and reliable assessment of food intake, as well as its effects on the body. Generally, food intake measurement is based on self-reported dietary intake questionnaires, which have inherent limitations. They can be overcome by the use of biomarkers, capable of objectively assessing food consumption without the bias of self-reported dietary assessment. Another major goal is to determine the biological effects of foods and their impact on health. Systems analysis of dynamic responses may help to identify biomarkers indicative of intake and effects on the body at the same time, possibly in relation to individuals' health/disease states. Such biomarkers could be used to quantify intake and validate intake questionnaires, analyse physiological or pathological responses to certain food components or diets, identify persons with specific dietary deficiency, provide information on inter-individual variations or help to formulate personalized dietary recommendations to achieve optimal health for particular phenotypes, currently referred as "precision nutrition." In this regard, holistic approaches using global analysis methods (omics approaches), capable of gathering high amounts of data, appear to be very useful to identify new biomarkers and to enhance our understanding of the role of food in health and disease.
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Affiliation(s)
- Catalina Picó
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics and Obesity), CIBER de Fisiopatología de la Obesidad y Nutrición (CIBERobn) and Instituto de Investigación Sanitaria Illes Balears (IdISBa), University of the Balearic Islands, ES-07122 Palma de Mallorca, Spain.
| | - Francisca Serra
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics and Obesity), CIBER de Fisiopatología de la Obesidad y Nutrición (CIBERobn) and Instituto de Investigación Sanitaria Illes Balears (IdISBa), University of the Balearic Islands, ES-07122 Palma de Mallorca, Spain.
| | - Ana María Rodríguez
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics and Obesity), CIBER de Fisiopatología de la Obesidad y Nutrición (CIBERobn) and Instituto de Investigación Sanitaria Illes Balears (IdISBa), University of the Balearic Islands, ES-07122 Palma de Mallorca, Spain.
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, PO Box 338, 6700 AH Wageningen, The Netherlands.
| | - Andreu Palou
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics and Obesity), CIBER de Fisiopatología de la Obesidad y Nutrición (CIBERobn) and Instituto de Investigación Sanitaria Illes Balears (IdISBa), University of the Balearic Islands, ES-07122 Palma de Mallorca, Spain.
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9
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Dufresne J, Bowden P, Thavarajah T, Florentinus-Mefailoski A, Chen ZZ, Tucholska M, Norzin T, Ho MT, Phan M, Mohamed N, Ravandi A, Stanton E, Slutsky AS, Dos Santos CC, Romaschin A, Marshall JC, Addison C, Malone S, Heyland D, Scheltens P, Killestein J, Teunissen CE, Diamandis EP, Michael Siu KW, Marshall JG. The plasma peptides of ovarian cancer. Clin Proteomics 2018; 15:41. [PMID: 30598658 PMCID: PMC6302491 DOI: 10.1186/s12014-018-9215-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/19/2018] [Indexed: 12/13/2022] Open
Abstract
Background It may be possible to discover new diagnostic or therapeutic peptides or proteins from blood plasma by using liquid chromatography and tandem mass spectrometry to identify, quantify and compare the peptides cleaved ex vivo from different clinical populations. The endogenous tryptic peptides of ovarian cancer plasma were compared to breast cancer and female cancer normal controls, other diseases with their matched or normal controls, plus ice cold plasma to control for pre-analytical variation. Methods The endogenous tryptic peptides or tryptic phospho peptides (i.e. without exogenous digestion) were analyzed from 200 μl of EDTA plasma. The plasma peptides were extracted by a step gradient of organic/water with differential centrifugation, dried, and collected over C18 for analytical HPLC nano electrospray ionization and tandem mass spectrometry (LC–ESI–MS/MS) with a linear quadrupole ion trap. The endogenous peptides of ovarian cancer were compared to multiple disease and normal samples from different institutions alongside ice cold controls. Peptides were randomly and independently sampled by LC–ESI–MS/MS. Precursor ions from peptides > E4 counts were identified by the SEQUEST and X!TANDEM algorithms, filtered in SQL Server, before testing of frequency counts by Chi Square (χ2), for analysis with the STRING algorithm, and comparison of precursor intensity by ANOVA in the R statistical system with the Tukey-Kramer Honestly Significant Difference (HSD) test. Results Peptides and/or phosphopeptides of common plasma proteins such as HPR, HP, HPX, and SERPINA1 showed increased observation frequency and/or precursor intensity in ovarian cancer. Many cellular proteins showed large changes in frequency by Chi Square (χ2 > 60, p < 0.0001) in the ovarian cancer samples such as ZNF91, ZNF254, F13A1, LOC102723511, ZNF253, QSER1, P4HA1, GPC6, LMNB2, PYGB, NBR1, CCNI2, LOC101930455, TRPM5, IGSF1, ITGB1, CHD6, SIRT1, NEFM, SKOR2, SUPT20HL1, PLCE1, CCDC148, CPSF3, MORN3, NMI, XTP11, LOC101927572, SMC5, SEMA6B, LOXL3, SEZ6L2, and DHCR24. The protein gene symbols with large Chi Square values were significantly enriched in proteins that showed a complex set of previously established functional and structural relationships by STRING analysis. Analysis of the frequently observed proteins by ANOVA confirmed increases in mean precursor intensity in ZFN91, TRPM5, SIRT1, CHD6, RIMS1, LOC101930455 (XP_005275896), CCDC37 and GIMAP4 between ovarian cancer versus normal female and other diseases or controls by the Tukey–Kramer HSD test. Conclusion Here we show that separation of endogenous peptides with a step gradient of organic/water and differential centrifugation followed by random and independent sampling by LC–ESI–MS/MS with analysis of peptide frequency and intensity by SQL Server and R revealed significant difference in the ex vivo cleavage of peptides between ovarian cancer and other clinical treatments. There was striking agreement between the proteins discovered from cancer plasma versus previous biomarkers discovered in tumors by genetic or biochemical methods. The results indicate that variation in plasma proteins from ovarian cancer may be directly discovered by LC–ESI–MS/MS that will be a powerful tool for clinical research. Electronic supplementary material The online version of this article (10.1186/s12014-018-9215-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jaimie Dufresne
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Pete Bowden
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Thanusi Thavarajah
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | | | - Zhuo Zhen Chen
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Monika Tucholska
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Tenzin Norzin
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Margaret Truc Ho
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Morla Phan
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Nargiz Mohamed
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Amir Ravandi
- 2Institute of Cardiovascular Sciences, St Boniface Hospital Research Center, University of Manitoba, Winnipeg, Canada
| | - Eric Stanton
- 3Division of Cardiology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Arthur S Slutsky
- 4Keenan Chair in Medicine, St. Michael's Hospital, University of Toronto, Toronto, Canada
| | - Claudia C Dos Santos
- 5Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada
| | - Alexander Romaschin
- 5Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada
| | - John C Marshall
- 5Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada
| | - Christina Addison
- 6Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Shawn Malone
- 6Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Daren Heyland
- 7Clinical Evaluation Research Unit, Kingston General Hospital, Kingston, Canada
| | - Philip Scheltens
- 8Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, The Netherlands
| | - Joep Killestein
- 9MS Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- 10Neurochemistry Lab and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - John G Marshall
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Ryerson University, Toronto, Canada.,13International Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (formerly CRP Sante Luxembourg), Strassen, Luxembourg.,14Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
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10
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Dufresne J, Bowden P, Thavarajah T, Florentinus-Mefailoski A, Chen ZZ, Tucholska M, Norzin T, Ho MT, Phan M, Mohamed N, Ravandi A, Stanton E, Slutsky AS, Dos Santos CC, Romaschin A, Marshall JC, Addison C, Malone S, Heyland D, Scheltens P, Killestein J, Teunissen C, Diamandis EP, Siu KWM, Marshall JG. The plasma peptidome. Clin Proteomics 2018; 15:39. [PMID: 30519149 PMCID: PMC6271647 DOI: 10.1186/s12014-018-9211-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/23/2018] [Indexed: 02/07/2023] Open
Abstract
Background It may be possible to discover new diagnostic or therapeutic peptides or proteins from blood plasma using LC–ESI–MS/MS to identify, with a linear quadrupole ion trap to identify, quantify and compare the statistical distributions of peptides cleaved ex vivo from plasma samples from different clinical populations. Methods A systematic method for the organic fractionation of plasma peptides was applied to identify and quantify the endogenous tryptic peptides from human plasma from multiple institutions by C18 HPLC followed nano electrospray ionization and tandem mass spectrometry (LC–ESI–MS/MS) with a linear quadrupole ion trap. The endogenous tryptic peptides, or tryptic phospho peptides (i.e. without exogenous digestion), were extracted in a mixture of organic solvent and water, dried and collected by preparative C18. The tryptic peptides from 6 institutions with 12 different disease and normal EDTA plasma populations, alongside ice cold controls for pre-analytical variation, were characterized by mass spectrometry. Each patient plasma was precipitated in 90% acetonitrile and the endogenous tryptic peptides extracted by a stepwise gradient of increasing water and then formic acid resulting in 10 sub-fractions. The fractionated peptides were manually collected over preparative C18 and injected for 1508 LC–ESI–MS/MS experiments analyzed in SQL Server R. Results Peptides that were cleaved in human plasma by a tryptic activity ex vivo provided convenient and sensitive access to most human proteins in plasma that show differences in the frequency or intensity of proteins observed across populations that may have clinical significance. Combination of step wise organic extraction of 200 μL of plasma with nano electrospray resulted in the confident identification and quantification ~ 14,000 gene symbols by X!TANDEM that is the largest number of blood proteins identified to date and shows that you can monitor the ex vivo proteolysis of most human proteins, including interleukins, from blood. A total of 15,968,550 MS/MS spectra ≥ E4 intensity counts were correlated by the SEQUEST and X!TANDEM algorithms to a federated library of 157,478 protein sequences that were filtered for best charge state (2+ or 3+) and peptide sequence in SQL Server resulting in 1,916,672 distinct best-fit peptide correlations for analysis with the R statistical system. SEQUEST identified some 140,054 protein accessions, or some ~ 26,000 gene symbols, proteins or loci, with at least 5 independent correlations. The X!TANDEM algorithm made at least 5 best fit correlations to more than 14,000 protein gene symbols with p-values and FDR corrected q-values of ~ 0.001 or less. Log10 peptide intensity values showed a Gaussian distribution from E8 to E4 arbitrary counts by quantile plot, and significant variation in average precursor intensity across the disease and controls treatments by ANOVA with means compared by the Tukey–Kramer test. STRING analysis of the top 2000 gene symbols showed a tight association of cellular proteins that were apparently present in the plasma as protein complexes with related cellular components, molecular functions and biological processes. Conclusions The random and independent sampling of pre-fractionated blood peptides by LC-ESI-MS/MS with SQL Server-R analysis revealed the largest plasma proteome to date and was a practical method to quantify and compare the frequency or log10 intensity of individual proteins cleaved ex vivo across populations of plasma samples from multiple clinical locations to discover treatment-specific variation using classical statistics suitable for clinical science. It was possible to identify and quantify nearly all human proteins from EDTA plasma and compare the results of thousands of LC–ESI–MS/MS experiments from multiple clinical populations using standard database methods in SQL Server and classical statistical strategies in the R data analysis system. Electronic supplementary material The online version of this article (10.1186/s12014-018-9211-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jaimie Dufresne
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St, Toronto, ON Canada
| | - Pete Bowden
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St, Toronto, ON Canada
| | - Thanusi Thavarajah
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St, Toronto, ON Canada
| | - Angelique Florentinus-Mefailoski
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St, Toronto, ON Canada
| | - Zhuo Zhen Chen
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St, Toronto, ON Canada
| | - Monika Tucholska
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St, Toronto, ON Canada
| | - Tenzin Norzin
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St, Toronto, ON Canada
| | - Margaret Truc Ho
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St, Toronto, ON Canada
| | - Morla Phan
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St, Toronto, ON Canada
| | - Nargiz Mohamed
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St, Toronto, ON Canada
| | - Amir Ravandi
- 2Institute of Cardiovascular Sciences, St Boniface Hospital Research Center, University of Manitoba, Winnipeg, Canada
| | - Eric Stanton
- 3Division of Cardiology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Arthur S Slutsky
- 4St. Michael's Hospital, Keenan Chair in Medicine, University of Toronto, Toronto, Canada
| | - Claudia C Dos Santos
- 5St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Alexander Romaschin
- 5St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - John C Marshall
- 5St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Christina Addison
- 6Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Shawn Malone
- 6Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Daren Heyland
- 7Clinical Evaluation Research Unit, Kingston General Hospital, Kingston, Canada
| | - Philip Scheltens
- 8Alzheimer Center, Department of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Joep Killestein
- 9MS Center, Department of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Charlotte Teunissen
- 10Neurochemistry Lab and Biobank, Department of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | | | - K W M Siu
- 12University of Windsor, Windsor, Canada
| | - John G Marshall
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St, Toronto, ON Canada.,13International Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (formerly CRP Sante Luxembourg), Strassen, Luxembourg
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11
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Dufresne J, Florentinus-Mefailoski A, Ajambo J, Ferwa A, Bowden P, Marshall J. Random and independent sampling of endogenous tryptic peptides from normal human EDTA plasma by liquid chromatography micro electrospray ionization and tandem mass spectrometry. Clin Proteomics 2017; 14:41. [PMID: 29234243 PMCID: PMC5721679 DOI: 10.1186/s12014-017-9176-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/26/2017] [Indexed: 12/12/2022] Open
Abstract
Background Normal human EDTA plasma samples were collected on ice, processed ice cold, and stored in a freezer at – 80 °C prior to experiments. Plasma test samples from the – 80 °C freezer were thawed on ice or intentionally warmed to room temperature. Methods Protein content was measured by CBBR binding and the release of alcohol soluble amines by the Cd ninhydrin assay. Plasma peptides released over time were collected over C18 for random and independent sampling by liquid chromatography micro electrospray ionization and tandem mass spectrometry (LC–ESI–MS/MS) and correlated with X!TANDEM. Results Fully tryptic peptides by X!TANDEM returned a similar set of proteins, but was more computationally efficient, than “no enzyme” correlations. Plasma samples maintained on ice, or ice with a cocktail of protease inhibitors, showed lower background amounts of plasma peptides compared to samples incubated at room temperature. Regression analysis indicated that warming plasma to room temperature, versus ice cold, resulted in a ~ twofold increase in the frequency of peptide identification over hours–days of incubation at room temperature. The type I error rate of the protein identification from the X!TANDEM algorithm combined was estimated to be low compared to a null model of computer generated random MS/MS spectra. Conclusion The peptides of human plasma were identified and quantified with low error rates by random and independent sampling that revealed 1000s of peptides from hundreds of human plasma proteins from endogenous tryptic peptides. Electronic supplementary material The online version of this article (10.1186/s12014-017-9176-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jaimie Dufresne
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | | | - Juliet Ajambo
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - Ammara Ferwa
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - Peter Bowden
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - John Marshall
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada.,Integrated BioBank of Luxembourg, 6 r. Nicolas-Ernest Barblé, Dudelange, 1210 Luxembourg
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12
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The proteins cleaved by endogenous tryptic proteases in normal EDTA plasma by C18 collection of peptides for liquid chromatography micro electrospray ionization and tandem mass spectrometry. Clin Proteomics 2017; 14:39. [PMID: 29213220 PMCID: PMC5712186 DOI: 10.1186/s12014-017-9174-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/21/2017] [Indexed: 02/08/2023] Open
Abstract
The tryptic peptides from ice cold versus room temperature plasma were identified by C18 liquid chromatography and micro electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS). Samples collected on ice showed low levels of endogenous tryptic peptides compared to the same samples incubated at room temperature. Plasma on ice contained peptides from albumin, complement, and apolipoproteins and others that were observed by the X!TANDEM and SEQUEST algorithms. In contrast to ice cold samples, after incubation at room temperature, greater numbers of tryptic peptides from well characterized plasma proteins, and from cellular proteins were observed. A total of 583,927 precursor ions and MS/MS spectra were correlated to 94,669 best fit peptides that reduced to 22,287 correlations to the best accession within a gene symbol and to 7174 correlations to at least 510 gene symbols with ≥ 5 independent MS/MS correlations (peptide counts) that showed FDR q-values ranging from E−9 (i.e. FDR = 0.000000001) to E−227. A set of 528 gene symbols identified by X!TANDEM and SEQUEST including C4B showed ≥ fivefold variation between ice cold versus room temperature incubation. STRING analysis of the protein gene symbols observed from endogenous peptides in normal plasma revealed an extensive protein-interaction network of cellular factors associated with cell signalling and regulation, the formation of membrane bound organelles, cellular exosomes and exocytosis network proteins. Taken together the results indicated that a pool of cellular proteins, or protein complexes, in plasma are apparently not stable and degrade soon after incubation at room temperature.
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13
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Streng AS, de Boer D, van Doorn WP, Kocken JM, Bekers O, Wodzig WK. Cardiac troponin T degradation in serum is catalysed by human thrombin. Biochem Biophys Res Commun 2016; 481:165-168. [DOI: 10.1016/j.bbrc.2016.10.149] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 10/31/2016] [Indexed: 12/21/2022]
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14
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Florentinus-Mefailoski A, Soosaipillai A, Dufresne J, Diamandis EP, Marshall JG. An enzyme-linked immuno-mass spectrometric assay with the substrate adenosine monophosphate. Anal Bioanal Chem 2014; 407:1119-30. [PMID: 25519722 DOI: 10.1007/s00216-014-8323-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/29/2014] [Accepted: 11/05/2014] [Indexed: 01/22/2023]
Abstract
An enzyme-linked immuno-mass spectrometric assay (ELIMSA) with the specific detection probe streptavidin conjugated to alkaline phosphatase catalyzed the production of adenosine from the substrate adenosine monophosphate (AMP) for sensitive quantification of prostate-specific antigen (PSA) by mass spectrometry. Adenosine ionized efficiently and was measured to the femtomole range by dilution and direct analysis with micro-liquid chromatography, electrospray ionization, and mass spectrometry (LC-ESI-MS). The LC-ESI-MS assay for adenosine production was shown to be linear and accurate using internal (13)C(15)N adenosine isotope dilution, internal (13)C(15)N adenosine one-point calibration, and external adenosine standard curves with close agreement. The detection limits of LC-ESI-MS for alkaline phosphatase-streptavidin (AP-SA, ∼190,000 Da) was tested by injecting 0.1 μl of a 1 pg/ml solution, i.e., 100 attograms or 526 yoctomole (5.26E-22) of the alkaline-phosphatase labeled probe on column (about 315 AP-SA molecules). The ELIMSA for PSA was linear and showed strong signals across the picogram per milliliter range and could robustly detect PSA from all of the prostatectomy patients and all of the female plasma samples that ranged as low as 70 pg/ml with strong signals well separated from the background and well within the limit of quantification of the AP-SA probe. The results of the ELIMSA assay for PSA are normal and homogenous when independently replicated with a fresh standard over multiple days, and intra and inter diem assay variation was less than 10 % of the mean. In a blind comparison, ELIMSA showed excellent agreement with, but was more sensitive than, the present gold standard commercial fluorescent ELISA, or ECL-based detection, of PSA from normal and prostatectomy samples, respectively.
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15
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Bilousova T, Taylor K, Emirzian A, Gylys R, Frautschy SA, Cole GM, Teng E. Parallel age-associated changes in brain and plasma neuronal pentraxin receptor levels in a transgenic APP/PS1 rat model of Alzheimer's disease. Neurobiol Dis 2014; 74:32-40. [PMID: 25449907 DOI: 10.1016/j.nbd.2014.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/31/2014] [Accepted: 11/04/2014] [Indexed: 11/26/2022] Open
Abstract
Neuronal pentraxin receptor (NPR) is a synaptic protein implicated in AMPA receptor trafficking at excitatory synapses. Since glutamate neurotransmission is disrupted in Alzheimer's disease (AD), NPR levels measured from plasma represent a potential biomarker for synaptic dysfunction associated with AD. We sought to determine the relationship between AD pathology and brain and plasma NPR levels by examining age-associated NPR levels in these compartments in a transgenic APP/PS1 rat model of AD. NPR levels in cortical homogenate were similar in wild-type (Wt) and APP/PS1 rats at 3 months of age (prior to Aβ plaque deposition), but significantly increased in APP/PS1 rats by 9 and 18-20 months of age (after the onset of plaque deposition). These age-dependent differences were driven by proportional increases in NPR in membrane-associated cortical fractions. Genotype-related differences in NPR expression were also seen in the hippocampus, which exhibits significant Aβ pathology, but not in the cerebellum, which does not. Plasma analyses revealed increased levels of a 26 kDa NPR fragment in APP/PS1 rats relative to Wt rats by 18-20 months of age, which correlated with the levels of full-length NPR in cortex. Our findings indicate that cerebral accumulation of NPR and Aβ occurs with similar temporal and regional patterns in the APP/PS1 model, and suggest that a 26 kDa plasma NPR fragment may represent a peripheral biomarker of this process.
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Affiliation(s)
- Tina Bilousova
- Department of Neurology, David Geffen School of Medicine, at UCLA, Los Angeles, CA, United States; Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, United States
| | - Karen Taylor
- Department of Neurology, David Geffen School of Medicine, at UCLA, Los Angeles, CA, United States; Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, United States
| | - Ana Emirzian
- Department of Neurology, David Geffen School of Medicine, at UCLA, Los Angeles, CA, United States
| | - Raymond Gylys
- Department of Neurology, David Geffen School of Medicine, at UCLA, Los Angeles, CA, United States
| | - Sally A Frautschy
- Department of Neurology, David Geffen School of Medicine, at UCLA, Los Angeles, CA, United States; Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, United States
| | - Gregory M Cole
- Department of Neurology, David Geffen School of Medicine, at UCLA, Los Angeles, CA, United States; Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, United States
| | - Edmond Teng
- Department of Neurology, David Geffen School of Medicine, at UCLA, Los Angeles, CA, United States; Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, United States.
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16
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Florentinus-Mefailoski A, Marshall JG. Pyridoxamine-5-phosphate enzyme-linked immune mass spectrometric assay substrate for linear absolute quantification of alkaline phosphatase to the yoctomole range applied to prostate specific antigen. Anal Chem 2014; 86:10684-91. [PMID: 25259405 DOI: 10.1021/ac502572a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is a need to measure proteins that are present in concentrations below the detection limits of existing colorimetric approaches with enzyme-linked immunoabsorbent assays (ELISA). The powerful enzyme alkaline phosphatase conjugated to the highly specific bacterial protein streptavidin binds to biotinylated macromolecules like proteins, antibodies, or other ligands and receptors with a high affinity. The binding of the biotinylated detection antibody, with resulting amplification of the signal by the catalytic production of reporter molecules, is key to the sensitivity of ELISA. The specificity and amplification of the signal by the enzyme alkaline phosphatase in ELISA together with the sensitivity of liquid chromatography electrospray ionization and mass spectrometry (LC-ESI-MS) to detect femtomole to picomole amounts of reporter molecules results in an ultrasensitive enzyme-linked immune mass spectrometric assay (ELIMSA). The novel ELIMSA substrate pyridoxamine-5-phosphate (PA5P) is cleaved by the enzyme alkaline phosphatase to yield the basic and hydrophilic product pyridoxamine (PA) that elutes rapidly with symmetrical peaks and a flat baseline. Pyridoxamine (PA) and (13)C PA were both observed to show a linear relationship between log ion intensity and quantity from picomole to femtomole amounts by liquid chromatography-electrospray ionization and mass spectrometry. Four independent methods, (i) internal (13)C isotope PA dilution curves, (ii) internal (13)C isotope one-point calibration, (iii) external PA standard curve, and (iv) external (13)C PA standard curve, all agreed within 1 digit in the same order of magnitude on the linear quantification of PA. Hence, a mass spectrometer can be used to robustly detect 526 ymol of the alkaline phosphatase streptavidin probe and accurately quantify zeptomole amounts of PSA against log linear absolute standard by micro electrospray on a simple ion trap.
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