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2018

2024

 

Qasrawi DO, Al-Ghabkari A, Khan RM, Petrotchenko EV, Montero-Odasso M, Borchers CH.

A Simplified Proteomics LC-MRM-MS Assay for Determination of apoE Genotypes in Plasma Samples.

J Proteome Res. 2024 Feb 27. DOI: 10.1021/acs.jproteome.3c00557. Online ahead of print.

PMID: 38412507

Luo V, Shen C, Worme S, Bhagrath A, Simo-Cheyou E, Findlay S, Hebert S, Poon W, Aryanpour Z, Zhang T, Zahedi R, Boulais J, Buchwald Z, Borchers CH, Cote J, Kleinman C, Mandl J, Orthwein A.

The Deubiquitylase Otub1 Regulates the Chemotactic Response of Splenic B Cells by Modulating the Stability of the γ-Subunit Gng2

Molecular and Cellular Biology 2024 Jan 29; 44:1, 1-16, DOI: 10.1080/10985549.2023.2290434

Mohammed Y, Tran K, Carlsten C, Ryerson C, Wong A, Lee T, Cheng MP, Vinh DC, Lee TC, Winston BW, Sweet D, Boyd JH, Walley KR, Haljan G, McGeer A, Lamontagne F, Fowler R, Maslove D, Singer J, Patrick DM, Marshall JC, Murthy S, Jain F, Borchers CH, Goodlett DR, Levin A, Russell JA; ARBs CORONA I Consortium.

Proteomic Evolution from Acute to Post-COVID-19 Conditions. 

J Proteome Res. 2024 Jan 5;23(1):52-70. DOI: 10.1021/acs.jproteome.3c00324.

PMID: 38048423 Free PMC article.

Sobsey CA, Mady N, Richard VR, LeBlanc A, Zakharov T, Borchers CH, Jagoe RT.

Measurement of CYP1A2 and CYP3A4 activity by a simplified Geneva cocktail approach in a cohort of free-living individuals: a pilot study.

Front Pharmacol. 2024 Feb 2;15:1232595. DOI: 10.3389/fphar.2024.1232595. eCollection 2024.

PMID: 38370474 Free PMC article.

Michaud SA, Pětrošová H, Sinclair NJ, Kinnear AL, Jackson AM, McGuire JC, Hardie DB, Bhowmick P, Ganguly M, Flenniken AM, Nutter LMJ, McKerlie C, Smith D, Mohammed Y, Schibli D, Sickmann A, Borchers CH.

Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues.

Commun Biol. 2024 Jan 2;7(1):6. DOI: 10.1038/s42003-023-05687-0.

PMID: 38168632

2023

Zhang A, Xia Y, Lin J, Chu K, Wang W, Ruiter T, Yang, J, Chen N, Chhuor J, Patil S, Cen H, Rideout E, Richard VR, Schaeffer D, Zahedi R, Borchers CH, Johnson J, Kopp J.

Hyperinsulinemia acts via acinar insulin receptors to initiate pancreatic cancer by increasing digestive enzyme production and inflammation

Cell Metabolism. 2023 Oct 31; ISSN 1550-4131, DOI: https://doi.org/10.1016/j.cmet.2023.10.003.

Wang K, Khoramjoo M, Srinivasan K, Gordon P, Mandal R, Jackson D, Sligl W, Grant M, Penninger J, Borchers CH, Wishart D, Prasad V, Oudit G.

Sequential multi-omics analysis identifies clinical phenotypes and predictive biomarkers for long COVID.

Cell Reports Medicine. 2023 Oct 26. DOI: https://doi.org/10.1016/j.xcrm.2023.101254.

Wakid M, Almeida D, Aouabed Z, Rahimian R, Davoli MA, Yerko V, Leonova-Erko E, Richard V, Zahedi R, Borchers CH, Turecki G, Mechawar N.

Universal method for the isolation of microvessels from frozen brain tissue: A proof-of-concept multiomic investigation of the neurovasculature.

Brain Behav Immun Health. 2023 Sep 21;34:100684. doi: 10.1016/j.bbih.2023.100684. eCollection 2023 Dec.

PMID: 37822873 Free PMC article.

Sultana M, Camicioli R, Dixon RA, Whitehead S, Pieruccini-Faria F, Petrotchenko E, Speechley M, Borchers CH, Montero-Odasso M.

A Metabolomics Analysis of a Novel Phenotype of Older Adults at Higher Risk of Dementia.

J Alzheimers Dis. 2023 Sep 28. doi: 10.3233/JAD-230683. Online ahead of print.

PMID: 37781807

Castillo-Castrejon M, Sankofi BM, Murguia SJ, Udeme AA, Cen HH, Xia YH, Thomas NS, Berry WL, Jones KL, Richard VR, Zahedi RP, Borchers CH, Johnson JD, Wellberg EA.

FGF1 supports glycolytic metabolism through the estrogen receptor in endocrine-resistant and obesity-associated breast cancer.

Breast Cancer Res. 2023 Aug 22;25(1):99. doi: 10.1186/s13058-023-01699-0.

PMID: 37608351 Free PMC article.

Shahid I, Han J, Hanook S, Borchers CH, El Enshasy HA, Mehnaz S.

Genome mining of Pseudomonas spp. hints towards the production of under-pitched secondary metabolites.

3 Biotech. 2023 Jun;13(6):182. doi: 10.1007/s13205-023-03607-x. Epub 2023 May 12.

PMID: 37193329

Preston SEJ, Richard VR, Del Rincón SV, Borchers CH, Zahedi RP.

Proteomic Assessment of the Murine Mammary Gland Extracellular Matrix.

Methods Mol Biol. 2023;2614:261-271. doi: 10.1007/978-1-0716-2914-7_16.

PMID: 36587130

Mohammed Y, Goodlett D, Borchers CH.

Absolute Quantitative Targeted Proteomics Assays for Plasma Proteins.

Methods Mol Biol. 2023;2628:439-473. doi: 10.1007/978-1-0716-2978-9_27.

PMID: 36781801

Petrotchenko EV, Nascimento EM, Witt JM, Borchers CH.

Determination of Protein Monoclonal-Antibody Epitopes by a Combination of Structural Proteomics Methods.

J Proteome Res. 2023 Sep 1;22(9):3096-3102. doi: 10.1021/acs.jproteome.3c00159. Epub 2023 Aug 1.

PMID: 37526474 Free PMC article.


Mohammed Y, Goodlett D, Borchers CH.

Bioinformatics Tools and Knowledgebases to Assist Generating Targeted Assays for Plasma Proteomics.

Methods Mol Biol. 2023;2628:557-577. doi: 10.1007/978-1-0716-2978-9_32.

PMID: 36781806

Yerra VG, Batchu SN, Kaur H, Kabir MDG, Liu Y, Advani SL, Tran DT, Sadeghian S, Sedrak P, Billia F, Kuzmanov U, Gramolini AO, Qasrawi DO, Petrotchenko EV, Borchers CH, Connelly KA, Advani A.

Pressure overload induces ISG15 to facilitate adverse ventricular remodeling and promote heart failure.

J Clin Invest. 2023 May 1;133(9):e161453. doi: 10.1172/JCI161453.

PMID: 37115698 Free PMC article.

Prabhu SA, Moussa O, Gonçalves C, LaPierre JH, Chou H, Huang F, Richard VR, Ferruzo PYM, Guettler EM, Soria-Bretones I, Kirby L, Gagnon N, Su J, Silvester J, Krisna SS, Rose AAN, Sheppard KE, Cescon DW, Mallette FA, Zahedi RP, Borchers CH, Del Rincon SV, Miller WH.

Inhibition of the MNK1/2-eIF4E Axis Augments Palbociclib-Mediated Antitumor Activity in Melanoma and Breast Cancer.

Mol Cancer Ther. 2023 Feb 1;22(2):192-204. doi: 10.1158/1535-7163.MCT-22-0092.

PMID: 36722142

Castillo-Castrejon M, Sankofi BM, Murguia SJ, Udeme AA, Cen HH, Xia YH, Thomas NS, Berry WL, Jones KL, Richard VR, Zahedi RP, Borchers CH, Johnson JD, Wellberg EA.

FGF1 supports glycolytic metabolism through the estrogen receptor in endocrine-resistant and obesity-associated breast cancer.

Breast Cancer Res. 2023 Aug 22;25(1):99. doi: 10.1186/s13058-023-01699-0.

PMID: 37608351 Free PMC article.

Sultana M, Camicioli R, Dixon RA, Whitehead S, Pieruccini-Faria F, Petrotchenko E, Speechley M, Borchers CH, Montero-Odasso M.

A Metabolomics Analysis of a Novel Phenotype of Older Adults at Higher Risk of Dementia.

J Alzheimers Dis. 2023 Sep 28. doi: 10.3233/JAD-230683. Online ahead of print.

PMID: 37781807

Mitsa G, Richard VR, Majedi Y, Lafleur J, Aguilar-Mahecha A, Basik M, Borchers CH.

Evaluation of a 'plug and play' nanoflow liquid chromatography system for MS-based proteomic characterization of clinical FFPE specimens.

Expert Rev Proteomics. 2023 Apr-Jun;20(4-6):87-92. doi: 10.1080/14789450.2023.2219844. Epub 2023 Jun 13.

PMID: 37309581

Reboucas P, Fillebeen C, Botta A, Cleverdon R, Steele AP, Richard V, Zahedi RP, Borchers CH, Burelle Y, Hawke TJ, Pantopoulos K, Sweeney G.

Discovery-Based Proteomics Identify Skeletal Muscle Mitochondrial Alterations as an Early Metabolic Defect in a Mouse Model of β-Thalassemia.

Int J Mol Sci. 2023 Feb 23;24(5):4402. doi: 10.3390/ijms24054402.

PMID: 36901833 Free PMC article.

Gaither C, Popp R, Richard VR, Zahedi RP, Borchers CH.

Offline Peptide Fractionation and Parallel Reaction Monitoring MS for the Quantitation of Low-Abundance Plasma Proteins.

Methods Mol Biol. 2023;2628:353-364. doi: 10.1007/978-1-0716-2978-9_23.

PMID: 36781797

Qasrawi DO, Petrotchenko EV, Borchers CH.

Amino acid analysis for peptide quantitation using reversed-phase liquid chromatography combined with multiple reaction monitoring mass spectrometry. Anal Bioanal Chem. 2023 Sep;415(22):5261-5267. doi: 10.1007/s00216-023-04840-2. Epub 2023 Jul 19.

PMID: 37468754 Free PMC article.

Wakid M, Almeida D, Aouabed Z, Rahimian R, Davoli MA, Yerko V, Leonova-Erko E, Richard VR, Zahedi R, Borchers C, Turecki G, Mechawar N.

Universal method for the isolation of microvessels from frozen brain tissue: A proof-of-concept multiomic investigation of the neurovasculature

Brain, Behavior, & Immunity - Health 34 (2023). https://doi.org/10.1016/j.bbih.2023.100684

Castillo-Castrejon, M., Sankofi, B.M., Murguia, Richard VRBorchers CH et al.

FGF1 supports glycolytic metabolism through the estrogen receptor in endocrine-resistant and obesity-associated breast cancer

Breast Cancer Res 25, 99 (2023). https://doi.org/10.1186/s13058-023-01699-0

Petrotchenko EV, Nascimento E, Witt J, Borchers CH.

Determination of Protein Monoclonal–Antibody Epitopes by a Combination of Structural Proteomics Methods 

Journal of Proteome Research Article ASAP (2023). doi: 10.1021/acs.jproteome.3c00159

Mitsa G, Richard R, Majedi Y, Lafeleur J, Aguilar-Maheca A, Basik M, Borchers CH.

Evaluation of a ‘plug and play’ nanoflow liquid chromatography system for MS-based proteomic characterization of clinical FFPE specimens.

Expert Review of Proteomics (2023). doi: 10.1080/14789450.2023.2219844.

Shahid I, Han J, Hanook S, Borchers CH, Enshasy H, Mehnaz S.

Genome mining of Pseudomonas spp. hints towards the production of under-pitched secondary metabolites.

3 Biotech 13, 182 (2023). https://doi.org/10.1007/s13205-023-03607-x.

Yerra GV, Batchu SN, Kaur, H, Kabir MD, Liu Youan, Adva ni S, Tran D, Sadeghian S, Sedrak P, Bilia F, Kuzmanov U, Gramolini A, Qasrawi D, Petrotchenko EV, Borchers CH, Connelly K, Advani A.

Pressure overload induces ISG15 to facilitate adverse ventricular remodeling and promote heart failure.

J Clin Invest. 2023 May; 133(9): e161453; doi: 10.1172/JCI161453.

PMID: 37115698

Reboucas P, Fillebeen C, Botta A, Cleverdon R, Steele AP, Richard VR, Zahede RP, Borchers CH, Burelle Y, Hawkes TJ, Pantopoulos K, Sweeney G.

Discovery-Based Proteomics Identify Skeletal Muscle Mitochondrial Alterations as an Early Metabolic Defect in a Mouse Model of β-Thalassemia

Int. J. Mol. Sci. 2023 Feb 23, 24(5), 4402; https://doi.org/10.3390/ijms24054402.

Mohammed Y, Goodlett D, Borchers CH.

Bioinformatics Tools and Knowledgebases to Assist Generating Targeted Assays for Plasma Proteomics

Methods Mol Biol. 2023 Feb 12; 2628: 557-577. doi: 10.1007/978-1-0716-2978-9_32.

PMID: 36781806

Mohammed Y, Goodlett D, Borchers CH.

Absolute Quantitative Targeted Proteomics Assays for Plasma Proteins

Methods Mol Biol. 2023 Feb 12; 2628: 439-473. doi: 10.1007/978-1-0716-2978-9_27.

PMID: 36781801

Prabhu SA, Moussa O, Gonçalves C, LaPierre JH, Chou H, Huang F, Richard VR, Ferruzo PYM, Guettler EM, Soria-Bretones I, Kirby L, Gagnon N, Su J, Silvester J, Krisna SS, Rose AAN, Sheppard KE, Cescon DW, Mallette FA, Zahedi RP, Borchers CH, Del Rincon SV, Miller WH.

Inhibition of the MNK1/2-eIF4E Axis Augments Palbociclib-Mediated Antitumor Activity in Melanoma and Breast Cancer

Mol Cancer Ther, 2023 Feb 1;22(2):192-204. doi: 10.1158/1535-7163.MCT-22-0092.

PMID: 36722142

Preston SEJ, Richard VR, Del Rincón SV, Borchers CH, Zahedi RP.

Proteomic Assessment of the Murine Mammary Gland Extracellular Matrix.

Methods Mol Biol, 2023;2614:261-271. doi: 10.1007/978-1-0716-2914-7_16.

PMID: 36587130

2022

Sobsey CA, Froehlich B, Batist G, Borchers CH.

Immuno-MALDI-MS for Accurate Quantitation of Targeted Peptides from

Volume-Restricted Samples.

In: Methods in Molecular Biology, 2515: 203-225 (2022).

Parra ALC, Freitas CDT, Souza PFN, von Aderkas P, Borchers CH, Beattie GA, Silva FDA, Thornburg RW.

Ornamental tobacco floral nectar is a rich source of antimicrobial peptides.

Plant Sci, 2022 Nov;324:111427. doi: 10.1016/j.plantsci.2022.111427. Epub 2022 Aug 23.

PMID: 36007629

Richard VR, Gaither C, Popp R, Chaplygina D, Brzhozovskiy A, Kononikhin A, Mohammed Y, Zahedi RP, Nikolaev EN, Borchers CH.

Early Prediction of COVID-19 Patient Survival by Targeted Plasma Multi-Omics and Machine Learning.

Mol Cell Proteomics, 2022 Oct;21(10):100277. doi: 10.1016/j.mcpro.2022.100277. Epub 2022 Aug 3.

PMID: 35931319

Smith-Byrne K, Cerani A, Guida F, Zhou S, Agudo A, Aleksandrova K, Barricarte A, Rodríguez-Barranco M, Borchers CH, Gram IT, Han J, Amos CI, Hung RJ, Grankvist K, Nøst TH, Imaz L, Chirlaque-López MD, Johansson M, Kaaks R, Kühn T, Martin RM, McKay JD, Pala V, Robbins HA, Sandanger TM, Schibli D, Schulze MB, Travis RC, Vineis P, Weiderpass E, Brennan P, Johansson M, Richards JB.

Circulating Isovalerylcarnitine and Lung Cancer Risk: Evidence from Mendelian Randomization and Pre-Diagnostic Blood Measurements.

Cancer Epidemiol Biomarkers Prev, 2022 Jul 15:EPI-21-1033. doi: 10.1158/1055-9965.EPI-21-1033. Online ahead of print.

PMID: 35839461

Preston SEJ, Bartish M, Richard VR, Aghigh A, Gonçalves C, Smith-Voudouris J, Huang F, Thebault P, Cleret-Buhot A, Lapointe R, Légaré F, Postovit LM, Zahedi RP, Borchers CH, Miller WH Jr, Del Rincón SV.
Phosphorylation of eIF4E in the stroma drives the production and spatial organisation of collagen type I in the mammary gland.

Matrix Biol, 2022 Jul 13:S0945-053X(22)00092-0. doi: 10.1016/j.matbio.2022.07.003. Online ahead of print.

PMID: 35842012

Pastushkova LK, Goncharov IN, Koloteva MI, Goncharova AG, Kashirina DN, Nosovsky AM, Glebova TM, Kononikhin AS, Borchers CH, Nikolaev EN, Larina IM.

Characteristics of blood plasma proteome changes associated with the hemorrhagic purpura of cosmonauts on the first day after long-term space missions.

Life Sci Space Res (Amst), 2022 May;33:7-12. doi: 10.1016/j.lssr.2022.01.001. Epub 2022 Jan 14.

PMID: 35491032

Mitsa G, Guo Q, Goncalves C, Preston SEJ, Lacasse V, Aguilar-Mahecha A, Benlimame N, Basik M, Spatz A, Batist G, Miller WH Jr, Del Rincon SV, Zahedi RP, Borchers CH.

A Non-Hazardous Deparaffinization Protocol Enables Quantitative Proteomics of Core Needle Biopsy-Sized Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Specimens.

Int J Mol Sci, 2022 Apr 18;23(8):4443. doi: 10.3390/ijms23084443.

PMID: 35457260

Laselva O, Petrotchenko EV, Hamilton CM, Qureshi Z, Borchers CH, Young RN, Bear CE.

A protocol for identifying the binding sites of small molecules on the cystic fibrosis transmembrane conductance regulator (CFTR) protein.

STAR Protoc, 2022 Apr 7;3(2):101258. doi: 10.1016/j.xpro.2022.101258. eCollection 2022 Jun 17.

PMID: 35434660

Mohammed Y, Touw CE, Nemeth B, van Adrichem RA, Borchers CH, Rosendaal FR, van Vlijmen BJ, Cannegieter SC.

Targeted proteomics for evaluating risk of venous thrombosis following traumatic lower-leg injury or knee arthroscopy.

J Thromb Haemost, 2022 Mar;20(3):684-699. doi: 10.1111/jth.15623. Epub 2022 Jan 6.

PMID: 34919779

Gaither C, Popp R, Zahedi RP, Borchers CH.

Multiple reaction monitoring-mass spectrometry enables robust quantitation of plasma proteins regardless of whole blood processing delays that may occur in the clinic.

Mol Cell Proteomics, 2022 May;21(5):100212. doi: 10.1016/j.mcpro.2022.100212. Epub 2022 Feb 17.

PMID: 35182769

Jennings MJ, Kagiava A, Vendredy L, Spaulding EL, Stavrou M, Hathazi D, Grüneboom A, De Winter V, Gess B, Schara U, Pogoryelova O, Lochmüller H, Borchers CH, Roos A, Burgess RW, Timmerman V, Kleopa KA, Horvath R.

NCAM1 and GDF15 are biomarkers of Charcot-Marie-Tooth disease in patients and mice.

Brain, 2022 Nov 21;145(11):3999-4015. doi: 10.1093/brain/awac055.

PMID: 35148379

Brzhozovskiy A, Kononikhin A, Bugrova AE, Kovalev GI, Schmit PO, Kruppa G, Nikolaev EN, Borchers CH.

The Parallel Reaction Monitoring-Parallel Accumulation-Serial Fragmentation (prm-PASEF) Approach for Multiplexed Absolute Quantitation of Proteins in Human Plasma.

Anal Chem, 2022 Jan 18. doi: 10.1021/acs.analchem.1c03782. Online ahead of print.

PMID: 35040635

Petrotchenko EV, Borchers CH.

Protein Chemistry Combined with Mass Spectrometry for Protein Structure Determination.

Chem Rev, 2022 Apr 27;122(8):7488-7499. doi: 10.1021/acs.chemrev.1c00302. Epub 2021 Dec 30.

PMID: 34968047

2021

Percy AJ, Borchers CH.

Detailed Method for Performing the ExSTA Approach in Quantitative Bottom-

up Plasma Proteomics.

In: Methods in Molecular Biology, 2228: 353-384 (2021).

Gaspar VP, Ibrahim S, Zahedi RP, Borchers CH.

Utility, Promise, and Limitations of LC-MS based Therapeutic Drug Monitoring in Precision Medicine.

Journal of Mass Spectrometry, 2021 Nov;56(11):e4788. doi: 10.1002/jms.4788. Epub 2021 Nov 4.

PMID: 34738286 

Review

Froehlich BC, Popp R, Sobsey CA, Ibrahim S, LeBlanc A, Mohammed Y, Buchanan M, Aguilar-Mahecha A, Pötz O, Chen MX, Spatz A, Basik M, Batist G, Zahedi RP, Borchers CH.

A multiplexed, automated immuno-matrix assisted laser desorption/ionization mass spectrometry assay for simultaneous and precise quantitation of PTEN and p110α in cell lines and tumor tissues.

Analyst, 2021 Oct 25, 146, 6566-6575 doi: 10.1039/d1an00165e. Epub 2021 Sep 29.

PMID: 34585690

Serpa JJ, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH.
Structure of prion β-oligomers as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations.

Proteomics, 2021 Sep 5:e2000298. doi: 10.1002/pmic.202000298. Online ahead of print.

PMID: 34482645

Ibrahim S, Lan C, Chabot C, Mitsa G, Buchanan M, Aguilar-Mahecha A, Elchebly M, Poetz O, Spatz A, Basik M, Batist G, Zahedi RP, Borchers CH.

Precise Quantitation of PTEN by Immuno-MRM: A Tool to Resolve the Breast Cancer Biomarker Controversy.

Anal Chem, 2021 Aug 10;93(31):10816-10824. doi: 10.1021/acs.analchem.1c00975. Epub 2021 Jul 29.

PMID: 34324311

Gaither C, Popp R, Borchers SP, Skarphedinsson K, Eiriksson FF, Thorsteinsdóttir M, Mohammed YBorchers CH.

Performance Assessment of a 125 Human Plasma Peptide Mixture Stored at Room Temperature for Multiple Reaction Monitoring-Mass Spectrometry.

J Proteome Res, 2021 Sep 3;20(9):4292-4302. doi: 10.1021/acs.jproteome.1c00249. Epub 2021 Jul 16.

PMID: 34270269

Skinnider MA, Rogalski J, Tigchelaar S, Manouchehri N, Prudova A, Jackson AM, Nielsen K, Jeong J, Chaudhary S, Shortt K, Gallagher-Kurtzke Y, So K, Fong A, Gupta R, Okon EB, Rizzuto MA, Dong K, Streijger F, Belanger L, Ritchie L, Tsang A, Christie S, Mac-Thiong JM, Bailey C, Ailon T, Charest-Morin R, Dea N, Wilson JR, Dhall S, Paquette S, Street J, Fisher CG, Dvorak MF, Shannon C, Borchers C, Balshaw R, Foster LJ, Kwon BK.

Proteomics portraits reveal evolutionarily conserved and divergent responses to spinal cord injury.

Mol Cell Proteomics, 2021 Jun 12:100096. doi: 10.1016/j.mcpro.2021.100096. Online ahead of print.

PMID: 34129941 

Tran JN, Günther OP, Sherwood KR, Fenninger F, Allan LL, Lan J, Sapir-Pichhadze R, Duquesnoy R, Claas F, Marsh SGE, McMaster WR, Keown PA; Genome Canada Transplant Consortium.

High-throughput sequencing defines donor and recipient HLA B-cell epitope frequencies for prospective matching in transplantation.

Commun Biol, 2021 May 14;4(1):583. doi: 10.1038/s42003-021-01989-3.

PMID: 33990681

Laselva O, Qureshi Z, Zeng ZW, Petrotchenko EV, Ramjeesingh M, Hamilton CM, Huan LJ, Borchers CH, Pomès R, Young R, Bear CE.

Identification of binding sites for ivacaftor on the cystic fibrosis transmembrane conductance regulator.

iScience, 2021 May 15;24(6):102542. doi: 10.1016/j.isci.2021.102542. eCollection 2021 Jun 25.

PMID: 34142049

Mohammed Y, Michaud SA, Pětrošová H, Yang J, Ganguly M, Schibli D, Flenniken AM, Nutter LMJ, Adissu HA, Lloyd KCK, McKerlie C, Borchers CH.

Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma.

NPJ Syst Biol Appl, 2021 May 28;7(1):25. doi: 10.1038/s41540-021-00184-8.

PMID: 34050187

Li FKK, Gale RT, Petrotchenko EV, Borchers CH, Brown ED, Strynadka NCJ.

Crystallographic analysis of TarI and TarJ, a cytidylyltransferase and reductase pair for CDP-ribitol synthesis in Staphylococcus aureus wall teichoic acid biogenesis.

J Struct Biol, 2021 Jun;213(2):107733. doi: 10.1016/j.jsb.2021.107733. Epub 2021 Apr 2.

PMID: 33819634

Bhowmick P, Roome S, Borchers CH, Goodlett DR, Mohammed Y.

An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community.

Proteome Res, 2021 Apr 2;20(4):2105-2115. doi: 10.1021/acs.jproteome.0c00961. Epub 2021 Mar 8.

PMID: 33683131

Mohammed Y, Bhowmick P, Michaud SA, Sickmann A, Borchers CH.

Mouse Quantitative Proteomics Knowledgebase: reference protein concentration ranges in 20 mouse tissues using 5000 quantitative proteomics assays.

Bioinformatics, 2021 Jan 23:btab018. doi: 10.1093/bioinformatics/btab018. Online ahead of print.

PMID: 33483739

Shahid I, Han J, Hardie D, Baig DN, Malik KA, Borchers CH, Mehnaz S.

Profiling of antimicrobial metabolites of plant growth promoting Pseudomonas spp. isolated from different plant hosts.

3 Biotech, 2021 Feb;11(2):48. doi: 10.1007/s13205-020-02585-8. Epub 2021 Jan 11.

PMID: 33489669

Michaud SA, Pětrošová H, Jackson AM, McGuire JC, Sinclair NJ, Ganguly M, Flenniken AM, Nutter LMJ, McKerlie C, Schibli D, Smith D, Borchers CH.

Process and Workflow for Preparation of Disparate Mouse Tissues for Proteomic Analysis.

J Proteome Res, 2021 Jan 1;20(1):305-316. doi: 10.1021/acs.jproteome.0c00399. Epub 2020 Nov 5.

PMID: 33151080

2020

Gaspar VP, Ibrahim S, Sobsey CA, Richard VR, Spatz A, Zahedi RP, Borchers CH.

Direct and Precise Measurement of Bevacizumab Levels in Human Plasma Based on Controlled Methionine Oxidation and Multiple Reaction Monitoring.

ACS Pharmacol Transl Sci, 2020 Nov 13;3(6):1304-1309. doi: 10.1021/acsptsci.0c00134. eCollection 2020 Dec 11.

PMID: 33344903

De Giorgi M, Jarrett KE, Burton JC, Doerfler AM, Hurley A, Li A, Hsu RH, Furgurson M, Patel KR, Han J, Borchers CH, Lagor WR.

Depletion of essential isoprenoids and ER stress induction following acute liver-specific deletion of HMG-CoA reductase.

J Lipid Res, 2020 Dec;61(12):1675-1686. doi: 10.1194/jlr.RA120001006. Epub 2020 Oct 27.

PMID: 33109681

Leitner A, Bonvin AMJJ, Borchers CH, Chalkley RJ, Chamot-Rooke J, Combe CW, Cox J, Dong MQ, Fischer L, Götze M, Gozzo FC, Heck AJR, Hoopmann MR, Huang L, Ishihama Y, Jones AR, Kalisman N, Kohlbacher O, Mechtler K, Moritz RL, Netz E, Novak P, Petrotchenko E, Sali A, Scheltema RA, Schmidt C, Schriemer D, Sinz A, Sobott F, Stengel F, Thalassinos K, Urlaub H, Viner R, Vizcaíno JA, Wilkins MR, Rappsilber J.

Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry.

Structure, 2020 Nov 3;28(11):1259-1268. doi: 10.1016/j.str.2020.09.011. Epub 2020 Oct 15.

PMID: 33065067

Richard VR, Zahedi RP, Eintracht S, Borchers CH.

An LC-MRM assay for the quantification of metanephrines from dried blood spots for the diagnosis of pheochromocytomas and paragangliomas.

Anal Chim Acta, 2020 Sep 1;1128:140-148. doi: 10.1016/j.aca.2020.06.020. Epub 2020 Jul 9.

PMID: 32825898 

Ibrahim S, Froehlich B, Aguilar-Mahecha A, Aloyz R, Poetz O, Basik M, Batist G, Zahedi RP, Borchers CH.

Using two peptide isotopologues as internal standards for the streamlined quantification of low-abundance proteins by immuno-MRM and immuno-MALDI.

Anal Chem, 2020 Aug 12. doi: 10.1021/acs.analchem.0c02157. Online ahead of print.

PMID: 32786432

Nikolaev EN, Indeykina MI, Brzhozovskiy AG, Bugrova AE, Kononikhin AS, Starodubtseva NL, Petrotchenko EV, Kovalev GI, Borchers CH, Sukhikh GT.

Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein.

J Proteome Res, 2020 Aug 19. doi: 10.1021/acs.jproteome.0c00412. Online ahead of print.

PMID: 32786682

Froehlich BC, Popp R, Sobsey CA, Ibrahim S, LeBlanc AM, Mohammed Y, Aguilar-Mahecha A, Poetz O, Chen MX, Spatz A, Basik M, Batist G, Zahedi RP, Borchers CH.

Systematic Optimization of the iMALDI Workflow for the Robust and Straightforward Quantification of Signaling Proteins in Cancer Cells.

Proteomics Clin Appl, 2020 Jul 8:e2000034. doi: 10.1002/prca.202000034. Online ahead of print.

PMID: 32643306

Kashirina DN, Brzhozovskiy AG, Pastushkova LKh, Kononikhin AS, Borchers CH, Nikolaev EN, Larina IM.

Semiquantitative Proteomic Research of Protein Plasma Profile of Volunteers in 21-Day Head-Down Bed Rest.

Front Physiol, 2020 Jul 24;11:678. doi: 10.3389/fphys.2020.00678. eCollection 2020.

PMID: 32848806 

Liu T, Wang RX, Han J, Qiu YL, Borchers CH, Ling V, Wang JS.

Changes in plasma bile acid profiles after partial internal biliary diversion in PFIC2 patients.

Ann Transl Med, 2020 Mar;8(5):185. doi: 10.21037/atm.2020.01.103.

PMID: 32309332 

Sobsey CA, Ibrahim S, Richard VR, Gaspar V, Mitsa G, Lacasse V, Zahedi RP, Batist G, Borchers CH.

Targeted and Untargeted Proteomics Approaches in Biomarker Development.

Proteomics. 2020 May;20(9):e1900029. doi: 10.1002/pmic.201900029. Epub 2020 Jan 30.

PMID: 31729135 

Review

Gaither C, Popp R, Mohammed Y, Borchers CH.

Determination of the concentration range for 267 proteins from 21 lots of commercial human plasma using highly multiplexed multiple reaction monitoring mass spectrometry.

Analyst, 2020 May 18;145(10):3634-3644. doi: 10.1039/c9an01893j.

PMID: 32255452

Tilburg J, Michaud SA, Maracle CX, Versteeg HH, Borchers CH, van Vlijmen BJM, Mohammed Y.

Plasma Protein Signatures of a Murine Venous Thrombosis Model and Slc44a2 Knockout Mice Using Quantitative-Targeted Proteomics.

Thromb Haemost, 2020 Mar;120(3):423-436. doi: 10.1055/s-0040-1702229. Epub 2020 Mar 5.

PMID: 32135565

Makepeace KAT, Mohammed Y, Rudashevskaya EL, Petrotchenko EV, Voegtle FN, Meisinger C, Sickmann A, Borchers CH.

Improving identification of in-organello protein-protein interactions using an affinity-enrichable, isotopically-coded, and mass spectrometry-cleavable chemical crosslinker.

Mol Cell Proteomics, 2020 Apr;19(4):624-639. doi: 10.1074/mcp.RA119.001839. Epub 2020 Feb 12.

PMID: 32051233 

Bhardwaj M, Weigl K, Tikk K, Holland-Letz T, Schrotz-King P, Borchers CH, Brenner H.

Multiplex quantitation of 270 plasma protein markers to identify a signature for early detection of colorectal cancer.

Eur J Cancer, 2020 Mar;127:30-40. doi: 10.1016/j.ejca.2019.11.021. Epub 2020 Jan 21.

PMID: 31972396

Shin JJH, Liu P, Chan LJ, Ullah A, Pan J, Borchers CH, Burke JE, Stefan C, Smits GJ, Loewen CJR.

pH Biosensing by PI4P Regulates Cargo Sorting at the TGN.

Dev Cell, 2020 Feb 24;52(4):461-476.e4.

doi: 10.1016/j.devcel.2019.12.010. Epub 2020 Jan 9. 

PMID: 31928972

Eshghi A, Pistawka AJ, Liu J, Chen M, Sinclair NJT, Hardie DB, Elliott M, Chen L, Newman R, Mohammed Y, Borchers CH.

Concentration determination of >200 proteins in dried blood spots for biomarker discovery and validation.

Mol Cell Proteomics, 2020 Mar;19(3):540-553. doi:10.1074/mcp.TIR119.001820. Epub 2020 Jan 2.

PMID: 31896676 

Silva F, Guirgis A, von Aderkas P, Borchers CH, Thornburg R.

LC-MS/MS based comparative proteomics of floral nectars reveal different mechanisms involved in floral defense of Nicotiana spp., Petunia hybrida and Datura stramonium.

J Proteomics, 2020 Feb 20;213:103618. 

doi: 10.1016/j.jprot.2019.103618. Epub 2019 Dec 14.

PMID: 31846763

Mohammed Y, Kootte RS, Kopatz WF, Borchers CH, Büller HR, Versteeg HH, Nieuwdorp M, van Mens TE.

The intestinal microbiome potentially affects thrombin generation in human subjects.

J Thromb Haemost, 2020 Mar;18(3):642-650. doi: 10.1111/jth.14699. Epub 2019 Dec 27.

PMID: 31808596

Sobsey CA, Ibrahim S, Richard VR, Gaspar V, Mitsa G, Lacasse V, Zahedi RP, Batist G, Borchers CH.

Targeted and Untargeted Proteomics Approaches in Biomarker Development.

Proteomics, 2020 May;20(9):e1900029. doi: 10.1002/pmic.201900029. Epub 2020 Jan 30.

PMID: 31729135

Makepeace KAT, Brodie NI, Popov KI, Gudavicius G, Nelson CJ, Petrotchenko EV, Dokholyan NV, Borchers CH.

Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations.

J Proteomics, 2020 Jan 16;211:103544. doi: 10.1016/j.jprot.2019.103544. Epub 2019 Nov 1.

PMID: 31683063

2019

Parker CE, Warren Hines MRE, Mocanu V, Greer SF, Borchers CH.

Mass Spectrometric Determination of Protein Ubiquitination.

In: Methods in Molecular Biology, 1934: 191-221 (2019).

 

Petrotchenko EV, Serpa JJ, Borchers CH

Cross-linking Applications in Structural Proteomics.

In: Proteomics for Biological Discovery, Wiley, 2019, 175-196, Veenstra TD

and JR Yates (Eds.).

Popov KI, Makepeace KAT, Petrotchenko EV, Dokholyan NV, Borchers CH.

Insight into the Structure of the "Unstructured" Tau Protein.

Structure, 2019 Nov 5;27(11):1710-1715.e4. doi: 10.1016/j.str.2019.09.003. Epub 2019 Oct 15.

PMID: 31628033

Martínez de Paz A, Khajavi L, Martin H, Claveria-Gimeno R, Tom Dieck S, Cheema MS, Sanchez-Mut JV, Moksa MM, Carles A, Brodie NI, Sheikh TI, Freeman ME, Petrotchenko EV, Borchers CH, Schuman EM, Zytnicki M, Velazquez-Campoy A, Abian O, Hirst M, Esteller M, Vincent JB, Malnou CE, Ausió J.

MeCP2-E1 isoform is a dynamically expressed, weakly DNA-bound protein with different protein and DNA interactions compared to MeCP2-E2.

Epigenetics Chromatin, 2019 Oct 10;12(1):63. doi: 10.1186/s13072-019-0298-1.

PMID: 31601272

Bhardwaj M, Gies A, Weigl K, Tikk K, Benner A, Schrotz-King P, Borchers CH, Brenner H.

Evaluation and Validation of Plasma Proteins Using Two Different Protein Detection Methods for Early Detection of Colorectal Cancer.

Cancers (Basel), 2019 Sep 25;11(10):1426. doi: 10.3390/cancers11101426.

PMID: 31557860 

Pires ES, Hardoim CCP, Miranda KR, Secco DA, Lobo LA, de Carvalho DP, Han J, Borchers CH, Ferreira RBR, Salles JF, Domingues RMCP, Antunes LCM.

The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon.

Front Microbiol, 2019 Sep 4;10:2003.

doi:10.3389/fmicb.2019.02003. eCollection 2019.

PMID: 31555238

Sirois I, Aguilar-Mahecha A, Lafleur J, Fowler E, Vu V, Scriver M, Buchanan M, Chabot C, Ramanathan A, Balachandran B, Legare S, Przybytkowski E, Lan C, Krzemien U, Cavallone L, Aleynikova O, Ferrario C, Guilbert MC, Benlimame N, Saad A, Alaoui-Jamali M, Saragovi HU, Josephy S, O'Flanagan C, Hursting SD, Richard VR, Zahedi RP, Borchers CH, Bareke E, Nabavi S, Tonellato P, Roy JA, Robidoux A, Marcus EA, Mihalcioiu C, Majewski J, Basik M.

A unique morphological phenotype in chemoresistant triple negative breast cancer reveals metabolic reprogramming and PLIN4 expression as a molecular vulnerability.

Mol Cancer Res, 2019 Dec;17(12):2492-2507.

doi: 10.1158/1541-7786.MCR-19-0264. Epub 2019 Sep 19.

PMID: 31537618

Oyama Y, Bartman CM, Bonney S, Lee JS, Walker LA, Han J, Borchers CH, Buttrick PM, Aherne CM, Clendenen N, Colgan SP, Eckle T.

Intense Light-Mediated Circadian Cardioprotection via Transcriptional Reprogramming of the Endothelium.

Cell Rep, 2019 Aug 6;28(6):1471-1484.e11.

doi: 10.1016/j.celrep.2019.07.020.

PMID: 31390562

Mao F, Liu T, Hou X, Zhao H, He W, Li C, Jing Z, Sui J, Wang F, Liu X, Han J, Borchers CH, Wang JS, Li W.

Increased sulfation of bile acids in mice and human subjects with sodium taurocholate cotransporting polypeptide deficiency.

J Biol Chem, 2019 Aug 2;294(31):11853-11862.

doi: 10.1074/jbc.RA118.007179. Epub 2019 Jun 14.

PMID: 31201272

Masson GR, Burke JE, Ahn NG, Anand GS, Borchers C, Brier S, Bou-Assaf GM, Engen JR, Englander SW, Faber J, Garlish R, Griffin PR, Gross ML, Guttman M, Hamuro Y, Heck AJR, Houde D, Iacob RE, Jørgensen TJD, Kaltashov IA, Klinman JP, Konermann L, Man P, Mayne L, Pascal BD, Reichmann D, Skehel M, Snijder J, Strutzenberg TS, Underbakke ES, Wagner C, Wales TE, Walters BT, Weis DD, Wilson DJ, Wintrode PL, Zhang Z, Zheng J, Schriemer DC, Rand KD.

Recommendations for performing, interpreting, and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments.

Nat Methods, 2019 Jul;16(7):595-602.

doi: 10.1038/s41592-019-0459-y. Epub 2019 Jun 27.

PMID: 31249422

Anwar MA, Dai DL, Wilson-McManus J, Smith D, Francis GA, Borchers CH, McManus BM, Hill JS, Cohen Freue GV.

Multiplexed LC/ESI-MRM-MS-based Assay for Identification of Coronary Artery Disease Biomarkers in Human Plasma.

Proteomics Clin Appl, 2019 Jul;13(4):e1700111.

doi: 10.1002/prca.201700111. Epub 2019 Jan 28.

PMID: 30632678

Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews PC, Bernfur K, Borchers CH, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis TN, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez CB, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Fereira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko EV, Piersimoni L, Plasencia M, Pukala TL, Rand KD, Rappsilber J, Reichman D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka MJ, Vilaseca M, Viner R, Xiang Y, Yılmaz Ş, Zelter A, Ziemianowicz DS, Leitner A, Sinz A.  

The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study.

Anal Chem, 2019 Jun 4;91(11):6953-6961.

doi: 10.1021/acs.analchem.9b00658. Epub 2019 May 22.

PMID: 31045356

Brodie NI, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH.

Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations.

PLoS Comput Biol, 2019 Mar 27;15(3):e1006859. doi: 10.1371/journal.pcbi.1006859. eCollection 2019 Mar.

PMID: 30917118 

Kashirina DN, Percy AJ, Pastushkova LK, Borchers CH, Kireev KS, Ivanisenko VA, Kononikhin AS, Nikolaev EN, Larina IM.

The molecular mechanisms driving physiological changes after long duration space flights revealed by quantitative analysis of human blood proteins.

BMC Med Genomics, 2019 Mar 13;12(Suppl 2):45. doi: 10.1186/s12920-019-0490-y.

PMID: 30871558 

Teixeira F, Tse E, Castro H, Makepeace KAT, Meinen BA, Borchers CH, Poole LB, Bardwell JC, Tomás AM, Southworth DR, Jakob U.

Chaperone activation and client binding of a 2-cysteine peroxiredoxin.

Nat Commun, 2019 Feb 8;10(1):659. doi: 10.1038/s41467-019-08565-8.

PMID: 30737390 

Shultis D, Mitra P, Huang X, Johnson J, Khattak NA, Gray F, Piper C, Czajka J, Hansen L, Wan B, Chinnaswamy K, Liu L, Wang M, Pan J, Stuckey J, Cierpicki T, Borchers CH, Wang S, Lei M, Zhang Y.

Changing the Apoptosis Pathway through Evolutionary Protein Design.

J Mol Biol, 2019 Feb 15;431(4):825-841.

doi: 10.1016/j.jmb.2018.12.016. Epub 2019 Jan 6.

PMID: 30625288

Wang R, Sheps JA, Liu L, Han J, Chen PSK, Lamontagne J, Wilson PD, Welch I, Borchers CH, Ling V.

Hydrophilic bile acids prevent liver damage caused by lack of biliary phospholipid in Mdr2-/-mice.

J Lipid Res, 2019 Jan;60(1):85-97. doi: 10.1194/jlr.M088070. Epub 2018 Nov 11.

PMID: 30416103 

Boczonadi V, King MS, Smith AC, Olahova M, Bansagi B, Roos A, Eyassu F, Borchers C, Ramesh V, Lochmüller H, Polvikoski T, Whittaker RG, Pyle A, Griffin H, Taylor RW, Chinnery PF, Robinson AJ, Kunji ERS, Horvath R.

Correction: Mitochondrial oxodicarboxylate carrier deficiency is associated with mitochondrial DNA depletion and spinal muscular atrophy-like disease.

Genet Med, 2019 Sep;21(9):2163-2164. doi: 10.1038/s41436-019-0506-1.

PMID: 31028354

2018

Eshghi A, Borchers CH.

Multiple Reaction Monitoring Using Double Isotopologue Peptide Standards 6

for Protein Quantification.

In: Methods in Molecular Biology, 1788: 193-214 (2018).

Popp R, Li H, Borchers CH.

Immuno-MALDI (iMALDI) mass spectrometry for the analysis of proteins in signaling pathways.

Expert Rev Proteomics, 2018 Sep;15(9):701-708. doi: 10.1080/14789450.2018.1516147. Epub 2018 Sep 17.

PMID: 30169113 

Han J, Higgins R, Lim MD, Atkinson K, Yang J, Lin K, Borchers CH.

Isotope-labeling derivatization with 3-nitrophenylhydrazine for LC/multiple-reaction monitoring-mass-spectrometry-based quantitation of carnitines in dried blood spots.

Anal Chim Acta, 2018 Dec 11;1037:177-187. doi: 10.1016/j.aca.2018.01.045. Epub 2018 Feb 5.

PMID: 30292292 

Michaud SA, Sinclair NJ, Pětrošová H, Palmer AL, Pistawka AJ, Zhang S, Hardie DB, Mohammed Y, Eshghi A, Richard VR, Sickmann A, Borchers CH.

Molecular phenotyping of laboratory mouse strains using 500 multiple reaction monitoring mass spectrometry plasma assays.

Common Biol, 2018 Jun 27;1:78. doi: 10.1038/s42003-018-0087-6. eCollection 2018.

PMID: 30271959 

Zahedi RP, Parker CE, Borchers CH.

Immuno-MALDI-TOF-MS in the Clinic.

Clin Chem, 2018 Sep;64(9):1271-1272. doi: 10.1373/clinchem.2018.292136. Epub 2018 Jul 17.

PMID: 30018057

Penn AM, Bibok MB, Saly VK, Coutts SB, Lesperance ML, Balshaw RF, Votova K, Croteau NS, Trivedi A, Jackson AM, Hegedus J, Klourfeld E, Yu AYX, Zerna C, Modi J, Barber PA, Hoag G, Borchers CH; SpecTRA study group.

Validation of a Proteomic Biomarker Panel to Diagnose Minor-Stroke and Transient Ischaemic Attack: Phase 2 of SpecTRA, a Large-Scale Translational Study.

Biomarkers, 2018 Dec;23(8):793-803. doi: 10.1080/1354750X.2018.1499130. Epub 2018 Aug 23.

PMID: 30010432 

Wölter M, Okai CA, Smith D, Ruß M, Rath W, Pecks U, Borchers CH, Glocker MO.

Maternal Apolipoprotein B100 Serum Levels are Diminished in Pregnancies with Intrauterine Growth Restriction and Differentiate from Controls.

Proteomics Clin Appl, 2018 Nov;12(6):e1800017.

doi: 10.1002/prca.201800017. Epub 2018 Jul 23.

PMID: 29956482

Mahdavi S, Jenkins DJA, Borchers CH, El-Sohemy A.

Genetic Variation in 9p21 and the Plasma Proteome.

J Proteome Res, 2018 Aug 3;17(8):2649-2656.

doi: 10.1021/acs.jproteome.8b00117. Epub 2018 Jul 19.

PMID: 29905076

Mnatsakanyan R, Shema G, Basik M, Batist G, Borchers CH, Sickmann A, Zahedi RP.

Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry.

Expert Rev Proteomics, 2018 Jun;15(6):515-535.

doi: 10.1080/14789450.2018.1483340.

PMID: 29893147

Bhowmick P, Mohammed Y, Borchers CH.

MRMAssayDB: an integrated resource for validated targeted proteomics assays.

Bioinformatics, 2018 Oct 15;34(20):3566-3571. doi: 10.1093/bioinformatics/bty385.

PMID: 29762640 

Popp R, Basik M, Spatz A, Batist G, Zahedi RP, Borchers CH.

How iMALDI can improve clinical diagnostics.

Analyst, 2018 May 15;143(10):2197-2203. doi: 10.1039/c8an00094h.

PMID: 29713694 

Parker CE, Borchers CH.

The Special Issue: Clinical Proteomics for Precision Medicine.

Proteomics Clin Appl, 2018 Mar;12(2). doi: 10.1002/prca.201600144.

PMID: 29521035 

Luehr TC, Koide EM, Wang X, Han J, Borchers CH, Helbing CC.

Metabolomic insights into the effects of thyroid hormone on Rana [Lithobates] catesbeiana metamorphosis using whole-body Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging (MALDI-MSI).

Gen Comp Endocrinol, 2018 Sep 1;265:237-245.

doi: 10.1016/j.ygcen.2018.02.012. Epub 2018 Feb 19.

PMID: 29470956

Liu T, Wang RX, Han J, Hao CZ, Qiu YL, Yan YY, Li LT, Wang NL, Gong JY, Lu Y, Zhang MH, Xie XB, Yang JC, You YJ, Li JQ, Knisely AS, Borchers CH, Ling V, Wang JS.

Comprehensive bile acid profiling in hereditary intrahepatic cholestasis: Genetic and clinical correlations.

Liver Int, 2018 Sep;38(9):1676-1685. doi: 10.1111/liv.13714. Epub 2018 Mar 12.

PMID: 29412511

Penn AM, Bibok MB, Saly VK, Coutts SB, Lesperance ML, Balshaw RF, Votova K, Croteau NS, Trivedi A, Jackson AM, Hegedus J, Klourfeld E, Yu AYX, Zerna C, Borchers CH.

Verification of a Proteomic Biomarker Panel to Diagnose Minor Stroke and Transient Ischaemic Attack: Phase 1 of SpecTRA, a Large-Scale Translational Study.

Biomarkers, 2018 May-Jun;23(4):392-405. doi: 10.1080/1354750X.2018.1434681. Epub 2018 Feb 12. 

PMID: 29385837

Penn AM, Saly V, Trivedi A, Lesperance ML, Votova K, Jackson AM, Croteau NS, Balshaw RF, Bibok MB, Smith DS, Lam KK, Morrison J, Lu L, Coutts SB, Borchers CH.

Differential Proteomics for Distinguishing Ischemic Stroke from Controls: a Pilot Study of the SpecTRA Project.

Transl Stroke Res, 2018 Dec;9(6):590-599. doi: 10.1007/s12975-018-0609-z. Epub 2018 Jan 24.

PMID: 29368175 

Dilworth D, Gudavicius G, Xu X, Boyce AKJ, O'Sullivan C, Serpa JJ, Bilenky M, Petrochenko EV, Borchers CH, Hirst M, Swayne LA, Howard P, Nelson CJ.

The prolyl isomerase FKBP25 regulates microtubule polymerization impacting cell cycle progression and genomic stability.

Nucleic Acids Res, 2018 Mar 16;46(5):2459-2478. doi: 10.1093/nar/gky008.

PMID: 29361176 

Perzanowska A, Fatalska A, Wojtas G, Lewandowicz A, Michalak A, Krasowski G, Borchers CH, Dadlez M, Domanski D.

An MRM-Based Cytokeratin Marker Assay as a Tool for Cancer Studies: Application to Lung-Cancer Pleural Effusions.

Proteomics Clin Appl,  2018 Mar;12(2). doi: 10.1002/prca.201700084. Epub 2018 Feb 7.

PMID: 29352525

Brodie NI, Huguet R, Zhang T, Viner R, Zabrouskov V, Pan J, Petrotchenko EV, Borchers CH.

Top-down hydrogen-deuterium exchange analysis of protein structures using ultraviolet photodissociation (UVPD).

Anal Chem,  2018 Mar 6;90(5):3079-3082. doi: 10.1021/acs.analchem.7b03655. Epub 2018 Feb 1.

PMID: 29336549

Jardim A, Hardie DB, Boitz J, Borchers CH.

Proteomic Profiling of Leishmania donovani Promastigote Subcellular Organelles.

J Proteome Res, 2018 Mar 2;17(3):1194-1215. doi: 10.1021/acs.jproteome.7b00817. Epub 2018 Feb 5.

PMID: 29332401

Han J, Higgins R, Lim MD, Lin K, Yang J, Borchers CH

Short-Term Stabilities of 21 Amino Acids in Dried Blood Spot. 

Clin Chem, 2018 Feb;64(2):400-402. doi: 10.1373/clinchem.2017.278457. Epub 2017 Nov 2.

PMID: 29097508

2017

Bowden JA, Heckert A, Ulmer CZ, Jones CM, Koelmel JP, Abdullah L, Ahonen L, Alnouti Y, Armando A, Asara JM, Bamba T, Barr JR, Bergquist J, Borchers CH, Brandsma J, Breitkopf SB, Cajka T, Cazenave-Gassiot A, Checa A, Cinel MA, Colas RA, Cremers S, Dennis EA, Evans JE, Fauland A, Fiehn O, Gardner MS, Garrett TJ, Gotlinger KH, Han J, Huang Y, Neo AH, Hyotylainen T, Izumi Y, Jiang H, Jiang H, Jiang J, Kachman M, Kiyonami R, Klavins K, Klose C, Kofeler HC, Kolmert J, Koal T, Koster G, Kuklenyik Z, Kurland IJ, Leadley M, Lin K, Maddipati KR, McDougall D, Meikle PJ, Mellett NA, Monnin C, Moseley MA, Nandakumar R, Oresic M, Patterson RE, Peake D, Pierce JS, Post M, Postle AD, Pugh R, Qui Y, Quehenberger O, Ramrup P, Rees J, Rembiesa B, Reynaud D, Roth MR, Sales S, Schuhmann K, Schwartzman ML, Serhan CN, Shevchenko A, Somerville SE, John-Williams LS, Surma MA, Takeda H, Thakare R, Thompson JW, Torta F, Triebl A, Trotzmuller M, Ubhayasekera SJK, Vuckovic D, Weir JM, Welti R, Wenk MR, Wheelock CE, Yao L, Yuan M, Zhao XH, Zhou S.

Harmonizing Lipidomics: NIST Interlaboratory Comparison Exercise for Lipidomics using Standard Reference Material 1950 Metabolites in Frozen Human Plasma.

J Lipid Res, 2017 Dec;58(12):2275-2288. doi: 10.1194/jlr.M079012. Epub 2017 Oct 6.

PMID: 28986437

Mohammed Y, Pan J, Zhang S, Han J, Borchers CH.

ExSTA: External Standard Addition Method for Accurate High-throughput Quantitation in Targeted Proteomics Experiments.

Proteomics Clin Appl, 2018 Mar;12(2):1600180. doi: 10.1002/prca.201600180. Epub 2017 Oct 25.

PMID: 28895300 

Urao N, Mirza RE, Corbiere TF, Hollander Z, Borchers CH, Koh TJ.

Thrombospondin-1 and disease progression in dysferlinopathy. 

Hum Mol Genet, 2017 Dec 15;26(24):4951-4960. doi: 10.1093/hmg/ddx378.

PMID: 29206970

Dilworth D, Upadhyay SK, Bonnafous P, Edoo AB, Bourbigot S, Pesek-Jardim F, Gudavicius G, Serpa JJ, Petrotchenko EV, Borchers CH, Nelson CJ, Mackereth CD.

The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module.

Nucleic Acids Res, 2017 Nov 16;45(20):11989-12004. doi:10.1093/nar/gkx852.

PMID: 29036638 

Popp R, Li H, LeBlanc A, Mohammed Y, Aguilar-Mahecha A, Chambers AG, Lan C, Poetz O, Basik M, Batist G, Borchers CH.

Immuno-Matrix-Assisted Laser Desorption/Ionization Assays for Quantifying AKT1 and AKT2 in Breast and Colorectal Cancer Cell Lines and Tumors.

Anal Chem, 2017 Oct 3;89(19):10592-10600. doi: 10.1021/acs.analchem.7b02934. Epub 2017 Sep 20.

PMID: 28853539

Pedde RD, Li H, Borchers CH, Akbari M.

Microfluidic-Mass Spectrometry Interfaces for Translational Proteomics.

Trends Biotechnol, 2017 Oct;35(10):954-970.

doi: 10.1016/j.tibtech.2017.06.006. Epub 2017 Jul 26.

PMID: 28755975

Richard VR, Domanski D, Percy AJ, Borchers CH.

An online 2D-reversed-phase - Reversed-phase chromatographic method for sensitive and robust plasma protein quantitation.

J Proteomics, 2017 Sep 25;168:28-36. doi: 10.1016/j.jprot.2017.07.018. Epub 2017 Jul 28.

PMID: 28757464 

Peixoto RJM, Alves ES, Wang M, Ferreira RBR, Granato A, Han J, Gill H, Jacobson K, Lobo LA, Domingues RMCP, Borchers CH, Davies JE, Finlay BB, Antunes LCM.

Repression of Salmonella host cell invasion by aromatic small molecules from the human fecal metabolome.

Appl Environ Microbiol, 2017 Sep 15;83(19):e01148-17.

doi: 10.1128/AEM.01148-17. Print 2017 Oct 1.

PMID: 28754707

Li H, Popp R, Frohlich B, Chen MX, Borchers CH.

Peptide and Protein Quantification Using Automated Immuno-MALDI (iMALDI).

J Vis Exp, 2017 Aug 18;(126):55933. doi: 10.3791/55933.

PMID: 28872133

Guarna MM, Hoover SE, Huxter E, Higo H, Moon KM, Domanski D, Bixby MEF, Melathopoulos AP, Ibrahim A, Peirson M, Desai S, Micholson D, White R, Borchers CH, Currie RW, Pernal SF, Foster LJ.

Peptide biomarkers used for the selective breeding of a complex polygenic trait in honeybees.

Sci Rep, 2017 Aug 21;7(1):8381. doi: 10.1038/s41598-017-08464-2.

PMID: 28827652

Larina IM, Percy AJ, Yang J, Borchers CH, M Nosovsky A, I Grigoriev A, N Nikolaev E.

Protein expression changes caused by spaceflight as measured for 18 Russian cosmonauts.

Sci Rep, 2017 Aug 15;7(1):8142. doi: 10.1038/s41598-017-08432-w.

PMID: 28811532

Brodie NI, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH.

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations.

Science Advances, 2017 Jul 7;3(7):e1700479. doi: 10.1126/sciadv.1700479. eCollection 2017 Jul.

PMID: 28695211 

LeBlanc A, Michaud SA, Percy AJ, Hardie DB, Yang J, Sinclair NJ, Proudfoot JI, Pistawka A, Smith DS, Borchers CH.

Multiplexed MRM-based Protein Quantitation Using Two Different Stable Isotope Labeled Peptides for Calibration.

J Proteome Res, 2017 Jul 7;16(7):2527-2536. doi: 10.1021/acs.jproteome.7b00094. Epub 2017 Jun 2.

PMID: 28516774

Wang X, Han J, Hardie DB, Yang J, Pan J, Borchers CH.

Metabolomic profiling of prostate cancer by matrix assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry imaging using Matrix Coating Assisted by an Electric Field (MCAEF).

Biochim Biophys Acta, 2017 Jul;1865(7):755-767. doi: 10.1016/j.bbapap.2016.12.012. Epub 2016 Dec 23.

PMID: 28017863

Mohammed Y, van Vlijmen BJ, Yang J, Percy AJ, Palmblad M, Borchers CH, Rosendaal FR.

Multiplexed targeted proteomic assay to assess coagulation factor concentrations and thrombosis-associated cancer.

Blood Advances, 2017 Jun 20;1(15):1080-1087. doi: 10.1182/bloodadvances.2017007955. eCollection 2017 Jun 27.

PMID: 29296750

Li H, Han J, Pan J, Liu T, Parker CE, Borchers CH.

Current Trends in Quantitative Proteomics -- an update.

J Mass Spectrom, 2017 May;52(5):319-341. doi: 10.1002/jms.3932.

PMID: 28418607 

Review

Qiu YL, Gong JY, Feng JY, Wang RX, Han J, Liu T, Lu Y, Li LT, Zhang MH, Sheps JA, Wang NL, Yan YY, Li JQ, Chen L, Borchers CH, Sipos B, Knisely AS, Ling V, Xing QH, Wang JS. 

Defects in MYO5B are associated with a spectrum of previously undiagnosed low γ-glutamyltransferase cholestasis.

Hepatology, 2017 May;65(5):1655-1669. doi: 10.1002/hep.29020. Epub 2017 Mar 23.

PMID: 28027573

Reynolds LA, Redpath SA, Yurist-Doutsch S, Gill N, Brown EM, van der Heijden J, Brosschot TP, Han J, Marshall NC, Woodward SE, Valdez Y, Borchers CH, Perona-Wright G, Finlay BB.

Enteric helminths promote Salmonella co-infection by altering the intestinal metabolome.

J Infect Dis, 2017 Apr 15;215(8):1245-1254. doi: 10.1093/infdis/jix141.

PMID: 28368463 

Streijger F, Skinnider M, Rogalski JC, Balshaw R, Shannon CP, Prudova A, Belanger LM, Ritchie L, Tsang A, Christie S, Parent S, Mac-Thiong JM, Bailey C, Urquhart J, Ailon T, Paquette SJ, Boyd MC, Street J, Fisher CG, Dvorak MF, Borchers CH, Foster LJ, Kwon BK.

A Targeted Proteomics Analysis of Cerebrospinal Fluid after Acute Human Spinal Cord Injury.

J Neurotrauma, 2017 Jun 15;34(12):2054-2068. doi:10.1089/neu.2016.4879. Epub 2017 Apr 7.

PMID: 28276985

Percy AJ, Michaud SA, Jardim A, Sinclair NJ, Zhang S, Mohammed Y, Palmer AL, Hardie DB, Yang J, LeBlanc AM, Borchers CH.

Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue.

Proteomics, 2017 Apr;17(7). doi: 10.1002/pmic.201600097. Epub 2016 Nov 18.

PMID: 27688154

Mohammed Y, Bhowmick P, Smith DS, Domanski D, Jackson AM, Michaud SA, Malchow S, Percy AJ, Chambers AG, Palmer A, Zhang S, Sickmann A, Borchers CH.

PeptideTracker: A knowledgebase for collecting and storing information on protein concentrations in biological tissues.

Proteomics, 2017 Apr;17(7). doi: 10.1002/pmic.201600210. Epub 2016 Dec 14.

PMID: 27683069

2016

Percy AJ, Yang J, Chambers AG, Mohammed Y, Miliotis, Borchers CH.

Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker

Assessments Through an MRM-with-Standard-Peptides Quantitative

Approach.

In: Modern Proteomics – Sample Preparation, Analysis and Practical

Applications, Advances in Experimental Medicine and Biology, Springer,

2016, Vol. 919, 515-531

 

Percy AJ, Yang J, Chambers AG, Borchers CH.

Increased Depth and Breadth of Plasma Protein Quantitation via Two-

Dimensional Liquid Chromatography/Multiple Reaction Monitoring-Mass

Spectrometry with Labeled Peptide Standards.

In: Methods in Molecular Biology, 1410: 1-21 (2016).

2015

 

Han J, Parker, CE, Borchers CH.

Chemical derivatization to enhance metabolomic analysis by LC/ESI–MS.

In: Advanced LC-MS Applications in Metabolomics, Future-Science eBook,

Han J, Parker, CE, Borchers CH, Borchers CH (Eds), 2015.

 

2014

Percy AJ, Chambers AG, Parker CE, Borchers CH.

MRM-based Protein Quantification with Labeled Standards for Biomarker

Discovery, Verification, and Validation in Human Plasma.

In: Quantitative Proteomics, Royal Society of Chemistry, 2014, Vol. 1, 316-325.

 

Parker CE, Domanski D, Percy AJ, Chambers AG, Camenzind AG, Smith DS, Borchers CH.

Mass Spectrometry in High-Throughput Clinical Biomarker Assays: Multiple

Reaction Monitoring.

In: Topics in Current Chemistry, Springer, 2014, Vol. 336, 117-138.

Petrotchenko EV, Makepeace KAT, Serpa JJ. Borchers CH.

Analysis of protein Structure by Crosslinking Combined with Mass

Spectrometry.

In: Methods in Molecular Biology, Humana Press, 2014, Vol. 1156, 447-463.

Percy AJ, Chambers AG, Parker CE, Borchers CH.

A Targeted Mass Spectrometric Approach for Quantitating Candidate Cancer

Biomarker Proteins in Undepleted and Non-Enriched Human Plasma.

In: The Research and Biology of Cancer, iConcept book, 2014, Vol. 1, 33-48.

 

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