2022
2018
2018
2024
Rahimian R, Perlman K, Fakhfouri G, Mpai R, Richard VR, Hercher C, Penney L, Davoli MA, Nagy C, Zahedi RP, Borchers CH, Giros B, Turecki G, Mechawar N.
Proteomic evidence of depression-associated astrocytic dysfunction in the human male olfactory bulb.
Brain Behav Immun 2024 Nov:122:110-121. DOI: 10.1016/j.bbi.2024.08.016. Epub 2024 Aug 14.
PMID: 39128570
Sobsey CA, Froehlich BC, Mitsa G, Ibrahim S, Popp R, Zahedi RP, de Bruin EC, Borchers CH, Batist G.
mTORC1-Driven Protein Translation Correlates with Clinical Benefit of Capivasertib within a Genetically Preselected Cohort of PIK3CA-Altered Tumors.
Clinical Trial.
Cancer Res Commun. 2024 Aug 1;4(8):2058-2074. DOI: 10.1158/2767-9764.CRC-24-0113.
PMID: 38954770
Blackburn DM, Sahinyan K, Hernández-Corchado A, Lazure F, Richard V, Raco L, Perron G, Zahedi RP, Borchers CH, Lepper C, Kawabe H, Jahani-Asl A, Najafabadi HS, Soleimani VD.
The E3 ubiquitin ligase Nedd4L preserves skeletal muscle stem cell quiescence by inhibiting their activation.
iScience 2024 Jun 11;27(7):110241. DOI: 10.1016/j.isci.2024.110241. eCollection 2024 Jul 19.
PMID: 39015146
Carvalho Cabral P, Richard VR, Borchers CH, Olivier M, Cermakian N.
Circadian Control of the Response of Macrophages to Plasmodium Spp.-Infected Red Blood Cells
Immunohorizons 2024 Jun 1;8(6):442-456. DOI: 10.4049/immunohorizons.2400021.
PMID: 38916585
Richard VR, Mitsa G, Eshghi A, Chaplygina D, Mohammed Y, Goodlett DR, Zahedi RP, Thevis M, Borchers CH.
Establishing Personalized Blood Protein Reference Ranges Using Noninvasive Microsampling and Targeted Proteomics: Implications for Antidoping Strategies
J Proteome Res 2024 May 3;23(5):1779-1787.
DOI: 10.1021/acs.jproteome.4c00020.Epub 2024 Apr 24. PMID: 38655860
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 VR, Borchers 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 Y, Borchers 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.