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Publications

 

2022

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. https://doi: 10.3390/ijms23084443

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. https://doi: 10.1016/j.xpro.2022.101258

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. https://doi: 10.1111/jth.15623

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. MCP. 2022 Feb 17. https://doi.org/10.1016/j.mcpro.2022.100212

 

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 Feb 10;awac055. doi: 10.1093/brain/awac055.

 

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.

Petrotchenko EV, Borchers CH. Protein Chemistry Combined with Mass Spectrometry for Protein Structure Determination. Chem Rev. 2021 Dec 30. doi: 10.1021/acs.chemrev.1c00302

2021

Gaspar VP, Ibrahim S, Zahedi RP, Borchers CH. Utility, promise, and limitations of liquid chromatography-mass spectrometry-based therapeutic drug monitoring in precision medicine. Journal of Mass Spectrometry. 2021 Oct.


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.

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 Jul 29. 

 

Gaither C, Popp R, Borchers SP, Skarphedinsson K, Eiriksson FF, Thorsteinsdottir M, Mohammed Y, Borchers CH. Performance Assessment of a 125 Human Plasma Peptide Mixture Stored at Room Temperature for Multiple Reaction MonitoringMass Spectrometry. J. Proteome Res. 2021 July.

Laselva O, Qureshi Z, Zeng ZW, Petrotchenko EV, Ramjeesingh M, Hamilton CM, Huan LJ, Borchers CH, Pomes R, Young R, Bear1 CE. Identification of binding sites for ivacaftor on the cystic fibrosis transmembrane conductance regulator. iScience. 2021 June 25; 24 (6):102542. 

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. 

Percy AJ, Borchers CH. Detailed Method for Performing the ExSTA Approach in Quantitative Bottom-Up Plasma Proteomics. Methods Mol Biol. 2021;2228:353-384. 

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.

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. 

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.

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 Apr. 

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.

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.

2020

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

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.;doi.org/10.1021/acsptsci.0c00134

 

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. 2020 Nov 5. doi: 10.1021/acs.jproteome.0c00399. Online ahead of print. PMID: 33151080

 

Marco GD, 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. jlr.RA120001006. First Published on October 27, 2020, doi:10.1194/jlr.RA120001006

 

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 Oct 12:S0969-2126(20)30336-1. doi: 10.1016/j.str.2020.09.011

 

Kopczynski D, Hentschel A, Coman C, Schebb NH, Hornemann T, Mashek DG, Hartung NM, Shevchuk O, Schött HF, Lorenz K, Torta F, Burla B, Zahedi RP, Sickmann A, Kreutz MR, Ejsing CS, Medenbach J, Ahrends R. Simple Targeted Assays for Metabolic Pathways and Signaling: A Powerful Tool for Targeted Proteomics. Anal Chem. 2020 Oct 20;92(20):13672-13676. doi: 10.1021/acs.analchem.0c02793. Epub 2020 Sep 21.PMID:32865986

 

Richard VR, P 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

 

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.

 

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 9. doi: 10.1021/acs.jproteome.0c00412. Online ahead of print.

 

Comer S, Nagy Z, Bolado A, von Kriegsheim A, Gambaryan S, Walter U, Pagel O, Zahedi RP, Jurk K, Smolenski A. The RhoA regulators Myo9b and GEF-H1 are targets of cyclic nucleotide-dependent kinases in platelets. J Thromb Haemost. 2020 Jul 21. doi: 10.1111/jth.15028. Online ahead of print.PMID:32692911

 

Scheidt T, Alka O, Gonczarowska-Jorge H, Gruber W, Rathje F, Dell'Aica M, Rurik M, Kohlbacher O, Zahedi RP, Aberger F, Huber CG. Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells. Cell Commun Signal. 2020 Jun 23;18(1):99. doi: 10.1186/s12964-020-00591-0.PMID ;32576205

 

Gaither C, Popp R1, 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 Apr 7. doi: 10.1039/c9an01893j.

 

Grimmer J, Helm S, Dobritzsch D, Hause G, Shema G, Zahedi RP, Baginsky S. Mild proteasomal stress improves photosynthetic performance in Arabidopsis chloroplasts. Nat Commun. 2020 Apr 3;11(1):1662. doi: 10.1038/s41467-020-15539-8.PMID ;32245955

 

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

 

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.;

 

Kumm EJ, Pagel O, Gambaryan S, Walter U, Zahedi RP, Smolenski A, Jurk K. The Cell Cycle Checkpoint System MAST(L)-ENSA/ARPP19-PP2A is Targeted by cAMP/PKA and cGMP/PKG in Anucleate Human Platelets. Cells. 2020 Feb 18;9(2):472. doi: 10.3390/cells9020472.PMID: 32085646

 

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 Jan 20;127:30-40. doi: 10.1016/j.ejca.2019.11.021. [Epub ahead of print];

 

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. pH Biosensing by PI4P Regulates Cargo Sorting at the TGN. Dev Cell. 2020 Jan 9. pii: S1534-5807(19)31031-7. doi: 10.1016/j.devcel.2019.12.010. [Epub ahead of print].

 

2019

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. pH Biosensing by PI4P Regulates Cargo Sorting at the TGN. Dev Cell. 2020 Jan 9. pii: S1534-5807(19)31031-7. doi: 10.1016/j.devcel.2019.12.010. 

 

Sirois I, Aguilar-Mahecha A, Lafleur J, Fowler E, Vu V, Scriver M, Buchanan M, Chabot C, Ramanathan A, Balachandran B, Légaré 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. 

 

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.

 

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. 2019 Dec 6. doi: 10.1111/jth.14699. 

 

Blank-Landeshammer B, Richard VR, Mitsa G, Marques M, LeBlanc A, Kollipara L, Feldmann I, Couetoux du Tertre M, Gambaro K, McNamara S, Spatz A, Zahedi RP, Sickmann A, Batist G, Borchers CH. Proteogenomics of Colorectal Cancer Liver Metastases: Complementing Precision Oncology with Phenotypic Data. Cancers (Basel). 2019 Dec 1;11(12). pii: E1907. doi: 10.3390/cancers11121907.

 

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. 2019 Nov 15:e1900029. doi: 10.1002/pmic.201900029. Review.

 

Parker CE, Warren Hines MRE, Mocanu V, Greer SF, Borchers CH. Mass Spectrometric Determination of Protein Ubiquitination. Methods Mol Biol. 2019;1934:191-221. doi: 10.1007/978-1-4939-9055-9_13.

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. 2019 Nov 1:103544. doi: 10.1016/j.jprot.2019.103544. 

 

Lategahn J, Keul M, Klövekorn P, Tumbrink HL, Niggenaber J, Müller MP, Hodson L, Flaßhoff M, Hardick J, Grabe T, Engel J, Schultz-Fademrecht C, Baumann M, Ketzer J, Mühlenberg T, Hiller W, Günther G, Unger A, Müller H, Heimsoeth A, Golz C, Blank-Landeshammer B, Kollipara L, Zahedi RP, Strohmann C, Hengstler JG, van Otterlo WAL, Bauer S, Rauh D.
Inhibition of osimertinib-resistant epidermal growth factor receptor EGFR-T790M/C797S. Chem Sci. 2019 Oct 4;10(46):10789-10801. doi: 10.1039/c9sc03445e. eCollection 2019 Dec 14.

 

 

Popov KI, Makepeace KAT, Petrotchenko EV, Dokholyan NV, Borchers CH. Insight into the Structure of the "Unstructured" Tau Protein. Structure. 2019 Oct 14. pii: S0969-2126(19)30309-0. doi: 10.1016/j.str.2019.09.003.

 

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.

 

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). pii: E1426. doi: 10.3390/cancers11101426.

 

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.

 

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.

 

Larina IM, Percy AJ, Yang J, Borchers CH, Nosovsky AM, Grigoriev AI, Nikolaev EN. Publisher Correction: Protein expression changes caused by spaceflight as measured for 18 Russian cosmonauts. Sci Rep. 2019 Jun 7;9(1):8570. doi: 10.1038/s41598-019-43121-w.

 

Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, 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-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann 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 M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A. 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.

 

Mnatsakanyan R, Markoutsa S, Walbrunn K, Roos A, Verhelst SHL, Zahedi RP. Proteome-wide detection of S-nitrosylation targets and motifs using bioorthogonal cleavable-linker-based enrichment and switch technique. Nat Commun. 2019 May 16;10(1):2195. doi: 10.1038/s41467-019-10182-4.

 

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.

 

Brunoro GVF, Carvalho PC, Barbosa VC, Pagnoncelli D, De Moura Gallo CV, Perales J, Zahedi RP, Valente RH, Neves-Ferreira AGDC. Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow. BMC Cancer. 2019 Apr 18;19(1):365. doi: 10.1186/s12885-019-5547-y.

 

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.

 

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.

 

2018

Popp R, Li H, Borchers C. 2018 Immuno-MALDI (iMALDI) mass spectrometry for the analysis of proteins in signaling pathways. Expert Rev. Proteomics , 1–8. (doi:10.1080/14789450.2018.1516147)

 

González Coraspe JA et al. 2018 Biochemical and pathological changes result from mutated Caveolin-3 in muscle. Skelet. Muscle 8, 28. (doi:10.1186/s13395-018-0173-y)

 

Zahedi RP, Parker CE, Borchers CH. 2018 Immuno-MALDI-TOF-MS in the Clinic. Clin. Chem. 64, 1271–1272. (doi:10.1373/clinchem.2018.292136)

 

Penn AM et al. 2018 Validation of a proteomic biomarker panel to diagnose minor-stroke and transient ischaemic attack: phase 2 of SpecTRA, a large scale translational study. Biomark. Biochem. Indic. Expo. Response Susceptibility Chem. , 1–11. (doi:10.1080/1354750X.2018.1499130)

 

Wölter M, Okai CA, Smith DS, Ruß M, Rath W, Pecks U, Borchers CH, Glocker MO. 2018 Maternal Apolipoprotein B100 Serum Levels are Diminished in Pregnancies with Intrauterine Growth Restriction and Differentiate from Controls. Proteomics Clin. Appl. , e1800017. (doi:10.1002/prca.201800017)

 

Mahdavi S, Jenkins DJA, Borchers CH, El-Sohemy A. 2018 Genetic Variation in 9p21 and the Plasma Proteome. J. Proteome Res. 17, 2649–2656. (doi:10.1021/acs.jproteome.8b00117)

 

Mnatsakanyan R, Shema G, Basik M, Batist G, Borchers CH, Sickmann A, Zahedi RP. 2018 Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry. Expert Rev. Proteomics 15, 515–535. (doi:10.1080/14789450.2018.1483340)

 

Walter C, Gonczarowska-Jorge H, Sickmann A, Zahedi RP, Meisinger C, Schmidt O. 2018 Advanced tools for the analysis of protein phosphorylation in yeast mitochondria. Anal. Biochem. 554, 23–27. (doi:10.1016/j.ab.2018.05.022)

 

Bhowmick P, Mohammed Y, Borchers CH. 2018 MRMAssayDB: an integrated resource for validated targeted proteomics assays. Bioinforma. Oxf. Engl. (doi:10.1093/bioinformatics/bty385)

 

Pett C et al. 2018 Effective Assignment of α2,3/α2,6-Sialic Acid Isomers by LC-MS/MS-Based Glycoproteomics. Angew. Chem. Int. Ed Engl. 57, 9320–9324. (doi:10.1002/anie.201803540)

 

Nguyen MTN, Shema G, Zahedi RP, Verhelst SHL. 2018 Protease Specificity Profiling in a Pipet Tip Using ‘Charge-Synchronized’ Proteome-Derived Peptide Libraries. J. Proteome Res. 17, 1923–1933. (doi:10.1021/acs.jproteome.8b00004)

 

Makhoul S, Walter E, Pagel O, Walter U, Sickmann A, Gambaryan S, Smolenski A, Zahedi RP, Jurk K. 2018 Effects of the NO/soluble guanylate cyclase/cGMP system on the functions of human platelets. Nitric Oxide Biol. Chem. 76, 71–80. (doi:10.1016/j.niox.2018.03.008)

 

Parker CE, Borchers CH. 2018 The Special Issue: Clinical Proteomics for Precision Medicine. Proteomics Clin. Appl. 12. (doi:10.1002/prca.201600144)

 

Luehr TC, Koide EM, Wang X, Han J, Borchers CH, Helbing CC. 2018 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. 265, 237–245. (doi:10.1016/j.ygcen.2018.02.012)

 

Liu T et al. 2018 Comprehensive bile acid profiling in hereditary intrahepatic cholestasis: Genetic and clinical correlations. Liver Int. Off. J. Int. Assoc. Study Liver 38, 1676–1685. (doi:10.1111/liv.13714)

 

Kösters M, Leufken J, Schulze S, Sugimoto K, Klein J, Zahedi RP, Hippler M, Leidel SA, Fufezan C. 2018 pymzML v2.0: introducing a highly compressed and seekable gzip format. Bioinforma. Oxf. Engl. 34, 2513–2514. (doi:10.1093/bioinformatics/bty046)

 

Penn AM et al. 2018 Verification of a proteomic biomarker panel to diagnose minor stroke and transient ischaemic attack: phase 1 of SpecTRA, a large scale translational study. Biomark. Biochem. Indic. Expo. Response Susceptibility Chem. 23, 392–405. (doi:10.1080/1354750X.2018.1434681)

 

Shema G, Nguyen MTN, Solari FA, Loroch S, Venne AS, Kollipara L, Sickmann A, Verhelst SHL, Zahedi RP. 2018 Simple, scalable, and ultrasensitive tip-based identification of protease substrates. Mol. Cell. Proteomics MCP 17, 826–834. (doi:10.1074/mcp.TIR117.000302)

 

Perzanowska A, Fatalska A, Wojtas G, Lewandowicz A, Michalak A, Krasowski G, Borchers CH, Dadlez M, Domanski D. 2018 An MRM-Based Cytokeratin Marker Assay as a Tool for Cancer Studies: Application to Lung Cancer Pleural Effusions. Proteomics Clin. Appl. 12. (doi:10.1002/prca.201700084)

 

Brodie NI, Huguet R, Zhang T, Viner R, Zabrouskov V, Pan J, Petrotchenko EV, Borchers CH. 2018 Top-Down Hydrogen-Deuterium Exchange Analysis of Protein Structures Using Ultraviolet Photodissociation. Anal. Chem. 90, 3079–3082. (doi:10.1021/acs.analchem.7b03655)

 

Jardim A, Hardie DB, Boitz J, Borchers CH. 2018 Proteomic Profiling of Leishmania donovani Promastigote Subcellular Organelles. J. Proteome Res. 17, 1194–1215. (doi:10.1021/acs.jproteome.7b00817)

 

Mohammed Y, Pan J, Zhang S, Han J, Borchers CH. 2018 ExSTA: External Standard Addition Method for Accurate High-Throughput Quantitation in Targeted Proteomics Experiments. Proteomics Clin. Appl. 12. (doi:10.1002/prca.201600180)

 

Eshghi A, Borchers CH. 2018 Multiple Reaction Monitoring Using Double Isotopologue Peptide Standards for Protein Quantification. Methods Mol. Biol. Clifton NJ 1788, 193–214. (doi:10.1007/7651_2017_112)

 

Urao N, Mirza RE, Corbiere TF, Hollander Z, Borchers CH, Koh TJ. 2017 Thrombospondin-1 and disease progression in dysferlinopathy. Hum. Mol. Genet. 26, 4951–4960. (doi:10.1093/hmg/ddx378)

 

Han J, Higgins R, Lim MD, Lin K, Yang J, Borchers CH. 2018 Short-Term Stabilities of 21 Amino Acids in Dried Blood Spots. Clin. Chem. 64, 400–402. (doi:10.1373/clinchem.2017.278457)

2017

Gonczarowska-Jorge H, Loroch S, Dell’Aica M, Sickmann A, Roos A, Zahedi RP. 2017 Quantifying Missing (Phospho)Proteome Regions with the Broad-Specificity Protease Subtilisin. Anal. Chem. 89, 13137–13145. (doi:10.1021/acs.analchem.7b02395)

 

Bowden JA et al. 2017 Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma. J. Lipid Res. 58, 2275–2288. (doi:10.1194/jlr.M079012)

 

Mohammed Y, van Vlijmen BJ, Yang J, Percy AJ, Palmblad M, Borchers CH, Rosendaal FR. 2017 Multiplexed targeted proteomic assay to assess coagulation factor concentrations and thrombosis-associated cancer. Blood Adv. 1, 1080–1087. (doi:10.1182/bloodadvances.2017007955)

 

Li H, Popp R, Frohlich B, Chen MX, Borchers CH. 2017 Peptide and Protein Quantification Using Automated Immuno-MALDI (iMALDI). J. Vis. Exp. JoVE (doi:10.3791/55933)

 

Popp R et al. 2017 Immuno-Matrix-Assisted Laser Desorption/Ionization Assays for Quantifying AKT1 and AKT2 in Breast and Colorectal Cancer Cell Lines and Tumors. Anal. Chem. 89, 10592–10600. (doi:10.1021/acs.analchem.7b02934)

 

Guarna MM et al. 2017 Peptide biomarkers used for the selective breeding of a complex polygenic trait in honey bees. Sci. Rep. 7, 8381. (doi:10.1038/s41598-017-08464-2)

 

M Larina I, Percy AJ, Yang J, Borchers CH, M Nosovsky A, I Grigoriev A, N Nikolaev E. 2017 Protein expression changes caused by spaceflight as measured for 18 Russian cosmonauts. Sci. Rep. 7, 8142. (doi:10.1038/s41598-017-08432-w)

 

Richard VR, Domanski D, Percy AJ, Borchers CH. 2017 An online 2D-reversed-phase - Reversed-phase chromatographic method for sensitive and robust plasma protein quantitation. J. Proteomics 168, 28–36. (doi:10.1016/j.jprot.2017.07.018)

 

Brodie NI, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. 2017 Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations. Sci. Adv. 3, e1700479. (doi:10.1126/sciadv.1700479)

 

LeBlanc A et al. 2017 Multiplexed MRM-Based Protein Quantitation Using Two Different Stable Isotope-Labeled Peptide Isotopologues for Calibration. J. Proteome Res. 16, 2527–2536. (doi:10.1021/acs.jproteome.7b00094)

 

Li H, Han J, Pan J, Liu T, Parker CE, Borchers CH. 2017 Current trends in quantitative proteomics - an update. J. Mass Spectrom. JMS 52, 319–341. (doi:10.1002/jms.3932)

 

Reynolds LA et al. 2017 Enteric Helminths Promote Salmonella Coinfection by Altering the Intestinal Metabolome. J. Infect. Dis. 215, 1245–1254. (doi:10.1093/infdis/jix141)

 

Li H, Popp R, Chen M, MacNamara EM, Juncker D, Borchers CH. 2017 Bead-Extractor Assisted Ready-to-Use Reagent System (BEARS) for Immunoprecipitation Coupled to MALDI-MS. Anal. Chem. 89, 3834–3839. (doi:10.1021/acs.analchem.6b04169)
Mohammed Y et al. 2017 PeptideTracker: A knowledge base for collecting and storing information on protein concentrations in biological tissues. Proteomics 17. (doi:10.1002/pmic.201600210)

CONTACT

Segal Cancer Proteomics Centre
E615
3755 Chemin de la Cote-Sainte-Catherine
Montreal, QC, H3T 1E2 Canada

Tel: +1 (514) 340-8222 ext: 27885
 

Segal Cancer Proteomics Centre

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