Reproducible protein quantitation of 270 human proteins at increased depth using nanoparticle-based fractionation and multiple reaction monitoring mass spectrometry with stable isotope-labelled internal standards

Claudia Gaither, Robert Popp, Aaron S. Gajadhar and Christoph H. Borchers

Analyst, 2025, 150, 353
DOI: 10.1039/D4AN00967C

Multiplexed Quantification of First-Trimester Serum Biomarkers in Healthy Pregnancy

Natalia Starodubtseva, Alisa Tokareva, Alexey Kononikhin, Alexander Brzhozovskiy, Anna Bugrova, Evgenii Kukaev, Alina Poluektova, Vladimir Frankevich, Evgeny Nikolaev and Gennady Sukhikh

IJMS, 2025, 26, 7970
DOI: 10.3390/ijms26167970

Mass Spectrometry Techniques: Principles and Practices for Quantitative Proteomics

Rocco J. Rotello and Timothy D. Veenstra

CPPS, 2021, 22, 121
DOI: 10.2174/1389203721666200921153513

Proteomic Markers and Early Prediction of Alzheimer’s Disease

Natalia V. Zakharova, Anna E. Bugrova, Maria I. Indeykina, Yana B. Fedorova, Igor V. Kolykhalov, Svetlana I. Gavrilova, Evgeny N. Nikolaev and Alexey S. Kononikhin

Biochemistry Moscow, 2022, 87, 762
DOI: 10.1134/S0006297922080089

Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells

Mirjam van Bentum, Bertram Klinger, Anja Sieber, Sheyda Naghiloo, Henrik Zauber, Nadine Lehmann, Mohamed Haji, Sylvia Niquet, Philipp Mertins, Nils Blüthgen and Matthias Selbach

Nat Commun, 2025, 16
DOI: 10.1038/s41467-025-59404-y

Multiplexed Quantitation of Plasma Proteins by Targeted Mass Spectrometry for Early Diagnosis of Pancreatic Ductal Adenocarcinoma

Dmitry N. Korobkov, Ivan A. Molodtsov, Alexey S. Kononikhin, Anna E. Bugrova, Maria I. Indeykina, Alexander G. Brzhozovskiy, Dmitry Yu. Kanner, Evgeny N. Nikolaev, Elena Vasilieva and Alexey A. Komissarov

IJMS, 2025, 26, 9219
DOI: 10.3390/ijms26189219

Novel biomarkers to detect occult cancer in patients with unprovoked venous thromboembolism: Rationale and design of the PLATO-VTE study

Noémie Kraaijpoel, Frits I. Mulder, Marc Carrier, Annabel van Lieshout, Tom Würdinger, Myron G. Best, Bart J.M. van Vlijmen, Yassene Mohammed, Luis Jara-Palomares, Pieter W. Kamphuisen, Marcello Di Nisio, Walter Ageno, Jan Beyer-Westendorf, Thomas Vanassche, Frederikus A. Klokm, Hans-Martin Otten, Mike J.L. Peters, Benilde Cosmi, Marije ten Wolde, Patrick M.M. Bossuyt, Harry R. Büller and Nick van Es

Thrombosis Update, 2021, 2, 100030
DOI: 10.1016/j.tru.2020.100030

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

Yassene Mohammed, Carolina E. Touw, Banne Nemeth, Raymond A. van Adrichem, Christoph H. Borchers, Frits R. Rosendaal, Bart J. van Vlijmen and Suzanne C. Cannegieter

Journal of Thrombosis and Haemostasis, 2022, 20, 684
DOI: 10.1111/jth.15623

Targeted MRM-analysis of plasma proteins in frozen whole blood samples from patients with COVID-19: a retrospective study

Anna E. Bugrova, Polina A. Strelnikova, Alexey S. Kononikhin, Natalia V. Zakharova, Elizaveta O. Diyachkova, Alexander G. Brzhozovskiy, Maria I. Indeykina, Ilya N. Kurochkin, Alexander V. Averyanov and Evgeny N. Nikolaev

Clinical Chemistry and Laboratory Medicine (CCLM), 2025, 63, 448
DOI: 10.1515/cclm-2024-0800

Absolute quantitative proteomics identifies patterns of plasma proteins associated with venous thromboembolism in patients with colorectal cancer

J.T. Buijs, N. van Es, C. Englisch, R.J.S. Anijs, F.T.M. Bosch, B.J.M. van Vlijmen, F.I. Mulder, I. Pabinger, C. Ay, H.H. Versteeg and Y. Mohammed

Thrombosis Research, 2026, 259, 109612
DOI: 10.1016/j.thromres.2026.109612

Blood Plasma Proteome: A Meta-Analysis of the Results of Protein Quantification in Human Blood by Targeted Mass Spectrometry

Anna A. Kliuchnikova, Svetlana E. Novikova, Ekaterina V. Ilgisonis, Olga I. Kiseleva, Ekaterina V. Poverennaya, Victor G. Zgoda, Sergei A. Moshkovskii, Vladimir V. Poroikov, Andrey V. Lisitsa, Alexander I. Archakov and Elena A. Ponomarenko

IJMS, 2023, 24, 769
DOI: 10.3390/ijms24010769

Longitudinal Plasma Proteomics Analysis Reveals Novel Candidate Biomarkers in Acute COVID-19

Yassene Mohammed, David R. Goodlett, Matthew P. Cheng, Donald C. Vinh, Todd C. Lee, Allison Mcgeer, David Sweet, Karen Tran, Terry Lee, Srinivas Murthy, John H. Boyd, Joel Singer, Keith R. Walley, David M. Patrick, Curtis Quan, Sara Ismail, Laetitia Amar, Aditya Pal, Rayhaan Bassawon, Lara Fesdekjian, Karine Gou, Francois Lamontagne, John Marshall, Greg Haljan, Robert Fowler, Brent W. Winston and James A. Russell

J. Proteome Res., 2022, 21, 975
DOI: 10.1021/acs.jproteome.1c00863

Targeted proteomics for cancer biomarker verification and validation

Seiryo Ogata, Takeshi Masuda, Shingo Ito, Sumio Ohtsuki and Kazufumi Honda

CBM, 2022, 33, 427
DOI: 10.3233/CBM-210218

Cross-platform clinical proteomics using the Charité open standard for plasma proteomics (OSPP)

Ziyue Wang, Vadim Farztdinov, Ludwig Roman Sinn, Pinkus Tober-Lau, Daniela Ludwig, Anja Freiwald, Fatma Amari, Kathrin Textoris-Taube, Agathe Niewienda, Anna Sophie Welter, Alan An Jung Wei, Luise Luckau, Florian Kurth, Matthias Selbach, Johannes Hartl, Michael Mülleder and Markus Ralser

Nat Commun, 2025, 16
DOI: 10.1038/s41467-025-67264-9

A plasma protein signature associated with cognitive function in men without severe cognitive impairment

Kanika Mehta, Mohammadreza Mohebbi, Julie A. Pasco, Lana J. Williams, Sophia X. Sui, Ken Walder, Boon Lung Ng and Veer Bala Gupta

Alz Res Therapy, 2023, 15
DOI: 10.1186/s13195-023-01294-7

Cerebrospinal fluid biomarkers for assessing Huntington disease onset and severity

Nicholas S Caron, Arsalan S Haqqani, Akshdeep Sandhu, Amirah E Aly, Hailey Findlay Black, Jeffrey N Bone, Jodi L McBride, Abedelnasser Abulrob, Danica Stanimirovic, Blair R Leavitt and Michael R Hayden

Brain Communications, 2022, 4
DOI: 10.1093/braincomms/fcac309

Cross‐Platform Proteomics and Machine Learning Algorithms Nominate Plasma Biomarkers of Stroke Diagnosis

Shubham Misra, Wooyoung Eric Jang, Sebastian Sanchez, Aditya Natu, Prateek Kumar, Michael Liu, Anmol Kaur, Victor Torres Lopez, Pinar Caglayan, Rolando Garcia‐Milian, Caroline M. Watson, Michael R. Frankel, Guido J. Falcone, Lauren H. Sansing and Srikant Rangaraju

JAHA, 2026, 15
DOI: 10.1161/JAHA.125.048249

Peculiarities of Hemostasis and Proteomics in Patients With Acute Myocardial Infarction and Healthy Volunteers After SARS-CоV-2 Infection

A. I. Kalinskaya, A. K. Elizarova, A. S. Anisimova, D. A. Vorobyeva, G. I. Rusakovich, E. V. Maryukhnich, O. A. Dukhin, O. I. Ivanova, A. E. Bugrova, A. G. Brzhozovskiy, M. I. Indeykina, A. S. Kononikhin, E. N. Nikolaev and E. Yu. Vasilieva

Kardiologiia, 2024, 64, 58
DOI: 10.18087/cardio.2024.9.n2752

Establishing Personalized Blood Protein Reference Ranges Using Noninvasive Microsampling and Targeted Proteomics: Implications for Antidoping Strategies

Vincent R. Richard, Georgia Mitsa, Azad Eshghi, Daria Chaplygina, Yassene Mohammed, David R. Goodlett, Rene P. Zahedi, Mario Thevis and Christoph H. Borchers

J. Proteome Res., 2024, 23, 1779
DOI: 10.1021/acs.jproteome.4c00020

Optimization of bottom-up proteomic sample preparation by design of experiments for absolute quantification of 257 proteins in human plasma using UPLC-MRM-MS

Kari Arnarson, Kristrun Y. Holm, Valdis Gunnarsdottir Thormar, Finnur F. Eiríksson, Yassene Mohammed, Christoph H. Borchers, Sigridur K. Bodvarsdottir and Margret Thorsteinsdottir

Expert Review of Proteomics, 2025, 22, 209
DOI: 10.1080/14789450.2025.2504994

Plasma Proteomic Profiling of a Group of Anxious Dogs by LC‐MS/MS: A Case–Control Study

Claudia Gaither, Robert Popp, Christoph H. Borchers, Francis Beaudry and Marion Desmarchelier

Proteomics Clinical Apps, 2025, 19
DOI: 10.1002/prca.70014

Proteomics in thrombosis research

Fredrik Edfors, Maria Jesus Iglesias, Lynn M. Butler and Jacob Odeberg

Research and Practice in Thrombosis and Haemostasis, 2022, 6, e12706
DOI: 10.1002/rth2.12706

Prognosis of Alzheimer’s Disease Using Quantitative Mass Spectrometry of Human Blood Plasma Proteins and Machine Learning

Alexey S. Kononikhin, Natalia V. Zakharova, Savva D. Semenov, Anna E. Bugrova, Alexander G. Brzhozovskiy, Maria I. Indeykina, Yana B. Fedorova, Igor V. Kolykhalov, Polina A. Strelnikova, Anna Yu. Ikonnikova, Dmitry A. Gryadunov, Svetlana I. Gavrilova and Evgeny N. Nikolaev

IJMS, 2022, 23, 7907
DOI: 10.3390/ijms23147907

Proteomic Evolution from Acute to Post-COVID-19 Conditions

Yassene Mohammed, Karen Tran, Chris Carlsten, Christopher Ryerson, Alyson Wong, Terry Lee, Matthew P. Cheng, Donald C. Vinh, Todd C. Lee, Brent W. Winston, David Sweet, John H. Boyd, Keith R. Walley, Greg Haljan, Allison McGeer, Francois Lamontagne, Robert Fowler, David Maslove, Joel Singer, David M. Patrick, John C. Marshall, Srinivas Murthy, Fagun Jain, Christoph H. Borchers, David R. Goodlett, Adeera Levin and James A. Russell

J. Proteome Res., 2024, 23, 52
DOI: 10.1021/acs.jproteome.3c00324

Targeted Quantification of Proteoforms in Complex Samples by Proteoform Reaction Monitoring

Che-Fan Huang, Jake T. Kline, Fernanda Negrão, Matthew T. Robey, Timothy K. Toby, Kenneth R. Durbin, Ryan T. Fellers, John J. Friedewald, Josh Levitsky, Michael M. I. Abecassis, Rafael D. Melani, Neil L. Kelleher and Luca Fornelli

Anal. Chem., 2024, 96, 3578
DOI: 10.1021/acs.analchem.3c05578

Multiple Reaction Monitoring-Mass Spectrometry Enables Robust Quantitation of Plasma Proteins Regardless of Whole Blood Processing Delays That May Occur in the Clinic

Claudia Gaither, Robert Popp, René P. Zahedi and Christoph H. Borchers

Molecular & Cellular Proteomics, 2022, 21, 100212
DOI: 10.1016/j.mcpro.2022.100212

Targeted MRM Quantification of Urinary Proteins in Chronic Kidney Disease Caused by Glomerulopathies

Alexey S. Kononikhin, Alexander G. Brzhozovskiy, Anna E. Bugrova, Natalia V. Chebotareva, Natalia V. Zakharova, Savva Semenov, Anatoliy Vinogradov, Maria I. Indeykina, Sergey Moiseev, Irina M. Larina and Evgeny N. Nikolaev

Molecules, 2023, 28, 3323
DOI: 10.3390/molecules28083323

Assessment of a 60-Biomarker Health Surveillance Panel (HSP) on Whole Blood from Remote Sampling Devices by Targeted LC/MRM-MS and Discovery DIA-MS Analysis

Stephen A. Whelan, Nathan Hendricks, Zachary L. Dwight, Qin Fu, Annie Moradian, Jennifer E. Van Eyk and Susan M. Mockus

Anal. Chem., 2023, 95, 11007
DOI: 10.1021/acs.analchem.3c01189

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

Claudia Gaither, Robert Popp, Sophia P. Borchers, Kjartan Skarphedinsson, Finnur F. Eiriksson, Margrét Thorsteinsdóttir, Yassene Mohammed and Christoph H. Borchers

J. Proteome Res., 2021, 20, 4292
DOI: 10.1021/acs.jproteome.1c00249

Absolute Quantitative Targeted Monitoring of Potential Plasma Protein Biomarkers: A Pilot Study on Healthy Individuals

Alexey S. Kononikhin, Natalia L. Starodubtseva, Alexander G. Brzhozovskiy, Alisa O. Tokareva, Daria N. Kashirina, Natalia V. Zakharova, Anna E. Bugrova, Maria I. Indeykina, Liudmila Kh. Pastushkova, Irina M. Larina, Vladimir A. Mitkevich, Alexander A. Makarov and Evgeny N. Nikolaev

Biomedicines, 2024, 12, 2403
DOI: 10.3390/biomedicines12102403

Proteomics of human biological fluids for biomarker discoveries: technical advances and recent applications

Loïc Dayon, Ornella Cominetti and Michael Affolter

Expert Review of Proteomics, 2022, 19, 131
DOI: 10.1080/14789450.2022.2070477

Quantitative targeted proteomics for occult cancer screening in patients with unprovoked venous thromboembolism: results from the prospective PLATO-VTE study

Noori A.M. Guman, Noémie Kraaijpoel, Frits I. Mulder, Marc Carrier, Luis Jara-Palomares, Marcello Di Nisio, Walter Ageno, Jan Beyer-Westendorf, Frederikus A. Klok, Thomas Vanassche, Johannes M.M.B. Otten, Benilde Cosmi, Mike J.L. Peters, Marije ten Wolde, Aurélien Delluc, Pieter W. Kamphuisen, Verónica Sánchez-López, Ettore Porreca, Jip Ramaker, Patrick M.M. Bossuyt, Harry R. Büller, Henri H. Versteeg, Bart J.M. van Vlijmen, Nick van Es and Yassene Mohammed

Research and Practice in Thrombosis and Haemostasis, 2025, 9, 103018
DOI: 10.1016/j.rpth.2025.103018

Identification of a novel apoB variant in a family exhibiting hypocholesterolemia: Mechanistic insights

Rachid Essalamani, Alexandra Evagelidis, Anna Roubtsova, Michael Chong, Nazia Pathan, Guillaume Pare, Evgeniy V. Petrochenko, Mart Reimund, Alan T. Remaley, Lorraine Chalifour, Morris Schweitzer and Nabil G. Seidah

Journal of Clinical Lipidology, 2026
DOI: 10.1016/j.jacl.2026.02.013

Plasma proteomic profiles of patients during oral anti‐coagulant treatment with vitamin K antagonists

Eleonora Camilleri, Bart J. M. van Vlijmen, Mettine H. A. Bos, Manfred Wuhrer, David R. Goodlett, Christoph H. Borchers, Suzanne C. Cannegieter, Nienke van Rein and Yassene Mohammed

Br J Haematol, 2026, 208, 763
DOI: 10.1111/bjh.70278

Machine Learning and Blood-Targeted Proteomics Enable Early Prediction and Etiological Discrimination of Hypertensive Pregnancy Disorders

Natalia Starodubtseva, Alisa Tokareva, Alexey Kononikhin, Anna Bugrova, Maria Indeykina, Evgenii Kukaev, Alina Poluektova, Alexander Brzhozovskiy, Evgeny Nikolaev and Gennady Sukhikh

IJMS, 2026, 27, 1402
DOI: 10.3390/ijms27031402

Targeted Blood Plasma Proteomics and Hemostasis Assessment of Post COVID-19 Patients with Acute Myocardial Infarction

Anna Kalinskaya, Daria Vorobyeva, George Rusakovich, Elena Maryukhnich, Alexandra Anisimova, Oleg Dukhin, Antonina Elizarova, Oxana Ivanova, Anna Bugrova, Alexander Brzhozovskiy, Alexey Kononikhin, Evgeny Nikolaev and Elena Vasilieva

IJMS, 2023, 24, 6523
DOI: 10.3390/ijms24076523

Potential of Proteomics in Forensic Phenotyping: A Focus on Biological Sex Estimation

Shirin Alex, Ruben Almey, Rachel Sian Dennis, Olivier Tytgat, Robbin Bouwmeester, Dieter Deforce, Marcel De Puit, Maarten Dhaenens and Laura De Clerck

J. Proteome Res., 2025, 24, 4888
DOI: 10.1021/acs.jproteome.5c00098