Citation Index

Agilent AssayMAP Bravo

In this citation index, you will gain fast access to the bibliographic information for all
the peer reviewed publications, as of September 2021, that use the AssayMAP Bravo
for protein sample preparation. This citation index illustrates the wide variety of ways
the AssayMAP Bravo platform has been used to help generate high quality dataand enable analysis on a scale that was previously considered unattainable. The
citations are organized chronologically by year and within each year alphabetically.
Each publication has keywords to make it easy to find publications that match yourresearch interest.

Searchable key words

AssayMAP cartridge type used

Areas of study–

C18 (Reversed Phase) (52)–CU (Cleanup) (5)–Fe(III)‑NTA (IMAC) (46)–

PAW (Protein A) (12)–PGW (Protein G) (6)–RPS (Reversed Phase‑small pore) (22)–

RPW (Reversed Phase‑wide pore) (2)–RX (Reaction) (4)–SAW (Streptavidin) (20)–

SCX (Strong Cation Exchange) (5)–TiO2 (Titanium Dioxide) (5)–Antibody Drug Conjugates (5)–Biomarkers (12)–Biopharma (21)–Clinical Research (27)–Glycans (6)–Glycoproteomics (1)–Immunopeptidomics (5)–Mechanism of Action (9)–Pharmacokinetics (13)–

Phosphoproteomics (41)–Protein‑Protein Interactions (13)–Proteomics (64)–Signal Transduction (27)–

Ubiquitination (1)Techniques–

BioID (8)–Immunocapture (20)–

PhosID (1)–PhoX (4)–

TMT labeling (1)2AssayMAP application used–

Affinity Purification (35)–Fractionation (15)–Glykoprep (4)–In‑Solution Digestion (15)–

On‑cartridge Reaction (8)–Peptide Cleanup (65)–

Phosphopeptide Enrichment (50)–Protein Cleanup (1)AssayMAP Bravo citations
2021
A New Mouse Model Related to SCA14 Carrying a Pseudosubstrate Domain Mutation in PKCγ
Shows Perturbed Purkinje Cell Maturation and Ataxic Motor Behavior
Authors: Etsuko Shimobayashi and Josef P. Kapfhammer
Journal Citation: The Journal of Neuroscience 2021, 41(9), 2053–2068
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
A Proteomics‑Based Assessment of Inflammation Signatures in Endotoxemia
Authors: Sean A. Burnap, Ursula Mayr, Manu Shankar‑Hari, Friederike Cuello, Mark R. Thomas,
Ajay M. Shah, Ian Sabroe, Robert F. Storey, and Manuel Mayr
Journal Citation: Molecular and Cellular Proteomics 2021, 20, 100021
Key words: C18, Peptide Cleanup, Clinical Research, Proteomics, Biomarkers
A serum proteome signature to predict mortality in severe COVID–19 patients
Authors: Franziska Vollmy, Henk van den Toorn, Riccardo Zenezini Chiozzi, Ottavio Zucchetti,
Alberto Papi, Carlo Alberto Volta, Luisa Marracino, Francesco Vieceli Dalla Sega, Francesca
Fortini, Vadim Demichev, Pinkus Tober‑Lau, Gianluca Campo, Marco Contoli, Markus Ralser,
Florian Kurth, Savino Spadaro, Paola Rizzo, and Albert J. R. Heck
Journal Citation: Life Science Alliance 2021, 4(9), e202101099
Key words: C18, Peptide Cleanup, Clinical Research, Proteomics, Biomarkers
A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine
Tie–Wnt signaling axis in the liver
Authors: Donato Inverso, Jingjing Shi, Ki Hong Lee, Moritz Jakab, Shani Ben‑Moshe, Shubhada R.
Kulkarni, Martin Schneider, Guanxiong Wang, Marziyeh Komeili, Paula Argos Velez, Maria Riedel,
Carleen Spegg, Thomas Ruppert, Christine Schaeffer‑Reiss, Dominic Helm, Indrabahadur Singh,
Michael Boutros, Sudhakar Chintharlapalli, Mathias Heikenwalder, Shalev Itzkovitz, and Hellmut
G. Augustin
Journal Citation: Developmental Cell 2021, 56(11), 1677–1693
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
A type 2C protein phosphatase activates high‑affinity nitrate uptake by dephosphorylating
NRT2.1
Authors: Yuri Ohkubo, Keiko Kuwata, and Yoshikatsu Matsubayashi
Journal Citation: Nature Plants 2021, 7, 310–316
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Proteomics, Signal Transduction

3

ABPP‑HT‑High‑Throughput Activity‑Based Profiling of Deubiquitylating Enzyme Inhibitors in a
Cellular Context
Authors: Hannah Jones, Raphael Heilig, Roman Fischer, Benedikt M. Kessler, and Adan
Pinto‑Fernandez
Journal Citation: Frontiers in Chemistry 2021, 9, 640105
Key words: PAW, Affinity Purification, Signal Transduction, Immunocapture
Afucosylated IgG characterizes enveloped viral responses and correlates with COVID–19 severity
Authors: Mads Delbo Larsen, Erik L. de Graff, Myrthe E. Sonneveld, H. Rosina Plomp, Jan Nouta,
Willianne Hoepel, Hung‑Jen Chen, Federica Linty, Remco Visser, Maximilian Briknkhaus, Tonci
Sustic, Steven W. de Taeye, Arthur E. H. Bentlage, Suvi Toivonen, Carolien A. M. Koeleman,
Susanna Sainio, Neeltje A. Kootstra, Philip J. M. Brouwer, Chiara Elisabeth Geyer, Ninotska I. L.
Derksen, Gertjan Wolbink, Menno de Winther, Rogier W. Sanders, Marit J. Van Gils, Sanne De
Bruin, Alexander P. J. Vlaar, Amsterdam UMC Covid–19, Biobank Study Group, Theo Rispens,
Jeroen Den Dunnen, Hans L. Zaaijer, Manfred Wuhrer, C. Ellen Van Der Schoot, and Gestur
Vidarsson
Journal Citation: Science 2021, 371(6532), eabc8378
Key words: PGW, Affinity Purification, Clinical research, Biomarkers
An EZH2‑dependent transcriptional complex promotes aberrant epithelial remodeling after injury
Authors: Huy Q. Le, Matthew A. Hill, Ines Kollak, Martina Keck, Victoria Schroeder, Johannes
Wirth, Wioletta Skronska‑Wasek, Eva Schruf, Benjamin Strobel, Heiko Stahl, Franziska E.
Herrmann, Alexandre R. Campos, Jun Li, Karsten Quast, Dagmar Knebel, Coralie Viollet, Matthew
J. Thomas, David Lamb, and James P. Garnett
Journal Citation: EMBO Reports 2021, 22(8), e52785
Key words: C18, Peptide Cleanup, Proteomics, Signal Transduction
Antibody toolkit reveals N‑terminally ubiquitinated substrates of UBE2W
Authors: Christopher W. Davies, Simon E. Vidal, Lilian Phu, Jawahar Sudhamsu, Trent B. Hinkle,
Scott Chan Rosenberg, Frances‑Rose Schumacher, Yi Jimmy Zeng, Carsten Schwerdtfeger,
Andrew S. Peterson, Jennie R. Lill, Christopher M. Rose, Andrey S. Shaw, Ingrid E. Wertz, Donald
S. Kirkpatrick, and James T. Koerber
Journal Citation: Nature Communications 2021, 12, 4608
Key words: RPS, Fractionation, Proteomics, Ubiquitination, Signal Transduction
Automated and Faster Affinity Capture Method for Biotransformation Assessment ofSite‑Specific Antibody Drug Conjugates
Authors: Aarti Jashnani, Srikanth Kotapati, Madhura Deshpande, Sayumi Yamazoe, Pavel Strop,
Arvind Rajpal, and Gavin Dollinger
Journal Citation: Analytical Chemistry 2021, 93(13), 5371–5376
Key words: SAW, Affinity Purification, On‑Cartridge Reaction, Biopharma, Antibody Drug
Conjugates, Pharmacokinetics, Immunocapture4Automated Ligand Purification Platform Accelerates Immunopeptidome Analysis by Mass
Spectrometry
Authors: Lichao Zhang, Patrick L. McAlpine, Marlene L. Heberling, and Joshua E. Elias
Journal Citation: Journal of Proteome Research 2021, 20(1), 393–408
Key words: PAW, RPS, Affinity Purification, Peptide Cleanup, Proteomics, Immunopeptidomics,
Immunocapture
Automated Phosphopeptide Enrichment for Gram‑Positive Bacteria
Authors: Marlène S. Birk, Emmanuelle Charpentier, and Christian K. Frese
Journal Citation: Journal of Proteome Research 2021, 20(10), 4886–4892
Key words: Fe(III)‑NTA, TiO2, Phosphopeptide Enrichment, Phosphoproteomics
Combined Inhibition of AKT and KIT Restores Expression of Programmed Cell Death 4 (PDCD4)in Gastrointestinal Stromal Tumor
Authors: Marya Kozinova, Shalina Joshi, Shuai Ye, Martin G. Belinsky, Dinara Sharipova, Jeffrey
M. Farma, Sanjay Reddy, Samuel Litwin, Karthik Devarajan, Alex Rosa Campos, Yi Yu, Brian
Schwartz, Margaret von Mehren, and Lori Rink
Journal Citation: Cancers 2021, 13(15), 3699
Key words: C18, Peptide Cleanup, Clinical Research, Proteomics, Signal Transduction
Comparing the efficacy and selectivity of Ck2 inhibitors. A phosphoproteomics approach
Authors: Christian Borgo, Luca Cesaro, Tsuyoshi Hirota, Keiko Kuwata, Claudio D’Amore, Thomas
Ruppert, Renata Blatnik, Mauro Salvi, Lorenzo A. Pinna
Journal Citation: European Journal of Medicinal Chemistry 2021, 214(15), 113217
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Clinical Research, Phosphoproteomics
Comprehensive micro‑scaled proteome and phosphoproteome characterization of archived
retrospective cancer repositories
Authors: Corinna Friedrich, Simon Schallenberg, Marieluise Kirchner, Matthias Ziehm, Sylvia
Niquet, Mohamed Haji, Christin Beier, Jens Neudecker, Frederick Klauschen and Philipp Mertins
Journal Citation: Nature Communications 2021, 12(1), 3576
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Clinical Research, Phosphoproteomics
Determination of Adenylate Nucleotides in Amphipod Gammarus fossarum by Ion‑Pair Reverse
Phase Liquid Chromatography: Possibilities of Positive Pressure Micro‑Solid Phase Extraction
Authors: Zuzana Redžovi´c, Marijana Erk, Ema Svetlicic, Lucija Doncevic, Sanja Gottstein, Amela
Hozic and Mario Cindric
Journal Citation: Separations 2021, 8(2), 20
Key words: Custom, Fractionation

5

Extensive remodeling of the extracellular matrix during aging contributes to age‑dependent
impairments of muscle stem cell functionality
Authors: Svenja C. Schüler, Joanna M. Kirkpatrick, Manuel Schmidt, Deolinda Santinha, Philipp
Koch, Simone Di Sanzo, Emilio Cirri, Martin Hemberg, Alessandro Ori, and Julia von Maltzahn
Journal Citation: Cell Reports 2021, 35(10), 109223
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
FRET‑Based Screening Identifies p38 MAPK and PKC Inhibition as Targets for Prevention of
Seeded α‑Synuclein Aggregation
Authors: Alexander Svanbergsson, Fredrik Ek, Isak Martinsson, Jordi Rodo, Di Liu, Edoardo
Brandi, Caroline Haikal, Laura Torres‑Garcia, Wen Li, Gunnar Gouras, Roger Olsson, Tomas
Björklund, and Jia‑Yi Li
Journal Citation: Neurotherapeutics 2021
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
Global proteomic analysis of extracellular matrix in mouse and human brain highlights relevanceto cerebrovascular disease
Authors: Alexandra Pokhilko, Gaia Brezzo, Lahiru Handunnetthi, Raphael Heilig, Rachel Lennon,
Colin Smith, Stuart M. Allan, Alessandra Granata, Sanjay Sinha, Tao Wang, Hugh S. Markus,
Alexandra Naba, Roman Fischer, Tom Van Agtmael, Karen Horsburgh, and M. Zameel Cader
Journal Citation: Journal of Cerebral Blood Flow and Metabolism 2021, 41(9), 2423–2438
Key words: RPS, Fractionation, Proteomics
High Endothelial Venules Accelerate Naive T Cell Recruitment by Tumor Necrosis Factor
Mediated R‑Ras Upregulation
Authors: Junko Sawada, Carole Y. Perrot, Linyuan Chen, Ashley E. Fournier‑Goss, Jeremiah Oyer,
Alicja Copik, and Masanobu Komatsu
Journal Citation: The American Journal of Pathology 2021, 191(2), 396–414
Key words: C18, Peptide Cleanup, Proteomics, Signal transduction
High titers and low fucosylation of early human anti‑SARS‑CoV–2 IgG promote inflammation by
alveolar macrophages
Authors: Willianne Hoepel, Hung‑Jen Chen, Chiara E. Geyer, Sona Allahverdiyeva, Xue D. Manz,
Steven W. de Taeye, Jurjan Aman, Lynn Mes, Maurice Steenhuis, Guillermo R. Griffith, Peter I.
Bonta, Philip J. M. Brouwer, Tom G. Caniels, Karlijn van der Straten, Korneliusz Golebski, René
E. Jonkers, Mads D. Larsen, Federica Linty, Jan Nouta, Cindy P. A. A. van Roomen, Frank E. H. P.
van Baarle, Cornelis M. van Drunen, Gertjan Wolbink, Alexander P. J. Vlaar, Godelieve J. de Bree,
Rogier W. Sanders, Lisa Willemsen, Annette E. Neele, Diederik van de Beek, Theo Rispens,
Manfred Wuhrer, Harm Jan Bogaard, Marit J. van Gils, Gestur Vidarsson, Menno de Winther, andJeroen den Dunnen
Journal Citation: Science Translational Medicine 2021, 13(596), eabf8654
Key words: PGW, Affinity Purification, Clinical Research, Biomarkers

6

Hypoxia‑induced acetylation of PAK1 enhances autophagy and promotes brain tumorigenesis via
phosphorylating ATG5
Authors: Xing Feng, Heng Zhang, Lingbing Meng, Huiwen Song, Qingxin Zhou, Chao Qu, PanZhao, Qinghua Li, Chang Zou, Xing Liu, and Zhiyong Zhang
Journal Citation: Autophagy 2021, 17(3), 723–742
Key words: SAW, Affinity Purification, Protein‑Protein Interactions, Proteomics, Signal
Transduction, BioID
Impairment of the ER/mitochondria compartment in human cardiomyocytes with PLN
p.Arg14del mutation
Authors: Friederike Cuello, Anika E. Knaust, Umber Saleem, Malte Loos, Janice Raabe, Diogo
Mosqueira, Sandra Laufer, Michaela Schweizer, Petra van der Kraak, Frederik Flenner, Barbel M.
Ulmer, Ingke Braren, Xiaoke Yin, Konstantinos Theofilatos, Jorge Ruiz‑Orera, Giannino Patone,
Birgit Klampe, Thomas Schulze, Angelika Piasecki, Yigal Pinto, Aryan Vink, Norbert Hubner, Sian
Harding, Manuel Mayr, Chris Denning, Thomas Eschenhagen, and Arne Hansen
Journal Citation: EMBO Molecular Medicine 2021, 13(6), e13074
Key words: C18, Peptide Cleanup, Clinical Research, Proteomics
In situ detection of protein interactions for recombinant therapeutic enzymes
Authors: Mojtaba Samoudi, Chih‑Chung Kuo, Caressa M. Robinson, Km Shams‑Ud‑Doha,
Song‑Min Schinn, Stefan Kol, Linus Weiss, Sara Petersen Bjorn, Bjorn G. Voldborg,
Alexandre Rosa Campos, and Nathan E. Lewis
Journal Citation: Biotechnology and Bioengineering 2021, 118(2), 890–904
Key words: C18, SAW, Affinity Purification, On‑Cartridge Reaction, Peptide Cleanup, Biopharma,
Protein‑Protein Interactions, Proteomics, BioID
Mechanisms of Regulation and Diverse Activities of Tau‑Tublin Kinase (TTBK) Isoforms
Authors: Channa Bao, Bekim Bajrami, Douglas J. Marcotte, Jayanth V. Chodaparambil, Hannah
M. Kerns, Jaclyn Henderson, Ru Wui, Benbo Gao, and Gregory M. Dillon
Journal Citation: Cellular and Molecular Neurobiology 2021, 41, 669–685
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics, Signal Transduction
Multilevel proteomics reveals host perturbation strategies of SARS‑CoV–2 and SARS‑CoV
Authors: Alexey Stukalov, Virginie Girault, Vincent Grass, Ozge Karayel, Valter Bergant, Christian
Urban, Darya A. Haas, Yiqi Huang, Lila Oubraham, Anqi Wang, Sabri M. Hamad, Antonio Piras,
Fynn M. Hansen, Maria Tanzer, Igor Paron, Luca Zinzula, Thomas Enghleitner, Maria Reinecke,
Teresa M. Lavacca, Rosina Ehmann, Roman Wölfel, Jörg Jores, Bernhard Kuster, Ulrike Protzer,
Roland Rad, John Ziebuhr, Volker Thiel, Pietro Scaturro, Matthias Mann, and Andreas Pichlmair
Journal Citation: Nature 2021, 594, 246–252
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics

7

Notch‑Jagged signaling complex defined by an interaction mosaic
Authors: Matthieu R. Zeronian, Oleg Klykov, Julia Portell i de Montserrat, Maria J. Konijnenberg,
Anamika Gaur, Richard A. Scheltema, and Bert J. C. Janssen
Journal Citation: PNAS 2021, 118(30), e2102502118
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Protein‑Protein Interactions, Signal
Transduction, PhoX
Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding
Authors: Michael Taschner, Jerome Basquin, Barbara Steigenberger, Ingmar Schaefer, Young‑Min
Soh, Claire Basquin, Esben Lorentzen, Markus Raschle, Richard A. Scheltema, Stephan Gruber
Journal Citation: The EMBO Journal 2021, 40(15), e107807
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Protein‑Protein Interactions, Signal
Transduction, PhoX
Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds
Authors: Deborah O. Dele‑Oni, Karen E. Christianson, Shawn B. Egri, Alvaro Sebastian Vaca
Jacome, Katherine C. DeRuff, James Mullahoo, Vagisha Sharma, Desiree Davison, Tak Ko,
Michael Bula, Joel Blanchard, Jennie Z. Young, Lev Litichevskiy, Xiaodong Lu, Daniel Lam, Jacob
K. Asiedu, Caidin Toder, Adam Officer, Ryan Peckner, Michael J. MacCoss, Li‑Huei Tsai, Steven A.
Carr, Malvina Papanastasiou, Jacob D. Jaffe
Journal Citation: Scientific Data 2021, 8, 226
Key words: Fe(III)‑NTA, RPS, Phosphopeptide Enrichment, Peptide Cleanup, Mechanism of
Action, Phosphoproteomics
Proteomics and Phosphoproteomics Profiling of Drug‑Addicted BRAFi‑Resistant Melanoma Cells
Authors: Bohui Li, Xiangjun Kong, Harm Post, Linsey Raaijmakers, Daniel S. Peeper, and Maarten
Altelaar
Journal Citation: Journal of Proteomics Research 2021, 20(9), 4381–4392
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics, Signal Transduction
Response of Saccharomyces cerevisiae W303 to Iron and Lead Toxicity in Overloaded Conditions
Authors: Gordana Čanadi Jurešić, Božena Ćurko‑Cofek, Martina Barbarić, Nermina Mumiši,
Branka Blagović, and Polona Jamnik
Journal Citation: Current Microbiology 2021, 78, 1188–1201
Key words: C18, Peptide Cleanup, Proteomics

8

SARS‑CoV–2 RNAemia and proteomic trajectories inform prognostication in COVID–19 patients
admitted to intensive care
Authors: Clemens Gutmann, Kaloyan Takov, Sean A. Burnap, Bhawana Singh, Hashim Ali,
Konstantinos Theofilatos, Ella Reed, Maria Hasman, Adam Nabeebaccus, Matthew Fish, MarkJ. W. McPhail, Kevin O’Gallagher, Lukas E. Schmidt, Christian Cassel, Marieke Rienks, Xiaoke
Yin, Georg Auzinger, Salvatore Napoli, Salma F. Mujib, Francesca Trovato, Barnaby Sanderson,
Blair Merrick, Umar Niazi, Mansoor Saqi, Konstantina Dimitrakopoulou, Rafael Fernandez‑Leiro,
Silke Braun, Romy Kronstein‑Wiedemann, Katie J. Doores, Jonathan D. Edgeworth, Ajay M. Shah,
Stefan R. Bornstein, Torsten Tonn, Adrian C. Hayday, Mauro Giacca, Manu Shankar‑Hari, andManuel Mayr
Journal Citation: Nature Communications 2021, 12(1), 3406
Key words: C18, Peptide Cleanup, Clinical Research, Proteomics
Sensitive and Quantitative Detection of MHC‑I Displayed Neoepitopes Using a SemiautomatedWorkflow and TOMAHAQ Mass Spectrometry
Authors: Samuel B. Pollock, Christopher M. Rose, Martine Darwish, Romain Bouziat, Lélia
Delamarre, Craig Blanchette, and Jennie R. Lill
Journal Citation: Molecular and Cellular Proteomics 2021, 20, 100108
Key words: PAW, C18, Affinity Purification, On‑Cartridge Reaction, Peptide Cleanup, Biopharma,
Immunopeptidomics, Proteomics, Immunocapture
Structure of the human signal peptidase complex reveals the determinants for signal peptide
cleavage
Authors: A. Manuel Liaci, Barbara Steigenberger, Paulo Cesar Telles de Souza, Sem Tamara,Mariska Gröllers‑Mulderij, Patrick Ogrissek, Siewert J. Marrink, Richard A. Scheltema, andFriedrich Förster
Journal Citation: Molecular Cell 2021
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Protein‑Protein Interactions, PhoX
Study of the venom proteome of Vipera ammodytes ammodytes (Linnaeus, 1758): A qualitative
overview, biochemical and biological profiling
Authors: Kristina Gopcevic, Ivanka Karadzic, Lidija Izrael‑Zivkovic, Ana Medic, Aleksandra
Isakovic, Marjan Popovi´, Dusan Kekic, Tatjana Stanojkovic, Amela Hozic, and Mario Cindric
Journal Citation: Comparative Biochemistry and Physiology‑Part D: Genomics and Proteomics
2021, 37, 100776
Key words: RPW, Protein Cleanup, Proteomics

9

The Human Melanoma Proteome Atlas—Complementing the melanoma transcriptome
Authors: Lazaro Hiram Betancourt, Jeovanis Gil, Aniel Sanchez, Viktória Doma, Magdalena Kuras,
Jimmy Rodriguez Murillo, Erika Velasquez, Uğur Çakır, Yonghyo Kim, Yutaka Sugihara, Indira Pla
Parada, Beáta Szeitz, Roger Appelqvist, Elisabet Wieslander, Charlotte Welinder, Natália Pintode Almeida, Nicole Woldmar, Matilda Marko‑Varga, Jonatan Eriksson, Krzysztof Pawłowski, Bo
Baldetorp, Christian Ingvar, Håkan Olsson, Lotta Lundgren, Henrik Lindberg, Henriett Oskolas,
Boram Lee, Ethan Berge, Marie Sjögren, Carina Eriksson, Dasol Kim, Ho Jeong Kwon, Beatrice
Knudsen, Melinda Rezeli, Johan Malm, Runyu Hong, Peter Horvath, A. Marcell Szász, József
Tímár, Sarolta Kárpáti, Peter Horvatovich, Tasso Miliotis, Toshihide Nishimura, Harubumi Kato,
Erik Steinfelder, Madalina Oppermann, Ken Miller, Francesco Florindi, Quimin Zhou, Gilberto B.
Domont, Luciana Pizzatti, Fábio C. S. Nogueira, Leticia Szadai, István Balázs Németh, Henrik
Ekedahl, David Fenyö, and György Marko‑Varga
Journal Citation: Clinical and Translational Medicine 2021, 11(7), e451
Key words: C18, Fe(III)‑NTA, Phosphopeptide Enrichment, Peptide Cleanup, Clinical Research,
Phosphoproteomics, Proteomics
The human melanoma proteome atlas—Defining the molecular pathology
Authors: Lazaro HiramBetancourt, Jeovanis Gil, Yonghyo Kim, Viktória Doma, Uğur Çakır, Aniel
Sanchez, Jimmy Rodriguez Murillo, Magdalena Kuras, Indira Pla Parada, Yutaka Sugihara, Roger
Appelqvist, Elisabet Wieslander, Charlotte Welinder, Erika Velasquez, Natália Pinto de Almeida,
Nicole Woldmar, Matilda Marko‑Varga, Krzysztof Pawłowski, Jonatan Eriksson, Beáta Szeitz, Bo
Baldetorp, Christian Ingvar, Håkan Olsson, Lotta Lundgren, Henrik Lindberg, Henriett Oskolas,
Boram Lee, Ethan Berge, Marie Sjögren, Carina Eriksson, Dasol Kim, Ho Jeong Kwon, Beatrice
Knudsen, Melinda Rezeli, Runyu Hong, Peter Horvatovich, Tasso Miliotis, Toshihide Nishimura,
Harubumi Kato, Erik Steinfelder, Madalina Oppermann, Ken Miller, Francesco Florindi, Qimin Zhou,
Gilberto B. Domont, Luiciana Pizzatti, Fábio C. S. Nogueira, Peter Horvath, Leticia Szadai, József
Tímár, Sarolta Kárpáti, A. Marcell Szász, JohanMalm, David Fenyö, Henrik Ekedahl, István Balázs
Németh, and György Marko‑Varga
Journal Citation: Clinical and Translational Medicine 2021, 11(7), e473
Key words: C18, Peptide Cleanup, Clinical Research, Proteomics
Transcriptomic, proteomic and phosphoproteomic underpinnings of daily exercise performanceand zeitgeber activity of training in mouse muscle
Authors: Geraldine Maier, Julien Delezie1, Pål O. Westermark, Gesa Santos, Danilo Ritz, andChristoph Handschin
Journal Citation: The Journal of Physiology 2021
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
Universal Automated Immunoaffinity Purification‑CE−MS Platform for Accelerating Next
Generation Biologic Design
Authors: Mei Han, Yunan Wang, Kevin Cook, Noor Bala, Marcus Soto, Dan A. Rock, Josh T.
Pearson, and Brooke M. Rock
Journal Citation: Analytical Chemistry 2021, 93(13), 5562–5569
Key words: SAW, Affinity Purification, Biopharma, Pharmacokinetics, Immunocapture

10

YAP and β‑Catenin Cooperate to Drive Oncogenesis in Basal Breast Cancer
Authors: Hazel Quinn, Regina Vogel, Oliver Popp, Philipp Mertins, Linxiang Lan, Clemens
Messerschmidt, Alexandro Landshammer, Kamil Lisek, Sophie Chateau‑Joubert, Elisabetta
Marangoni, Elle Koren, Yaron Fuchs, and Walter Birchmeier
Journal Citation: Cancer Research 2021, 81, 2116–2127
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics

2020
A mass spectrometry‑based proteome map of drug action in lung cancer cell lines
Authors: Benjamin Ruprecht, Julie Di Bernardo, Zhao Wang, Xuan Mo, Oleg Ursu, Matthew
Christopher, Rafael B. Fernandez, Li Zheng, Brian D. Dill, Huijun Wang, Yuting Xu, Andy Liaw,
Jonathan D. Mortison, Nirodhini Siriwardana, Brian Andresen, Meir Glick, James R. Tata, Victoria
Kutilek, Ivan Cornella‑Taracido and An Chi
Journal Citation: Nature Chemical Biology 2020, 16, 1111–1119
Key words: C18, Peptide Cleanup, Mechanism of Action, Proteomics
A rapid method for relative quantification of N‑glycans from a therapeutic monoclonal antibody
during trastuzumab biosimilar development
Authors: Zaneer Segu, Todd Stone, Claudia Berdugo, Anthony Roberts, Emma Doud, andYunsong Li
Journal Citation: mABs 2020, 12(1), 1750794
Key words: PA50, Glycans
Avant‑garde: an automated data‑driven DIA data curation tool
Authors: Alvaro Sebastian Vaca Jacome, Ryan Peckner, Nicholas Shulman, Karsten Krug,
Katherine C. DeRuff, Adam Officer, Karen E. Christianson, Brendan MacLean, Michael J.
MacCoss, Steven A. Carr and Jacob D. Jaffe
Journal Citation: Nature Methods 2020, 17, 1237–1244
Key words: Fe(III)‑NTA, RPS, Phosphopeptide Enrichment, Peptide Cleanup, Mechanism of
Action, Phosphoproteomics
Chronic glucose‑dependent insulinotropic polypeptide receptor (GIPR) agonism desensitizes
adipocyte GIPR activity mimicking functional GIPR antagonism
Authors: Elizabeth A. Killion, Michelle Chen, James R. Falsey, Glenn Sivits, Todd Hager, Larissa
Atangan, Joan Helmering, Jae Lee, Hongyan Li, Bin Wu, Yuan Cheng, Murielle M. Véniant, andDavid J. Lloyd
Journal Citation: Nature Communications 2020, 11, 4981
Key words: PAW, Affinity Purification, Pharmacokinetics, Immunocapture11Collagen‑rich omentum is a premetastatic niche for integrin α2‑mediated peritoneal metastasis
Authors: Yen‑Lin Huang, Ching‑Yeu Liang, Danilo Ritz, Ricardo Coelho, Dedy Septiadi, Manuela
Estermann, Cecile Cumin, Natalie Rimmer, Andreas Schotzau, Monica Nunez Lopez, Andre´
Fedier, Martina Konantz, Tatjana Vlajnic, Diego Calabrese, Claudia Lengerke, Leonor David,
Barbara Rothen‑Rutishauser, Francis Jacob, and Viola Heinzelmann‑Schwarz
Journal Citation: elife 2020, 9, e59442
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
Combined EGFR and ROCK Inhibition in Triple‑negative Breast Cancer Leads to Cell Death Via
Impaired Autophagic Flux
Authors: Stamatia Rontogianni, Sedef Iskit, Sander van Doorn, Daniel S. Peeper and Maarten
Altelaar
Journal Citation: Molecular and Cellular Proteomics 2020, 19(2), 261–277
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Mechanism of Action, Phosphoproteomics
Comparative Application of BioID and TurboID for Protein‑Proximity Biotinylation
Authors: Danielle G. May, Kelsey L. Scott, Alexandre R. Campos, and Kyle J. Roux
Journal Citation: Cells 2020, 9(5), 1070–1090
Key words: C18, Peptide Cleanup, Protein‑Protein Interactions, BioID
Data, Reagents, Assays and Merits of Proteomics for SARS‑CoV–2 Research and Testing
Authors: Jana Zecha, Chien‑Yun Lee, Florian P. Bayer, Chen Meng, Vincent Grass, Johannes
Zerweck, Karsten Schnatbaum, Thomas Michler, Andreas Pichlmair, Christina Ludwig andBernhard Kuster
Journal Citation: Molecular and Cellular Proteomics 2020, 19(9), 1503–1522
Key words: RPS, Peptide Cleanup, Proteomics
Development and validation of a platform reduced intact mass method for process monitoring of
monoclonal antibody glycosylation during routine manufacturing
Authors: Michael Schilling, Pamela Feng, Zoran Sosic, and Stacey L. Traviglia
Journal Citation: Bioengineered 2020, 11(1), 1301–1312
Key words: PAW, Affinity Purification, Biopharma, Glycans
Dynamic remodeling of the human host cell proteome and phosphoproteome upon enterovirus
infection
Authors: Piero Giansanti, Jeroen R. P. M. Strating, Kyra A. Y. Defourny, Ieva Cesonyte, Alexia M.
S. Bottino, Harm Post, Ekaterina G. Viktorova, Vien Quang Tri Ho, Martijn A. Langereis, George A.
Belov, Esther N. M. Nolte‑‘t Hoen, Albert J. R. Heck and Frank J. M. van Kuppeveld
Journal Citation: Nature Communications 2020, 11, 4332
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics, Proteomics

12

E3 Ubiquitin Ligase Fbw7 Regulates the Survival of Mature B Cells
Authors: Parham Ramezani‑Rad, Charlotte R. Leung, John R. Apgar, and Robert C. Rickert
Journal Citation: Journal of Immunology 2020, 204(6), 1535–1542
Key words: C18, Peptide Cleanup, Proteomics
Effects of electron‑transfer/higher‑energy collisional dissociation (EThcD) on phosphopeptide
analysis by data‑independent acquisition.
Authors: Thierry Schmidlin, Maarten Altelaar
Journal Citation: International Journal of Mass Spectrometry 2020, 452, 116336
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
Enhancer reprograming driven by high‑order assemblies of transcription factor promotes
phenotypic plasticity and breast cancer endocrine resistance
Authors: Mingjun Bi, Zhao Zhang, Yi‑Zhou Jiang, Pengya Xue, Hu Wang, Zhao Lai, Xiaoyong Fu,
Carmine De Angelis, Yue Gong, Zhen Gao, Jianhua Ruan, Victor X. Jin, Elisabetta Marangoni,
Elodie Montaudon, Christopher K. Glass, Wei Li, Tim Hui‑Ming Huang, Zhi‑Ning Shao, Rachel
Schiff, Lizhen Chen, and Zhijie Liu
Journal Citation: Nature Cell Biology 2020, 22, 701–715
Key words: C18, Peptide Cleanup, Protein‑Protein Interactions, Signal Transduction, BioID
Fishing for newly synthesized proteins with phosphonate‑handles
Authors: Fleur Kleinpenning, Barbara Steigenberger, Wei Wu, and Albert J. R. Heck
Journal Citation: Nature Communications 2020, 11, 3244
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Proteomics, PhosID
High‑Throughput Stool Metaproteomics: Method and Application to Human Specimens
Authors: Carlos G. Gonzalez, Hannah C. Wastyk, Madeline Topf, Christopher D. Gardner, Justin L.
Sonnenburg, and Joshua E. Elias
Journal Citation: mSystems 2020, 5(3), e00200–20
Key words: RPS, Peptide Cleanup, Proteomics
Identification of pathogens from native urine samples by Maldi‑TOF/TOF tandem mass
spectrometry
Authors: Damir Oros, Marina Ceprnja, Jurica Zucko, Mario Chindric, Amela Hozic, Jasenka Skrlin,
Karmela Barisic, Ena Melvan, Ksenija Uroic, Blazenka Kos, and Antonio Starcevic
Journal Citation: Clinical Proteomics 2020, 17, 25
Key words: SCX, Fractionation, Clinical Research, Proteomics

13

Improving the throughput of immunoaffinity purification and enzymatic digestion of therapeuticproteins using membrane‑immobilized reagent technology
Authors: Michelle R. Robinson, Lisa A. Vasicek, Christian Hoppmann, Mandy Li, Gia Jokhadze,
Daniel S. Spellman
Journal Citation: Analyst 2020, 145, 3148–3156
Key words: PAW, Affinity Purification, In‑Solution Digestion, Biopharma
Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human
Proteome Project
Authors: Michael R. Hoopmann, Ulrike Kusebauch, Magnus Palmblad, Nuno Bandeira, David D.
Shteynberg, Lingjie He, Bin Xia, Stoyan H. Stoychev, Gilbert S. Omenn, Susan T. Weintraub, andRobert L. Moritz
Journal Citation: Journal of Proteome Research 2020, 19(12), 4754–4765
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
Laccases 2 & 3 as biomarkers of Botrytis cinerea infection in sweet white wines
Authors: S. Ployon, A. Attina, J. Vialaret, A. S. Walker, C. Hirtz, and C. Saucier
Journal Citation: Food Chemistry 2020, 315, 126233
Key words: C18, Peptide Cleanup, Biomarkers, Proteomics
Metabolic changes related to the IDH1 mutation in gliomas preserve TCA‑cycle activity: An
investigation at the protein level
Authors: Lennard J. M. Dekker, Suying Wu, Cherise Jurriëns, Dana A. N. Mustafa, Frederieke
Grevers, Peter C. Burgers, Peter A. E. Sillevis Smitt, Johan M. Kros, and Theo M. Luider
Journal Citation: The FASEB Journal 2020, 34(3), 3636–3657
Key words: C18, Peptide Cleanup, Proteomics
Modulation of Human Adipose Stem Cells’ Neurotrophic Capacity Using a Variety of Growth
Factors for Neural Tissue Engineering Applications: Axonal Growth, Transcriptional, andPhosphoproteomic Analyses In Vitro
Authors: Katharina M. Prautsch, Alexander Schmidt, Viola Paradiso, Dirk J. Schaefer, Raphael
Guzman, Daniel F. Kalbermatten and Srinivas Madduri
Journal Citation: Cells 2020, 9(9), 1939
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
Multi‑omic comparison of Alzheimer’s variants in human ESC‑derived microgila reveals
convergence at APOE
Authors: Tongfei Liu, Bing Zhu, Yan Liu, Xiaoming Zhang, Jun Yin, Xiaoguang Li, LuLin Jiang,
Andrew P. Hodges, Sara Brin Rosenthal, Lisa Zhou, Joel Yancey, Amanda McQuade, Mathew
Blurton‑Jones, Rudolph E. Tanzi, Timothy Y. Huang, and Huaxi Xu
Journal Citation: Journal of Experimental Medicine 2020, 217(12), e20200474
Key words: C18, Peptide Cleanup, Proteomics

14

Mutation position is an important determinant for predicting cancer neoantigens
Authors: Aude‑Hélène Capietto, Suchit Jhunjhunwala, Samuel B. Pollock, Patrick Lupardus,
Jim Wong, Lena Hänsch, James Cevallos, Yajun Chestnut, Ajay Fernandez, Nicolas Lounsbury,
Tamaki Nozawa, Manmeet Singh, Zhiyuan Fan, Cecile C. de la Cruz, Qui T. Phung, Lucia
Taraborrelli, Benjamin Haley, Jennie R. Lill, Ira Mellman, Richard Bourgon, and Lélia Delamarre
Journal Citation: Journal of Experimental Medicine 2020, 217(4), e20190179
Key words: C18, PAW, Affinity Purification, On‑Cartridge Reaction, Peptide Cleanup, Biopharma,
Immunopeptidomics, Immuocapture
Phosphorylation Ratio Determination in Fresh‑Frozen and Formalin‑Fixed Paraffin‑Embedded
Tissue with Targeted Mass Spectrometry
Authors: Lona Zeneyedpour, Christoph Stingl, Lennard J. Dekker. Dana A. M. Mustafa, Johan M.
Kros, and Theo M. Luider
Journal Citation: Journal of Proteome Research 2020, 19(10), 4179–4190
Key words: C18, Fe(III)‑NTA, Peptide Cleanup, Phosphopeptide Enrichment, Proteomics
PKCλ/ι Loss Induces Autophagy, Oxidative Phosphorylation, and NRF2 to Promote Liver Cancer
Progression
Authors: Yotaro Kudo, Masayuki Sugimoto, Esperanza Arias, Hiroaki Kasashima, Thekla Cordes,
Juan F. Linares, Angeles Duran, Yuki Nakanishi, Naoko Nakanishi, Antoine L’Hermitte, Alex
Campos, Nadia Senni, Tarmo Rooslid, Lewis R. Roberts, Ana Maria Cuervo, Christian M. Metallo,
Michael Karin, Maria T. Diaz‑Meco, and Jorge Moscat
Journal Citation: Cancer Cell 2020, 38(2), P247–262 e11
Key words: C18, SAW, Affinity Purification, On‑Cartridge Reaction, Peptide Cleanup,
Protein‑Protein Interactions, Proteomics, Signal Transduction, BioID
Post‑hoc assessment of the immunogenicity of three antibodies reveals distinct immune
stimulatory mechanisms
Authors: Robin E. Walsh, Megan Lannan, Yi Wen, Xiaoli Wang, Christopher A. Moreland, Jill
Willency, Michael D. Knierman, Laura Spindler, Ling Liu, Wei Zeng, Guilherme V. Rocha, Victor
Obungu, Jirong Lu, Arunan Kaliyaperumal, Andrea Ferrante, Robert Siegel and Laurent P.
Malherbe
Journal Citation: mABs 2020, 12(1), 1764829
Key words: SAW, Affinity Purification, Clinical Research, Biopharma, Immunopeptidomics,
Immunocapture
Prevention of dsRNA‑induced interferon signaling by AGO1x is linked to breast cancer cellproliferation
Authors: Souvik Ghosh, Joao C. Guimaraes, Manuela Lanzafame, Alexander Schmidt, Afzal
Pasha Syed, Beatrice Dimitriades, Anastasiya Börsch, Shreemoyee Ghosh, Nitish Mittal, Thomas
Montavon, Ana Luisa Correia, Johannes Danner, Gunter Meister, Luigi M. Terracciano, Sébastien
Pfeffer, Salvatore Piscuoglio, and Mihaela Zavolan
Journal Citation: The EMBO Journal 2020, 39(18), e103922
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment15Process‐wide control and automation of an integrated continuous manufacturing platform for
antibodies
Authors: Fabian Feidl, Sebastian Vogg, Moritz Wolf, Matevz Podobnik, Caterina Ruggeri, Nicole
Ulmer, Ruben Wälchli, Jonathan Souquet, Hervé Broly, Alessandro Butté, and Massimo Morbidelli
Journal Citation: Biotechnology Bioengineering 2020, 117(5), 1367–1380
Key words: CU, RX, GlykoPrep, Glycans
Quantitative Longitudinal Inventory of the N‑Glycoproteome of Human Milk from a Single Donor
Reveals the Highly Variable Repertoire and Dynamic Site‑Specific Changes
Authors: Jing Zhu, Yu‑Hsien Lin, Kelly A. Dingess, Marko Mank, Bernd Stahl, and Albert J. R. Heck
Journal Citation: Journal of Proteome Research 2020, 19(5), 1941–1952
Key words: CU, Fractionation, Glycoproteomics
Quantitative proteomics discloses monacolin K‑induced alterations in triple‑negative breast
cancer cell proteomes and phosphoproteomes
Authors: Federica del Gaudio, Ida Chiara Guerrera, Raffaele Riccio and Maria Chiara Monti
Journal Citation: Molecular Omics 2020, 16, 19–30
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
RNF43 truncations trap CK1 to drive niche‑independent self‑renewal in cancer
Authors: Maureen Spit, Nicola Fenderico, Ingrid Jordens, Tomasz Radaszkiewicz, Rik GH
Lindeboom, Jeroen M. Bugter, Alba Cristobal, Lars Ootes, Max van Osch, Eline Janssen, Kim E.
Boonekamp, Katerina Hanakova, David Potesil, Zbynek Zdrahal, Sylvia F. Boj, Jan Paul Medema,Vitezslav Bryja, Bon‑Kyoung Koo, Michiel Vermeulen and Madelon M. Maurice
Journal Citation: The EMBO Journal 2020, 39(18), e103932
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics, Signal Transduction
Robust, reproducible, and quantitative analysis of thousands of proteomes by micro‑flow
LC–MS/MS
Authors: Yangyang Bian, Runsheng Zheng, Florian P. Bayer, Cassandra Wong, Yun‑Chien
Chang, Chen Meng, Daniel P. Zolg, Maria Reinecke, Jana Zecha, Svenja Wiechmann, Stephanie
Heinzlmeir, Johannes Scherr, Bernhard Hemmer, Mike Baynham, Anne‑Claude Gingras, Oleksandr
Boychenko, and Bernhard Kuster
Journal Citation: Nature Communications 2020, 11, 157
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
Soluble SORLA Enhances Neurite Outgrowth and Regeneration through Activation of the EGF
Receptor/ERK Signaling Axis
Authors: Jessica Stupack, Xiao‑Peng Xiong, Lu‑Lin Jiang, Tongmei Zhang, Lisa Zhou, Alex
Campos, Barbara Ranscht, William Mobley, Elena B. Pasquale, Huaxi Xu, and Timothy Y. Huang
Journal Citation: The Journal of Neuroscience 2020, 40(31), 5908–5921
Key words: C18, Fe(III)‑NTA, Peptide Cleanup, Phosphopeptide Enrichment, Phosphoproteomics

16

Targeting CLK3 inhibits the progression of cholangiocarcinoma by reprograming nucleotide
metabolism
Authors: Qingxin Zhou, Meihua Lin, Xing Feng, Fei Ma, Yuekun Zhu, Xing Liu, Chao Qu, Hong Sui,
Bei Sun, Anlong Zhu, Heng Zhang, He Huang, Zhi Gao, Yongxiang Zhao, Jiangyun Sun, Yuxian Bai,
Jufei Jin, Xuehui Hong, Chang Zou, and Zhiyong Zhang
Journal Citation: Journal of Experimental Medicine 2020, 217(8), e20191779
Key words: SAW, Affinity Purification, Protein‑Protein Interactions, Signal Transduction, BioID
Temporal Quantitative Proteomics of mGluR induced Protein Translation and Phosphorylation in
Neurons
Authors: Charlotte A. G. H. van Gelder, Renske Penning, Tim S. Veth, Lisa A. E. Catsburg, Casper
C. Hoogenraad, Harold D. MacGillavry, and Maarten Altelaar
Journal Citation: Molecular and Cellular Proteomics 2020, 19(12), 1952–1968
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics, Signal Transduction
The Human Leukocyte Antigen Class II Immunopeptidome of the SARS‑CoV–2 Spike
Glycoprotein
Authors: Michael D. Knierman, Megan B. Lannan, Laura J. Spindler, Carl L. McMillian, Robert J.
Konrad, and Robert W. Siege
Journal Citation: Cell Reports 2020, 33(9), 108454
Key words: SAW, Affinity Purification, Clinical Research, Biopharma, Immunopeptidomics,
Proteomics, Immunocapture
Variation of human salivary alpha‑amylase proteoforms in three stimulation models
Authors: María D. Contreras‑Aguilar, Jerome Vialaret, Dominique Deville de Périère, Damián
Escribano, Sylvain Lehmann, Fernando Tecles, Jose J. Cerón, and Christophe Hirtz
Journal Citation: Clinical and Oral Investigations 2020, 24, 475–486
Key words: C18, Peptide Cleanup, Clinical Research, Proteomics

2019
A Non‑canonical Role of YAP/TEAD Is Required for Activation of Estrogen‑Regulated Enhancers
in Breast Cancer
Authors: Chi Zhu, Li Li, Zhao Zhang, Mingjun Bi, Hu Wang, Wenyue Su, Karen Hernandez,
Pingping Liu, Junqiang Chen, Mingqiu Chen, Tim Hui‑Ming Huang, Lizhen Chen, and Zhijie Liu
Journal Citation: Molecular Cell 2019, 75(4), 791–806
Key words: C18, Peptide Cleanup, Protein‑Protein Interactions, Proteomics, Signal Transduction,
BioID

17

A small‑molecule inhibitor of BamA impervious to efflux and the outer membrane permeability
barrier
Authors: Elizabeth M. Hart, Angela M. Mitchell, Anna Konovalova, Marcin Grabowicz, Jessica
Sheng, Xiaoqing Han, Frances P. Rodriguez‑Rivera, Adam G. Schwaid, Juliana C. Malinverni, Carl
J. Balibar, Smaranda Bodea, Qian Si, Hao Wang, Michelle F. Homsher, Ronald E. Painter, Anthony
K. Ogawa, Holly Sutterlin, Terry Roemer, Todd A. Black, Deborah M. Rothman, Scott S. Walker, andThomas J. Silhavy
Journal Citation: PNAS 2019, 116(43), 21748–21757
Key words: C18, Peptide Cleanup, Mechanism of Action
Absolute Quantification of Apolipoproteins Following Treatment with Omega–3 Carboxylic Acids
and Fenofibrate Using a High Precision Stable Isotope‑labeled Recombinant Protein Fragments
Based SRM Assay
Authors: Andreas Hober, Fredrik Edfors, Maria Ryaboshapkina, Jonas Malmqvist, Louise
Rosengren, Andrew J. Percy, Lars Lind, Bjorn Forsstrom, Mathias Uhlen, Jan Oscarsson, andTasso Miliotis
Journal Citation: Molecular and Cellular Proteomics 18(12), 2433–2446
Key words: RPS, Peptide Cleanup, Clinical Research, Biomarkers
An amino‑terminal threonine/serine motif is necessary for activity of the Crp/Fnr homolog, MrpC
and for Myxococcus xanthus developmental robustness
Authors: Brooke E. Feeley, Vidhi Bhardwaj, Patrick T. McLaughlin, Stephen Diggs, Gregor M. Blaha
and Penelope I. Higgs
Journal Citation: Molecular Microbiology 2019, 112(5), 1531–1551
Key words: TiO2, Phosphopeptide Enrichment, Signal Transduction
ANKRD44 Gene Silencing: A Putative Role in Trastuzumab Resistance in Her2‑Like Breast Cancer
Authors: Marco La Ferla, Francesca Lessi, Paolo Aretini, Davide Pellegrini, Sara Franceschi, Elena
Tantillo, Michele Menicagli, Ivo Marchetti, Claudia Scopelliti, Prospero Civita, Claudia De Angelis,
Lucrezia Diodati, Ilaria Bertolini, Manuela Roncella, Liam A. McDonnell, Jacob Hochman, Marzia
Del Re, Cristian Scatena, Antonio G. Naccarato, Andrea Fontana, and Chiara M. Mazzanti
Journal Citation: Frontiers in Oncology 2019, 9, 547
Key words: RPS, Fractionation, Proteomics
Apolipoprotein Profiles in Very Preterm and Term‑Born Preschool Children
Authors: Anna Posod, Raimund Pechlaner, Xiaoke Yin, Sean Anthony Burnap, Sophia Julia Kiechl,
Johann Willeit, Joseph L. Witztum, Manuel Mayr, Stefan Kiechl, and Ursula Kiechl‑Kohlendorfer
Journal Citation: Journal of the American Heart Association 2019, 8(8), e011199
Key words: C18, Peptide Cleanup

18

Assessing Automated Sample Preparation Technologies for High‑Throughput Proteomics ofFrozen Well Characterized Tissues from Swedish Biobanks
Authors: Magdalena Kuras, Lazaro Hiram Betancourt, Melinda Rezeli, Jimmy Rodriguez, Marcell
Szasz, Qimin Zhou, Tasso Miliotis, Roland Andersson, and Gyorgy Marko‑Varga
Journal Citation: Journal of Proteome Research 2019, 18(1), 548–556
Key words: C18, RPS, Fractionation, In‑Solution Digestion, Peptide Cleanup, Clinical Research,
Proteomics
Augmenting Immunotherapy Impact by Lowering Tumor TNF Cytotoxicity Threshold
Authors: David W. Vredevoogd, Thomas Kuilman, Maarten A. Ligtenberg, Julia Boshuizen, Kelly E.
Stecker, Beaunelle de Bruijn, Oscar Krijgsman, Xinyao Huang, Juliana C. N. Kenski, Ruben Lacroix,
Riccardo Mezzadra, Raquel Gomez‑Eerland, Mete Yildiz, Ilknur Dagidir, Georgi Apriamashvili,
Nordin Zandhuis, Vincent van der Noort, Nils L. Visser, Christian U. Blank, Maarten Altelaar, Ton N.
Schumacher, and Daniel S. Peeper
Journal Citation: Cell 2019, 178(3), 585–599
Key words: C18, Fe(III)‑NTA, Peptide Cleanup, Phosphopeptide Enrichment, Phosphoproteomics,
Proteomics
Chronic Low Dose Oral Exposure to Microcystin‑LR Exacerbates Hepatic Injury in a Murine Modelof Non‑Alcoholic Fatty Liver Disease
Authors: Apurva Lad, Robin C. Su, Joshua D. Breidenbach, Paul M. Stemmer, Nicholas J.
Carruthers, Nayeli K. Sanchez, Fatimah K. Khalaf, Shungang Zhang, Andrew L. Kleinhenz,
Prabhatchandra Dube, Chrysan J. Mohammed, Judy A. Westrick, Erin L. Crawford, Dilrukshika
Palagama, David Baliu‑Rodriguez, Dragan Isailovic, Bruce Levison, Nikolai Modyanov, Amira F.
Gohara, Deepak Malhotra, Steven T. Haller, and David J. Kennedy
Journal Citation: Toxins 2019, 11(9), 486
Key words: TiO2, Phosphopeptide Enrichment, Phosphoproteomics
Clinical protein science in translational medicine targeting malignant melanoma
Authors: Jeovanis Gil, Lazaro Hiram Betancourt, Indira Pla, Aniel Sanchez, Roger Appelqvist,
Tasso Miliotis, Magdalena Kuras, Henriette Oskolas, Yonghyo Kim, Zsolt Horvath, Jonatan
Eriksson, Ethan Berge, Elisabeth Burestedt, Göran Jönsson, Bo Baldetorp, Christian Ingvar, Håkan
Olsson, Lotta Lundgren, Peter Horvatovich, Jimmy Rodriguez Murillo, Yutaka Sugihara, Charlotte
Welinder, Elisabet Wieslander, Boram Lee, Henrik Lindberg, Krzysztof Pawłowski, Ho Jeong
Kwon, Viktoria Doma, Jozsef Timar, Sarolta Karpati, A. Marcell Szasz, István Balázs Németh,Toshihide Nishimura, Garry Corthals, Melinda Rezeli, Beatrice Knudsen, Johan Malm, and György
Marko‑Varga
Journal Citation: Cell Biology and Toxicology 2019, 35, 293–332
Key words: In‑Solution Digestion, Clinical Research, Phosphoproteomics, Proteomics

19Comparative proteomic study of phytotoxic effects of silver nanoparticles and silver ions on
tobacco plants
Authors: Petra Peharec Štefanić, Martina Jarnević, Petra Cvjetko, Renata Biba, Sandra Šikić, Mirta
Tkalec, Mario Cindrić, Ilse Letofsky‑Papst, and Biljana Balen
Journal Citation: Environmental Science and Pollution Research 2019, 26, 22529–22550
Key words: RPS, Peptide Cleanup, Proteomics
Comparison of Proteomic, Metabolic, and Growth Profiles for Brettanomyces bruxellensis Isolates
from Croatian Wines
Authors: Stela Krizanovic, Leo Gracin, Mario Cindric, Marina Tomasevic, Karla Kelsin, Katarina
Lukic, and Karin Kovacevic Ganic
Journal Citation: American Journal of Enology and Viticulture 2019, 70, 77–87
Key words: C18, SCX, Fractionation, Proteomics
Direct quantitation of therapeutic antibodies for pharmacokinetic studies using
immuno‑purification and intact mass analysis
Authors: Lisa A. Vasicek, Xin Zhu, Daniel S. Spellman, Kevin P. Bateman
Journal Citation: Bioanalysis 2019, 11(3), 203–213
Key words: SAW, Affinity Purification, In‑Solution Digestion, On‑Cartridge Reaction, Biopharma,
Pharmacokinetics, Immunocapture
Glucocorticoids promote breast cancer metastasis
Authors: Milan M. S. Obradović, Baptiste Hamelin, Nenad Manevski, Joana Pinto Couto, Atul
Sethi, Marie‑May Coissieux, Simone Münst, Ryoko Okamoto, Hubertus Kohler, Alexander Schmidt,
and Mohamed Bentires‑Alj
Journal Citation: Nature 2019, 567, 540–544
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
High resolution two‑dimensional liquid chromatography coupled with mass spectrometry forrobust and sensitive characterization of therapeutic antibodies at the peptide level
Authors: Dwight R. Stoll, Hayley R. Lhotka, David C. Harmes, Ben Madigan, Jordy J. Hsiao,
Gregory O. Staples
Journal Citation: Journal of Chromatography B 2019, 1134–1135, 121832
Key words: C18, In‑Solution Digestion, Peptide CleanupHigh Throughput Assessment of Kinome‑wide Activation States
Authors: Thierry Schmidlin, Donna O. Debets, Charlotte A. G. H. van Gelder, Kelly E. Stecker,
Stamatia Rontogianni, Bart L. van den Eshof, Kristel Kemper, Esther H. Lips, Maartje van den
Biggelaar, Daniel S. Peeper, Albert J. R. Heck, and Maarten Altelaar
Journal Citation: Cell Systems 2019, 9(4), 366–374
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Clinical Research, Phosphoproteomics

20

Increased Serine and One‑Carbon Pathway Metabolism by PKCλ/ι Deficiency Promotes
Neuroendocrine Prostate Cancer
Authors: Miguel Reina‑Campos, Juan F. Linares, Angeles Duran, Thekla Cordes, Antoine
L’Hermitte, Mehmet G. Badur, Munveer S. Bhangoo, Phataraporn K. Thorson, Alicia Richards,
Tarmo Rooslid, Dolores C. Garcia‑Olmo, Syongh Y. Nam‑Cha, Antonio S. Salinas‑Sanchez, Ken
Eng, Himisha Beltran, David A. Scott, Christian M. Metallo, Jorge Moscat, and Maria T. Diaz‑Meco
Journal Citation: Cancer Cell 2019, 35(3), 385–400
Key words: C18, SAW, Affinity Purification, On‑Cartridge Reaction, Peptide Cleanup,
Protein‑Protein Interactions, Proteomics, Signal Transduction, BioID
Integrative proteomics and pharmacogenomics analysis of methylphenidate treatment response
Authors: Bruna S. da Silva, Douglas T. Leffa, Walter O. Beys‑da‑Silva, Iraci L. S. Torres, Diego L.
Rovaris, Marcelo M. Victor, Luis A. Rohde, Nina R. Mota, Carla de Oliveira, Markus Berger, John R.
Yates III, Renuka Sabnis, Ramón Díaz Peña, Alexandre Rosa Campos, Eugenio H. Grevet, Lucelia
Santi, Claiton H. D. Bau, and Verônica Contini
Journal Citation: Translational Psychiatry 2019, 9, 308
Key words: C18, Peptide Cleanup, Mechanism of Action, Proteomics
Isomer separation of sialylated O‑ and N‑linked glycopeptides using reversed‑phase LC–MS/MS
at high temperature
Authors: Eun Sun Ji, Hyun Kyoung Lee, Gun Wook Park, Kwang Hoe Kim, Jin Young Kim, andJong Shin Yoo
Journal Citation: Journal of Chromatography B 2019, 1110–1111, 101–107
Key words: RPS, Peptide Cleanup
Omomyc Reveals New Mechanisms To Inhibit the MYC Oncogene
Authors: Mark J. Demma, Claudio Mapelli, Angie Sun, Smaranda Bodea, Benjamin Ruprecht,
Sarah Javaid, Derek Wiswell, Eric Muise, Shiying Chen, John Zelina, Federica Orvieto, Alessia
Santoprete, Simona Altezza, Federica Tucci, Enrique Escandon, Brian Hall, Kallol Ray, Abbas Walji,
and Jennifer O’Neil
Journal Citation: Molecular and Cellular Biology 2019, 39(22), e00248–19
Key words: C18, Peptide Cleanup, Mechanism of Action
PhoX: An IMAC‑Enrichable Cross‑Linking Reagent
Authors: Barbara Steigenberger, Roland J. Pieters, Albert J. R. Heck, and Richard A. Scheltema
Journal Citation: ACS Central Science 2019, 5(9), 1514–1522
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Protein‑Protein Interactions, Proteomics,
Signal Transduction, PhoX

21

Process design and development of a mammalian cell perfusion culture in shake‐tube andbenchtop bioreactors
Authors: Moritz K. F. Wolf, Andrea Müller, Jonathan Souquet, Hervé Broly, and Massimo
Morbidelli
Journal Citation: Biotechnology and Bioengineering 2019, 116(8), 1973–1985
Key words: CU, RX, GlykoPrep, Biopharma, Glycans
Proteome profiling of triple negative breast cancer cells overexpressing NOD1 and NOD2
receptors unveils molecular signatures of malignant cell proliferation
Authors: Fernando J. Velloso, Alexandre R. Campos, Mari C. Sogayar, and Ricardo G. Correa
Journal Citation: BMC Genomics 2019, 20, 152
Key words: C18, Peptide Cleanup, Proteomics
Proteomic atlas of organ vasculopathies triggered by Staphylococcus aureus sepsis
Authors: Alejandro Gómez Toledo, Gregory Golden, Alexandre Rosa Campos, Hector Cuello,
James Sorrentino, Nathan Lewis, Nissi Varki, Victor Nizet, Jeffrey W. Smith, and Jeffrey D. Esko
Journal Citation: Nature Communications 2019, 10, 4656
Key words: C18, SAW, Affinity Purification, On‑Cartridge Reaction, Peptide Cleanup, Proteomics
Proteomic profiling of extracellular vesicles allows for human breast cancer subtyping
Authors: Stamatia Rontogianni, Eleni Synadaki, Bohui Li, Marte C. Liefaard, Esther H. Lips, Jelle
Wesseling, Wei Wu, and Maarten Altelaar
Journal Citation: Communications Biology 2019, 2, 325
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Biomarkers, Phosphoproteomics
Proteomics of Rat Lungs Infected by Cryptococcus gattii Reveals a Potential Warburg‑like EffectAuthors: Rafael L. Rosa, Markus Berger, Lucélia Santi, David Driemeier, Paula Barros Terraciano,
Alexandre R. Campos, Jorge A. Guimarães, Marilene H. Vainstein, John R. Yates III, and Walter O.
Beys‑da‑Silva
Journal Citation: Journal of Proteome Research 2019, 18(11), 3885–3895
Key words: C18, Peptide Cleanup, Proteomics
Quantitative Microproteomics Based Characterization of the Central and Peripheral Nervous
System of a Mouse Model of Krabbe Disease
Authors: Davide Pellegrini, Ambra del Grosso, Lucia Angella, Nadia Giordano, Marialaura Dilillo,
Ilaria Tonazzini, Matteo Caleo, Marco Cecchini, and Liam A. McDonnell
Journal Citation: Molecular and Cellular Proteomics 2019, 18(6), 1227–1241
Key words: RPS, Fractionation, Proteomics

22

Suspension Trapping (S‑Trap) Is Compatible with Typical Protein Extraction Buffers andDetergents for Bottom‑Up Proteomics
Authors: Dalia Elinger, Alexandra Gabashvili, and Yishai Levin
Journal Citation: Journal of Proteome Research 2019, 18(3), 1441–1445
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
Targeting proline in (phospho)proteomics
Authors: Saar A. M. van der Laarse, Charlotte A. G. H. van Gelder, Marshall Bern, Michiel Akeroyd,
Maurien M. A. Olsthoorn, and Albert J. R. Heck
Journal Citation: The FEBS Journal 2019, 287(14), 2979–2997
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics
The Hidden Story of Heterogeneous B‑raf V600E Mutation Quantitative Protein Expression in
Metastatic Melanoma—Association with Clinical Outcome and Tumor Phenotypes
Authors: Lazaro Hiram Betancourt, A. Marcell Szasz, Magdalena Kuras, Jimmy Rodriguez
Murillo, Yutaka Sugihara, Indira Pla, Zsolt Horvath, Krzysztof Pawłowski, Melinda Rezeli, Kenichi
Miharada, Jeovanis Gil, Jonatan Eriksson, Roger Appelqvist, Tasso Miliotis, Bo Baldetorp,
Christian Ingvar, Håkan Olsson, Lotta Lundgren, Peter Horvatovich, Charlotte Welinder, Elisabet
Wieslander, Ho Jeong Kwon, Johan Malm, Istvan Balazs Nemeth, Göran Jönsson, David Fenyö,
Aniel Sanchez, and György Marko‑Varga
Journal Citation: Cancers 2019), 11(12), 1981
Key words: RPS, In‑Solution Digestion, Peptide Cleanup, Clinical Research, Proteomics
Validation of a Fully Automated Immunoaffinity Workflow for the Detection and Quantification of
Insulin Analogs by LC–MS‑MS in Postmortem Vitreous Humor
Authors: Kevin M. Legg, Laura M. Labay, Sally S. Aiken, Barry K. Logan
Journal Citation: Journal of Analytical Toxicology 2019, 43(7), 505–511
Key words: PGW, Affinity Purification, Forensics, Immunocapture

2018
A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses
to Drug Perturbations
Authors: Lev Litichevskiy, Ryan Peckner, Jennifer G. Abelin, Jacob K. Asiedu, Amanda L. Creech,
John F. Davis, Desiree Davison, Caitlin M. Dunning, Jarrett D. Egertson, Shawn Egri, Joshua Gould,
Tak Ko, Sarah A. Johnson, David L. Lahr, Daniel Lam, Zihan Liu, Nicholas J. Lyons, Xiaodong Lu,
Brendan X. MacLean, Alison E. Mungenast, Adam Officer, Ted E. Natoli, Malvina Papanastasiou,
Jinal Patel, Vagisha Sharma, Courtney Toder, Andrew A. Tubelli, Jennie Z. Young, Steven A. Carr,
Todd R. Golub, Aravind Subramanian, Michael J. MacCoss, Li‑Huei Tsai, and Jacob D. Jaffe
Journal Citation: Cell Systems 2018, 6(4), 424–443
Key words: Fe(III)‑NTA, RPS, Peptide Cleanup, Phosphopeptide Enrichment, Phosphoproteomics,
Signal Transduction23

An Integrated, High‑Throughput Strategy for Multiomics Systems Level Analysis
Authors: Danielle B. Gutierrez, Randi L. Gant‑Branum, Carrie E. Romer, Melissa A. Farrow, Jamie
L. Allen, Nikesh Dahal, Yuan‑Wei Nei, Simona G. Codreanu, Ashley T. Jordan, Lauren D. Palmer,
Stacy D. Sherrod, John A. McLean, Eric P. Skaar, Jeremy L. Norris, and Richard M. Caprioli
Journal Citation: Journal of Proteome Research 2018, 17(10), 3396–3408
Key words: C18, In‑Solution Digestion, Peptide Cleanup, Proteomics
Assessing a multiplex‑targeted proteomics approach for the clinical diagnosis of periodontitis
using saliva samples
Authors: Brenda Mertens, Valerie Orti, Jerome Vialaret, Philippe Gibert, Aroa Relano‑Ginesk,
Sylvain Lehmann, Dominique Deville de Periere, and Christophe Hirtz
Journal Citation: Bioanalysis 2018, 10(1), 35–45
Key words: C18, In‑Solution Digestion, Peptide Cleanup, Biomarkers, Clinical Research,
Proteomics
Assessment of susceptible chemical modification sites of trastuzumab and endogenous humanimmunoglobulins at physiological conditions
Authors: Ingrid Schmid, Lea Bonnington, Monika Gerl, Katrin Bomans, Anna Louisa Thaller,
Katharina Wagner, Tilman Schlothauer, Roberto Falkenstein, Boris Zimmermann, Jugen Kopitz,
Max Hasmann, Frieder Bauss, Markus Haberger, Dietmar Reusch, and Patrick Bulau
Journal Citation: Communications Biology 2018, 1, 28
Key words: PAW, Affinity Purification, Biopharma, Pharmacokinetics
Automated phosphopeptide enrichment from minute quantities of frozen malignant melanoma
tissueAuthors: Jimmy Rodriguez Murillo, Magdalena Kuras, Melinda Rezeli, Tasso Milliotis, Lazaro
Betancourt, and Gyorgy Marko‑Varga
Journal Citation: PLOS One 2018, 13(12), e0208562
Key words: C18, Fe(III)‑NTA, RPS, Fractionation, Peptide Cleanup, Phosphopeptide Enrichment,
Clinical Research, Phosphoproteomics
Calpain‑mediated tau fragmentation is altered in Alzheimer’s disease progression
Authors: Hsu‑Hsin Chen, Peter Liu, Paul Auger, Seung‑Hye Lee, Oskar Adolfsson, Lorianne
Rey‑Bellet, Julien Lafrance‑Vanasse, Brad A. Friedman, Maria Pihlgren, Andreas Muhs, Andrea
Pfeifer, James Ernst, Gai Ayalon, Kristin R. Wildsmith, Thomas G. Beach, and Marcel P. van der
Brug
Journal Citation: Scientific Reports 2018, 8, 16725
Key words: RPW, In‑Solution Digestion, Peptide Cleanup, Clinical Research
Ceramide‑Protein Interactions Modulate Ceramide‑Associated Lipotoxic Cardiomyopathy
Authors: Stanley M. Walls, Anthony Cammarato, Dale A. Chatfield, Karen Ocorr, Greg L. Harris,and Rolf Bodmer
Journal Citation: Cell Reports 2018, 22(10), 2702–2715
Key words: C18, Peptide Cleanup, Proteomics

24Characterization of Degraded Proteins in Paintings Using Bottom‑Up Proteomic Approaches:
New Strategies for Protein Digestion and Analysis of Data
Authors: Sibilla Orsini, Avinash Yadav, Marialaura Dilillo, Liam A. McDonnell, and Ilaria Bonaduce
Journal Citation: Analytical Chemistry 2018, 90(11), 6403–6408
Key words: C18, Peptide Cleanup, Proteomics
Data from a targeted proteomics approach to discover biomarkers in saliva for the clinicaldiagnosis of periodontitis
Authors: V. Orti, B. Mertens, J. Vialaret, P. Gilbert, A. Relano‑Gines, S. Lehmann, D. Deville dePeriere, and C. Hirtz
Journal Citation: Data in Brief 2018, 18, 294–299
Key words: C18, In‑Solution Digestion, Peptide Cleanup, Biomarkers, Clinical Research,
Proteomics
Determination of Site‑Specific Phosphorylation Ratios in Proteins with Targeted Mass
Spectrometry
Authors: Lennard J. M. Dekker, Lona Zeneyedpour, Sandor Snoeijers, Jos Joore, Sieger Leenstra,
and Theo M. Luider
Journal Citation: Journal of Proteome Research 2018, 17(4), 1654–1663
Key words: C18, RPS, TiO2, Fractionation, Peptide Cleanup, Phosphopeptide Enrichment,
Phosphoproteomics, Proteomics, Signal Transduction
Micro‑Data‑Independent Acquisition for High‑Throughput Proteoimcs and Sensitive Peptide
Mass Spectrum Identification
Authors: Michael R. Heaven, Archie L. Cobbs, Yuan‑Wei Nei, Danielle B. Gutierrez, Anthony W.
Herren, Harsha P. Gunawardena, Richard M. Caprioli, and Jeremy L. Norris
Journal Citation: Analytical Chemistry 2018, 90(15), 8905–8911
Key words: C18, Peptide Cleanup, Proteomics
Physiological, ultrastructural and proteomic responses of tobacco seedlings exposed to silver
nanoparticles and silver nitrate
Authors: Petra Peharec Stefanic, Petra Cvjetko, Renata Biba, Ana‑Marija Domijan, Ilse
Letofsky‑Papst, Mirta Tkalec, Sandra Sikic, Mario Cindric, and Biljana Balen
Journal Citation: Chemosphere 2018, 209, 640–653
Key words: RPS, Peptide Cleanup, Proteomics
Quantitation of a Therapeutic Antibody in Serum Using Intact Sequential Affinity Capture, Trypsin
Digestion and LC‑MS/MS
Authors: Lisa A. Vasicek, Daniel S. Spellman, SuChun Hseih, Wolfgang Seghezzi, Shuli Zhang,Michael Santostefano, and Kevin P. Bateman
Journal Citation: Analytical Chemistry 2018, 90(1), 866–871
Key words: PAW, SAW, Affinity Purification, In‑Solution Digestion, Biopharma, Pharmacokinetics,
Immunocapture25

Selective Substrates and Activity‑Based Probes for Imaging of the Human Constitutive 20S
Proteasome in Cells and Blood Samples
Authors: Wioletta Rut, Marcin Poręba, Paulina Kasperkiewicz, Scott J. Snipas, and Marcin DrągJournal Citation: Journal of Medicinal Chemistry 2018, 61(12), 5222–5234
Key words: C18, Peptide Cleanup, Proteomics
What sample preparation should be chosen for targeted MS monoclonal antibody quantificationin human serum
Authors: Jerome Vialaret, Sophie Broutin, Celia Pugnier, Sophie Santele, Aurore Jaffuel, Alan
Barnes, Laurent Tiers, Laurent Pelletier, Sylvain Lehmann, Angelo Paci, and Christophe Hirtz
Journal Citation: Bioanalysis 2018, 10(10), 723–746
Key words: PGW, Affinity Purification

2017
A multiplexed immunocapture liquid chromatography tandem mass spectrometry assay for thesimultaneous measurement of myostatin and GDF–11 in rat serum using an automated sample
preparation platform
Authors: Yue Zhao, Guowen Liu, Frank C. Zambito, Yan J. Zhang, Binodh S. DeSilva, Alexander T.
Kozhich, and Jim X. Shen
Journal Citation: Analytica Chimica Acta 2017, 979, 36–44
Key words: SAW, Affinity Purification, Biopharma, Pharmacokinetics, Immunocapture
Mass Spectrometry Imaging, Laser Capture Microdissection, and LC‑MS/MS of the Same Tissue
SectionAuthors: Marialaura Dilillo, Davide Pellegrini, Rima Ait‑Belkacem, Erik L. de Graaf, Matteo Caleo,
and Liam A. McDonnell
Journal Citation: Journal of Proteome Research 2017, 16(8), 2993–3001
Key words: C18, Peptide Cleanup, Proteomics
Proteasome Activation by Small Molecules
Authors: Yves Leestemaker, Annemieke de Jong, Katharina F. Witting, Renske Penning, Katianne
Schuurman, Boris Rodenko, Esther A. Zaal, Bert van de Kooij, Stefan Laufer, Albert J. R. Heck,
Jannie Borst, Wiep Scheper, Celia R. Berkers, and Huib Ovaa
Journal Citation: Cell Chemical Biology 2017, 24(6), 725–736
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Mechanism of Action, Phosphoproteomics
Robust, Sensitive, and Automated Phosphopeptide Enrichment Optimized for Low Sample
Amounts Applied to Primary Hippocampal Neurons
Authors: Harm Post, Renske Penning, Martin A. Fitzpatrick, Luc B. Garrigues, Wei Wu, Harold D.
MacGillavry, Casper C. Hoogenraad, Albert J. R. Heck, and A. F. Maarten Altelaar
Journal Citation: Journal of Proteome Research 2017, 16(2), 728–737
Key words: Fe(III)‑NTA, TiO2, Phosphopeptide Enrichment, Phosphoproteomics

26Strain effect on extracellular laccase activities from Botrytis cinera
Authors: N. Quijada‑Morin, F. Garcia, K. Lambert, A.‑S. Walker, L. Tiers, M. Viaud, F.‑X. Sauvage, C.
Hirtz, and C. Saucier
Journal Citation: Australian Journal of Grape and Wine Research 2017, 24, 241–251
Key words: C18, Peptide Cleanup

2016
Absolute quantification of 35 plasma biomarkers in human saliva using targeted MS
Authors: Christophe Hirtz, Jerome Vialaret, Nora Nowak, Audey Gabelle, Dominique Deville dePeriere, Sylvain Lehmann
Journal Citation: Bioanalysis 2016, 8(1), 43–53
Key words: C18, In‑Solution Digestion, Peptide Cleanup, Biomarkers, Clinical research,
Proteomics
Antibody‑drug conjugate bioanalysis using LB‑LC‑MS/MS hybrid assays: strategies, methodology
and correlation to ligand‑binding assays
Authors: Jian Wang, Huidong Gu, Ang Liu, Alexander Kovhich, Vangipuram Rangan, Heather
Myler, Linlin Luo, Richard Wong, Huadong Sun, Bonnie Wang, Heather E. Vezina, Shrikant
Deshpande, Yan Zhang, Zheng Yang, Timothy Olah, Anne‑Francoise Aubry, Mark Arnold, Renuka
Pillutla, and Binodh DeSilva
Journal Citation: Bioanalysis 2016, 8(13), 1383–1401
Key words: PAW, PGW, SAW, Affinity Purification, Antibody Drug Conjugates, Biopharma,
Pharmacokinetics, Immunocapture
Automated DBS microsampling, microscale automation and microflow LC‑MS for therapeuticprotein PK
Authors: Qian Zhang, Daniela Tomazela, Lisa A. Vasicek, Daniel S. Spellman, Maribel Beaumont,
BaoJen Shyong, Jacqueline Kenny, Scott Fauty, Kerry Fillgrove, Jan Harrelson, and Kevin P.
Bateman
Journal Citation: Bioanalysis 2016, 8(7), 649–659
Key words: PAW, Affinity Purification, In‑Solution Digestion, Biopharma, Pharmacokinetics
Automated Microchromatography Enables Multiplexing of Immunoaffinity Enrichment of
Peptides to Greater than 150 for Targeted MS‑Based Assays
Authors: Paul J. Ippoliti, Eric Kuhn, D. R. Mani, Lola Fagbami, Hasmik Keshishian, Michael W.
Burgress, Jacob D. Jaffe, and Steven A. Carr
Journal Citation: Analytical Chemistry 2016, 88(15), 7548–7555
Key words: PGW, Affinity Purification, Biomarkers, Proteomics, Signal Transduction,
Immunocapture27

CLK2 inhibition ameliorates autistic features associated with SHANK3 deficiency
Authors: Michael Bidinosti, Paolo Botta, Sebastian Kruttner, Catia C. Proenca, Natacha Stoehr,
Mario Bernhard, Isabelle Fruh, Matthias Mueller, Debora Bonenfant, Hans Voshol, Walter Carbone,
Sarah J. Neal, Stephanie M. Mctighe, Guglielmo Roma, Richardo E. Dolmetsch, Jeffrey Porter,
Pico Caroni, Tewis Bouwmeester, Andreas Luthi, and Ivan Galimberti
Journal Citation: Science 2016, 351(6278), 1199–1203
Key words: Fe(III)‑NTA, Phosphopeptide Enrichment, Phosphoproteomics, Signal Transduction
Discovery of Pyrophosphate Diesters as Tunable, Soluble and Bioorthogonal Linkers forSite‑Specific Antibody‑Drug Conjugates
Authors: Jeffrey C. Kern, Mark Cancilla, Deborah Dooney, Kristen Kwasnjuk, Rena Zhang, Maribel
Beaumont, Isabel Figueroa, SuChun Hsieh, Linda Liang, Daniela Tomazela, Jeffrey Zhang,Philip E. Brandish, Anthony Palmieri, Peter Stivers, Mangeng Cheng, Guo Feng, Prasanthi Geda,
Sanjiv Shah, Andrew Beck, Damien Bresson, Juhi Firdos, Dennis Gately, Nick Knudsen, Anthony
Manibusan, Peter G. Schultz, Ying Sun, and Robert M. Garbaccio
Journal Citation: Journal of the American Chemical Society 2016, 138(4), 1430–1445
Key words: SAW, Affinity Purification, Antibody Drug Conjugates, Biopharma, Pharmacokinetics,
Immunocapture
Electrophysiology of glioma: a Rho GTPase‑activating protein reduces tumor growth and spares
neuron structure and function
Authors: Eleonora Vannini, Francesco Olimpico, Silvia Middei, Martine Ammassari‑Teule, Erik L.
de Graaf, Liam McDonell, Gudula Schmidt, Alessia Fabbri, Carla Fiorentini, Laura Baronceei, Mario
Costa, and Matteo Caleo
Journal Citation: Neuro‑oncology 2016, 18(12), 1634–1643
Key words: RPS, Fractionation, Proteomics, Signal Transduction
Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling
Networks in B‑Catenin‑Active Cancers
Authors: Joseph Rosenbluh, Johnathan Mercer, Yashaswi Shrestha, Rachel Oliver, Pablo Tamayo,
John G. Doench, Itay Tirosh, Federica Piccioni, Ella Hartenian, Heiko Horn, Lola Fagbami, David E.
Root, Jacob Jaffe, Kasper Lage, Jesse S. Boehm, and William C. Hahn
Journal Citation: Cell Systems 2016, 3(3), 302–316
Key words: RPS, SCX, Fractionation, Peptide Cleanup, Protein‑Protein Interactions, Proteomics,
Signal Transduction
Human S100A10 plays a crucial role in the acquisition of the endometrial receptivity phenotype
Authors: Laurence Bissonnette, Loubna Drissennek, Yannick Antoine, Laurent Tiers, Christophe
Hirtz, Sylmain Lehmann, Helene Perrochia, Francois Bissonnnette, Isaac‑Jacques Kadoch,
Delphine Haouzi, and Samir Hamamah
Journal Citation: Cell Adhesion & Migration 2016, 10(3), 282–298
Key words: C18, In‑Solution Digestion, Peptide Cleanup, Biomarkers, Clinical Research,
Proteomics

28Reduced‑representation Phosphosignatures Measured by Quantitative Targeted MS Capture
Cellular States and Enable Large‑Scale Comparison of Drug‑Induced Phenotypes
Authors: Jennifer G. Abelin, Jinal Patel, Xiaodong Lu, Caitlin M. Feeney, Lola Fagbami, Amanda
L. Creech, Roger Hu, Daniel Lam, Desiree Davison, Lindsay Pino, Jana W. Qiao, Eric Kuhn, Adam
Officer, Jianxue Li, Susan Abbatiello, Aravind Subramanian, Richard Sidman, Evan Snyder, Steven
A. Carr, and Jacob D. Jaffe
Journal Citation: Molecular and Cellular Proteomics 2016, 15(5), 1622–1641
Key words: Fe(III)‑NTA, RPS, Peptide Cleanup, Phosphopeptide Enrichment, Phosphoproteomics,
Signal Transduction, Mechanism of Action
Set of Novel Automated Quantitative Microproteomics Protocols for Small Sample Amounts and
Its Application to Kidney Tissue Substrates
Authors: Erik Leonardus de Graaf, Davide Pelligrini, and Liam McDonnell
Journal Citation: Journal of Proteome Research 2016, 15(12), 4722–4730
Key words: C18, RPS, SCX, Fractionation, Peptide Cleanup, Proteomics, TMT labeling2015
An integrated multiplatform bioanalytical strategy for antibody–drug conjugates: a novel casestudy
Authors: Heather Myler, Vangipuram S. Rangan, Jian Wang, Alexander Kozhich, Jennifer
A. Cummings, Robert Neely, Donna Dail, Ang Liu, Bonnie Wang, Heather E. Vezina, Wendy
Freebern, Mei‑Chen Sung, David Passmore, Shrikant Deshpande, Thomas Kempe, Huidong
Gu, Mark Saewert, Amy Manney, John Lute, Frank Zambito, Richard L. Wong, Steven P. Piccoli,
Anne‑Françoise Aubry, Renuka Pillutla, Mark Arnold, and Binodh DeSilva
Journal Citation: Bioanalysis 2015, 7(13), 1569–1582
Key words: SAW, Affinity Purification, Antibody Drug Conjugates, Biopharma, Pharmacokinetics,
Immunocapture
Enhancing the Quality of Antibodies to HIV–1 Envelope by GagPol‑Specific Th Cells
Authors: Michael Storcksdieck genannt Bonsmann, Thomas Niezold, Vladimir Temchura, Franco
Pissani, Katrin Ehrhardt, Eric P. Brown, Nan Yaw Osei‑Owusu, Drew Hannaman, Hartmut Hengel,
Margaret E. Ackerman, Hendrik Steeck, Ghulam Nabi, Matthias Tenbusch, and Klaus Uberla
Journal Citation: The Journal of Immunology, 2015, 195(10), 4861–72
Key words: SAW, Affinity Purification, Immunocapture
Microscale purification of antigen‑specific antibodies
Authors: Eric P. Brown, Erica Normandin, Nana Yaw Osei‑Owusu, Alison E. Mahan, Ying N. Chan,
Jennifer I. Lai, Monica Vaccari, Mangala Rao, Genoveffa Franchini, Galit Alter, and Margaret E.
Ackerman
Journal Citation: Journal of Immunology Methods 2015, 425, 27–36
Key words: SAW, Affinity Purification, Immunocapture29

Quantitative bioanalysis of antibody‑conjugated payload in monkey plasma using a hybrid
immuno‑capture LC‑MS/MS approach: Assay development, validation, and a case study
Authors: Ang Liu, Alexander Kozhich, David Passmore, Huidong Gu, Frank Zambito, Vangipuram
S. Rangan, Heather, Myler, Anne‑Francoise Aubry, Mark E. Arnold, and Jian Wang
Journal Citation: Journal of Chromatography B 2015, 1002, 54–62
Key words: SAW, Affinity Purification, Antibody Drug Conjugates, Biopharma, Pharmacokinetics,
Immunocapture
Stable Isotope Labeling by Amino acid in Vivo (SILAV): a new method to explore protein
metabolism
Authors: Sylvain Lehmann, Jérôme Vialaret, Guillaume Gras Combe, Luc Bauchet, Olivier Hanon,
Marine Girard, Audrey Gabelle, and Christophe Hirtz
Journal Citation: Rapid Communications Mass Spectrometry 2015, 29(20), 1917–1925
Key words: C18, SCX, Fractionation, In‑Solution Digestion, Peptide Cleanup, Clinical Research,
Proteomics

2014
Overexpression of microRNAs enhances recombinant protein production in Chinese hamster
ovary cells
Authors: Wan Ping Loh, Bernard Loo, Lihan Zhou, Peiqing Zhang, Dong‐Yup Lee, YuanshengYang, and Kong Peng Lam
Journal Citation: Biotechnology Journal 2014, 9(9), 1140–1151
Key words: CU, RX, GlykoPrep, Biopharma, Glycans
Targeting an acid labile aspartyl–prolyl amide bond as a viable alternative to trypsin digestion to
generate a surrogate peptide for LC–MS/MS analysis
Authors: Eliza N. Fung, Frank Zambito, Jonathan Haulenbeek, Steven P. Piccoli, Yan Zhang,
Binodh DeSilva, Mark Arnold, and Alexander Kozhich
Journal Citation: Bioanalysis 2014, 6(22), 2985–2998
Key words: SAW, Affinity Purification, Biopharma, Pharmacokinetics, Immunocapture

2011
A High‑Throughput Microchromatography Platform for Quantitative Analytical Scale Protein
Sample Preparation
Authors: Scott Fulton, Steve Murphy, Jenn Reich, Zachary Van Den Heuvel, Robert Sakowski,
Ronald Smith, Susan Agee
Journal Citation: Journal of Laboratory Automation 2011, 16(6), 457–467
Key words: CU, PAW, RX, Affinity Purification, GlykoPrep, Glycans

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