Mucosal or systemic microbiota exposures shape the B cell repertoire.
Nature. 2020; 584: 274-278
Functions of antibodies.
Microbiol. Spectr. 2014; 2: 1-17
Know your enemy or find your friend? Induction of IgA at mucosal surfaces.
Immunol. Rev. 2021; ()
Next generation antibody drugs: pursuit of the ’high-hanging fruit’.
Nat. Rev. Drug Discov. 2017; 17: 197-223
Early high-titer plasma therapy to prevent severe Covid-19 in older adults.
N. Engl. J. Med. 2021; 384: 610-618
Molecular landscape of anti-drug antibodies reveals the mechanism of the immune response following treatment with TNFα Antagonists.
Front. Immunol. 2019; 10: 2921
Antibodies in diagnostics – from immunoassays to protein chips.
Immunol. Today. 2000; 21: 379-382
Monoclonal antibody-based biosensor for point-of-care detection of type III secretion system expressing pathogens.
Anal. Chem. 2021; 93: 928-935
AIRR-C Glossary of Terms.
zenodo. 2021; https://doi.org/10.5281/zenodo.5095380
Novel approaches to analyze immunoglobulin repertoires.
Trends Immunol. 2017; 38: 471-482
Bioinformatic and statistical analysis of adaptive immune repertoires.
Trends Immunol. 2015; 36: 738-749
Sequencing the functional antibody repertoire – diagnostic and therapeutic discovery.
Nat. Rev. Rheumatol. 2014; 11: 171-182
Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning.
Nat. Biomed. Eng. 2021; 5: 600-612
Studying the antibody repertoire after vaccination: practical applications.
Trends Immunol. 2014; 35: 319-331
Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires.
Front. Immunol. 2018; 9: 224
Practical guidelines for B-cell receptor repertoire sequencing analysis.
Genome Med. 2015; 7: 121
Proteomics-directed cloning of circulating antiviral human monoclonal antibodies.
Nat. Biotechnol. 2012; 30: 1039-1043
A proteomics approach for the identification and cloning of monoclonal antibodies from serum.
Nat. Biotechnol. 2012; 30: 447-452
Serology in the 21st century: the molecular-level analysis of the serum antibody repertoire.
Curr. Opin. Immunol. 2015; 35: 89-97
Proteogenomics: concepts, applications and computational strategies.
Nat. Methods. 2014; 11: 1114-1125
Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination.
Nat. Med. 2016; 22: 1456-1464
Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response.
Proc. Natl. Acad. Sci. 2013; 110: 2993-2998
Next-generation sequencing and protein mass spectrometry for the comprehensive analysis of human cellular and serum antibody repertoires.
Curr. Opin. Chem. Biol. 2015; 24: 112-120
Proteomic analysis of Pemphigus autoantibodies indicates a larger, more diverse, and more dynamic repertoire than determined by B cell genetics.
Cell Rep. 2017; 18: 237-247
Strong clonal relatedness between serum and gut IgA despite different plasma cell origins.
Cell Rep. 2017; 20: 2357-2367
Sera antibody repertoire analyses reveal mechanisms of broad and pandemic strain neutralizing responses after human norovirus vaccination.
Immunity. 2019; 50: 1530-1541
Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2.
Science. 2020; 370: 1479-1484
Identification and characterization of the constituent human serum antibodies elicited by vaccination.
Proc. Natl. Acad. Sci. 2014; 111: 2259-2264
Human Plasma IgG1 Repertoires Are Simple, Unique, and Dynamic.
Social Science Research Network, 2020
Persistence of intrathecal oligoclonal B cells and IgG in multiple sclerosis.
J. Neuroimmunol. 2019; 333: 576966
Persistent antibody clonotypes dominate the serum response to influenza over multiple years and repeated vaccinations.
Cell Host Microbe. 2019; 25: 367-376
Intrathecal BCR transcriptome in multiple sclerosis versus other neuroinflammation: equally diverse and compartmentalized, but more mutated, biased and overlapping with the proteome.
Clin. Immunol. 2015; 160: 211-225
Methods for sequence and structural analysis of B and T cell receptor repertoires.
Comput. Struct. Biotechnol. J. 2020; 18: 2000-2011
Light chain of natural antibody plays a dominant role in protein antigen binding.
Biochem. Biophys. Res. Commun. 2000; 268: 390-394
The association of heavy and light chain variable domains in antibodies: implications for antigen specificity.
FEBS J. 2011; 278: 2858-2866
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding.
Cell Rep. 2021; 34: 108856
Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies.
Cell Syst. 2021; 12: 220-234
Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes.
Science. 2021; 372: 1108-1112
‘Background’ immunoglobulin production: measurement, biological significance and regulation.
Immunol. Today. 1982; 3: 243-249
Duration of humoral immunity to common viral and vaccine antigens.
N. Engl. J. Med. 2007; 357: 1903-1915
The role of antibody concentration and avidity in antiviral protection.
Science. 1997; 276: 2024-2027
Serum proteomics expands on high-affinity antibodies in immunized rabbits than deep B-cell repertoire sequencing alone.
BioRxiv. 2020; ()
Beyond bulk single-chain sequencing: getting at the whole receptor.
Curr. Opin. Syst. Biol. 2020; 24: 93-99
Differences in self-recognition between secreted antibody and membrane-bound B cell antigen receptor.
J. Immunol. 2019; 202: 1417-1427
More than one antibody of individual B cells revealed by single-cell immune profiling.
Cell Discov. 2019; 5 ()
IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.
Bioinformatics. 2015; 31: i53-i61
The bone marrow: the major source of serum immunoglobulins, but still a neglected site of antibody formation.
Clin. Exp. Immunol. 1981; 46: 1-8
Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires.
Mol. Syst. Des. Eng. 2019; 4: 701-736
Advanced methodologies in high-throughput sequencing of immune repertoires.
Trends Biotechnol. 2016; 35: 203-214
High-throughput mapping of B cell receptor sequences to antigen specificity.
Cell. 2019; 179: 1636-1646
Direct determination of antibody chain pairing by top-down and middle-down mass spectrometry using electron capture dissociation and ultraviolet photodissociation.
Anal. Chem. 2020; 92: 766-773
Understanding the human antibody repertoire.
mAbs. 2020; 12: 1729683
A 3D structural affinity model for multi-epitope in silico germinal center simulations.
BioRxiv. 2019; ()
Induction of broadly neutralizing antibodies in germinal centre simulations.
Curr. Opin. Biotechnol. 2018; 51: 137-145
How a well-adapted immune system is organized.
Proc. Natl. Acad. Sci. 2015; 112: 5950-5955
A minimal model of peptide binding predicts ensemble properties of serum antibodies.
BMC Genomics. 2012; 13: 79
Breaking the law: unconventional strategies for antibody diversification.
Nat. Rev. Immunol. 2019; 19: 355-368
Five computational developability guidelines for therapeutic antibody profiling.
Proc. Natl. Acad. Sci. U. S. A. 2019; 116: 4025-4030
The neonatal Fc receptor (FcRn): a misnomer?.
Front. Immunol. 2019; 10: 1540
Post-translational structural modifications of immunoglobulin G and their effect on biological activity.
Anal. Bioanal. Chem. 2015; 407: 79-94
Afucosylated IgG characterizes enveloped viral responses and correlates with COVID-19 severity.
Science. 2021; 371eabc8378
Antibody fucosylation predicts disease severity in secondary dengue infection.
Science. 2021; 372: 1102-1105
Changes in antigen-specific IgG1 Fc N-glycosylation upon influenza and tetanus vaccination.
Mol. Cell. Proteomics. 2012; 11M111.014563
The emerging landscape of single-molecule protein sequencing technologies.
Nat. Methods. 2021; 18: 604-617
Beyond mass spectrometry, the next step in proteomics.
Sci. Adv. 2020; 6eaax8978
iReceptor: a platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories.
Immunol. Rev. 2018; 284: 24-41
The analysis of clonal expansions in normal and autoimmune B cell repertoires.
Philos. Trans. R. Soc. B. 2015; 370: 20140239
Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting.
Sci. Adv. 2016; 2e1501371
Protein analysis by shotgun/bottom-up proteomics.
Chem. Rev. 2013; 113: 2343-2394
Sample preparation techniques for the untargeted LC-MS-based discovery of peptides in complex biological matrices.
J. Biomed. Biotechnol. 2011; 2011e245291
Protein A and protein G purification of antibodies.
Cold Spring Harb. Protoc. 2019; 2019prot099143
Antibody purification: ammonium sulfate fractionation or gel filtration.
in: Oliver C. Jamur M.C. Immunocytochemical Methods and Protocols. Humana Press, 2010: 15-26
Blood plasma from survivors of COVID-19: a novel and next frontier approach to fight against pandemic coronavirus.
Int. J. Immunol. Immunother. 2020; 7: 045
Proteomic identification of monoclonal antibodies from serum.
Anal. Chem. 2014; 86: 4758-4766
Mass spectrometry applied to bottom-up proteomics: entering the high-throughput era for hypothesis testing.
Annu. Rev. Anal. Chem. 2016; 9: 449-472
Value of using multiple proteases for large-scale mass spectrometry-based proteomics.
J. Proteome Res. 2010; 9: 1323-1329
Maximum entropy models for antibody diversity.
Proc. Natl. Acad. Sci. 2010; 107: 5405-5410
Proteomics beyond trypsin.
FEBS J. 2015; 282: 2612-2626
Interlaboratory study for characterizing monoclonal antibodies by top-down and middle-down mass spectrometry.
J. Am. Soc. Mass Spectrom. 2020; 31: 1783-1802
Breaking the affinity ceiling for antibodies and T cell receptors.
Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 10679-10681
A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics.
Mol. Cell. Proteomics. 2018; 17: 2284-2296
Multiplexed, quantitative workflow for sensitive biomarker discovery in plasma yields novel candidates for early myocardial injury.
Mol. Cell. Proteomics. 2015; 14: 2375-2393
Enhanced detection of low abundance human plasma proteins using a tandem IgY12-SuperMix immunoaffinity aeparation atrategy.
Mol. Cell. Proteomics. 2008; 7: 1963-1973
Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona.
Nat. Commun. 2020; 11: 3662
Online parallel accumulation–serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer.
Mol. Cell. Proteomics. 2018; 17: 2534-2545
Comprehensive single-shot proteomics with FAIMS on a hybrid orbitrap mass spectrometer.
Anal. Chem. 2018; 90: 9529-9537
BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes.
Nat. Methods. 2018; 15: 440-448
Ultra-fast proteomics with scanning SWATH.
Nat. Biotechnol. 2021; 39: 846-854
Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial.
Mol. Syst. Biol. 2018; 14e8126
TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples.
Nat. Methods. 2020; 17: 399-404
Plasma proteome profiling to assess human health and disease.
Cell Syst. 2016; 2: 185-195
Analysis of 1508 plasma samples by capillary-flow data-independent acquisition profiles proteomics of weight loss and maintenance.
Mol. Cell. Proteomics. 2019; 18: 1242-1254
A human interactome in three quantitative dimensions organized by stoichiometries and abundances.
Cell. 2015; 163: 712-723
The BioPlex network: a systematic exploration of the human interactome.
Cell. 2015; 162: 425-440
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.
Nat. Biotechnol. 2008; 26: 1367-1372
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry.
Rapid Commun. Mass Spectrom. 2003; 17: 2337-2342
MS-GF+ makes progress towards a universal database search tool for proteomics.
Nat. Commun. 2014; 5: 5277
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics.
Nat. Methods. 2017; 14: 513-520
Proteome Discoverer – a community enhanced data processing suite for protein informatics.
Proteomes. 2021; 9: 15
PASA: proteomic analysis of serum antibodies web server.
PLoS Comput. Biol. 2021; 17e1008607
Complete de novo assembly of monoclonal antibody sequences.
Sci. Rep. 2016; 6: 31730
Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry.
Nat. Commun. 2017; 8: 291
A multicenter study benchmarks software tools for label-free proteome quantification.
Nat. Biotechnol. 2016; 34: 1130-1136
Analysis of the resolution limitations of peptide identification algorithms.
J. Proteome Res. 2011; 10: 5555-5561
The lysosomal endopeptidases Cathepsin D and L are selective and effective proteases for the middle-down characterization of antibodies.
FEBS J. 2021; ()
Generating informative sequence tags from antigen-binding regions of heavily glycosylated IgA1 antibodies by native top-down electron capture dissociation.
J. Am. Soc. Mass Spectrom. 2021; 32: 1326-1335
Mining adaptive immune receptor repertoires for biological and clinical information using machine learning.
Curr. Opin. Syst. Biol. 2020; 24: 109-119
Inferring processes underlying B-cell repertoire diversity.
Philos. Trans. R. Soc. B. 2015; 370: 20140243
Learning the high-dimensional immunogenomic features that predict public and private antibody repertoires.
J. Immunol. 2017; 199: 2985-2997
Germline immunoglobulin genes: disease susceptibility genes hidden in plain sight?.
Curr. Opin. Syst. Biol. 2020; 24: 100-108
The individual and population genetics of antibody immunity.
Trends Immunol. 2017; 38: 459-470
Diversity in the CDR3 region of VH is sufficient for most antibody specificities.
Immunity. 2000; 13: 37-45
Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire.
Proc. Natl. Acad. Sci. U. S. A. 2009; 06: 20216-20221
Number and distribution of lymphocytes in man. A critical analysis.
J. Mol. Med. 1974; 52: 511-515
The generation of antibody-secreting plasma cells.
Nat. Rev. Immunol. 2015; 15: 160-171
The secretion of antibody by isolated lymph node cells.
J. Biol. Chem. 1961; 236: 464
Single-cell deep phenotyping of IgG-secreting cells for high-resolution immune monitoring.
Nat. Biotechnol. 2017; 35: 977-982
Immunoglobulin responses at the mucosal interface.
Annu. Rev. Immunol. 2011; 29: 273-293
Maintenance of serum antibody levels.
Annu. Rev. Immunol. 2005; 23: 367-386
The half-lives of serum immunoglobulins in adult mice.
Eur. J. Immunol. 1988; 18: 313-316
Balancing charge in the complementarity-determining regions of humanized mAbs without affecting pI reduces non-specific binding and improves the pharmacokinetics.
mAbs. 2015; 7: 483-493
Charge-mediated influence of the antibody variable domain on FcRn-dependent pharmacokinetics.
Proc. Natl. Acad. Sci. U. S. A. 2015; 112: 5997-6002
A high-throughput pipeline for validation of antibodies.
Nat. Methods. 2018; 15: 909
Autoantigen discovery with a synthetic human peptidome.
Nat. Biotechnol. 2011; 29: 535-541
The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops.
Protein Eng. Des. Sel. 2013; 26: 599-609
Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization.
Science. 2013; 340: 751-756
One by one – insights into complex immune responses through functional single-cell analysis.
Chim. Int. J. Chem. 2020; 74: 716-723
Quantitative and qualitative analysis of humoral immunity reveals continued and personalized evolution in chronic viral infection.
Cell Rep. 2020; 30: 997-1012
High-throughput single-cell activity-based screening and sequencing of antibodies using droplet microfluidics.
Nat. Biotechnol. 2020; 38: 715-721
Top-down mass spectrometry: recent developments, applications and perspectives.
Analyst. 2011; 136: 3854-3864
Proteomics in heart failure: top-down or bottom-up?.
Pflugers Arch. 2014; 466: 1199-1209
Top down proteomics: facts and perspectives.
Biochem. Biophys. Res. Commun. 2014; 445: 683-693
The benefits (and misfortunes) of SDS in top-down proteomics.
J. Proteome. 2018; 175: 75-86
Direct quantitation of therapeutic antibodies for pharmacokinetic studies using immuno-purification and intact mass analysis.
Bioanalysis. 2019; ()
Top-down proteomics: ready for prime time?.
Anal. Chem. Wash. 2018; 90: 110-127
Top-down mass spectrometry analysis of human serum autoantibody antigen-binding fragments.
Sci. Rep. 2019; 9: 2345
A whole-molecule immunocapture LC–MS approach for the in vivo quantitation of biotherapeutics.
Bioanalysis. 2016; 8: 2103-2114
Generic hybrid ligand binding assay liquid chromatography high-resolution mass spectrometry-based workflow for multiplexed human immunoglobulin G1 quantification at the intact protein level: application to preclinical pharmacokinetic studies.
Anal. Chem. 2017; 89: 2628-2635
Selectivity over coverage in de novo sequencing of IgGs.
Chem. Sci. 2020; 11: 11886-11896
Mass spectrometry-based proteomic exploration of the human immune system: focus on the inflammasome, global protein secretion, and T cells.
Expert Rev. Proteomics. 2017; 14: 395-407
Toward sensitive and accurate analysis of antibody biotherapeutics by liquid chromatography coupled with mass spectrometry.
Drug Metab. Dispos. 2014; 42: 1858-1866
PepNovo: de novo peptide sequencing via probabilistic network modeling.
Anal. Chem. 2005; 77: 964-973
NovoHMM: a hidden Markov model for de novo peptide sequencing.
Anal. Chem. 2005; 77: 7265-7273
Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides.
J. Proteome Res. 2013; 12: 2846-2857
Automated de novo protein sequencing of monoclonal antibodies.
Nat. Biotechnol. 2008; 26: 1336-1338
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