timsTOF Pro Bibliography

Introduction

 

timsTOF Pro Bibliography  

The timsTOF Pro powered by PASEF boosts the research capability of the labs having acquired it by offering an unprecedented, uncompromised combination of speed, sensitivity, selectivity and robustness. The reproducible measurement of Collisional Cross Section (CCS) values for every peptide has allowed to develop innovative 4D proteomics/lipidomics/metabolomics approaches, making the best use of the instrument’s selectivity. New acquisition modes are rolled out on a regular basis, like dia-PASEF introduced at HUPO 2019. The peer-reviewed communications listed below is a non-exhaustive list from the work initiated on the first instruments, and many more are to come.  

Biology – timsTOF Pro - COVID-19 section

Biology – timsTOF Pro - COVID-19 section

Title Authors Publication Link
Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study IMPACC Manuscript Writing Team†, on behalf of the IMPACC Network Steering Committee‡ Sci. Immunol. 6, 2021, eabf3733 https://doi.org/10.1126/sciimmunol.abf3733
DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients Mun, D.-G., Vanderboom, P.M. et al. J. Proteome Res. 20, 2021, 4165–4175 https://doi.org/10.1021/acs.jproteome.1c00506
Proteomic Analysis Identifies Prolonged Disturbances in Pathways Related to Cholesterol Metabolism and Myocardium Function in the COVID-19 Recovery Stage Chen, Y.; Yao, H.; Wong, C.C.L. et al. J. Proteome Res 2021 https://doi.org/10.1021/acs.jproteome.1c00054
SARS-CoV-2 infects human pancreatic ß cells and elicits ß cell impairment Wu, C.-T.; Lidsky, P.V.; Jackson, P.K. et al. Cell Metabolism 2021 https://doi.org/10.1016/j.cmet.2021.05.013
Second-Generation Antibodies Neutralize Emerging SARS-CoV-2 Variants of Concern Kovacech, B.; Fialova, L. et al. preprint; Microbiology 2021 https://doi.org/10.1101/2021.06.09.447527
A Blood Atlas of COVID-19 Defines Hallmarks of Disease Severity and Specificity; COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium Ahern, D. J.; Ai, Z.; Fischer, R. et al. preprint; Infectious Diseases (except HIV/AIDS) 2021 https://doi.org/10.1101/2021.05.11.21256877
Systematic Functional Analysis of SARS-CoV-2 Proteins Uncovers Viral Innate Immune Antagonists and Remaining Vulnerabilities Hayn, M.; Hirschenberger, M. et al. Cell Reports 2021, 109126 https://doi.org/10.1016/j.celrep.2021.109126
Large Scale Discovery of Coronavirus-Host Factor Protein Interaction Motifs Reveals SARS-CoV-2 Specific Mechanisms and Vulnerabilities Kruse, T.; Benz, C.; Mann, M. et al. Biochemistry 2021 https://doi.org/10.1101/2021.04.19.440086
The COVIDome Explorer Researcher Portal Sullivan, K. D.; Galbraith, M. D. et al. Allergy and Immunology 2021 https://doi.org/10.1101/2021.03.04.21252945
Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Native Top-Down Mass Spectrometry Roberts, D. S.; Mann, M. W.; Ge, Y. et al. preprint; Biochemistry 2021 https://doi.org/10.1101/2021.02.28.433291
Structural and Functional Characterization of SARS-CoV-2 RBD Domains Produced in Mammalian Cells Gstöttner, C.; Zhang, T.; Wuhrer, M. et al. preprint; Biochemistry 2021 https://doi.org/10.1101/2021.02.23.432424
High-Resolution Longitudinal Serum Proteome Trajectories in COVID-19 Reveal Patients-Specific Seroconversion Geyer, P. E.; Arend, F. M. et al. preprint; Infectious Diseases (except HIV/AIDS) 2021 https://doi.org/10.1101/2021.02.22.21252236
The Host Interactome of Spike Expands the Tropism of SARS-CoV-2 Bamberger, C.; Pankow, S.; Yates, J. et al. preprint; Molecular Biology 2021 https://doi.org/10.1101/2021.02.16.431318
Evidence of Structural Protein Damage and Membrane Lipid Remodeling in Red Blood Cells from COVID-19 Patients Thomas, T.; Stefanoni, D. et al. Proteome Res. 2020, 19 (11), 4455–4469 https://doi.org/10.1021/acs.jproteome.0c00606
Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein (preprint). Nikolaev, E.; Indeykina, M.; Borchers, C. et al. Molecular Biology 2020 https://doi.org/10.1101/2020.05.24.113043
Immune Suppression in the Early Stage of COVID-19 Disease Tian, W.; Zhang, N.; Wong, C. C. L. et al. Nat Commun 2020, 11 (1), 5859 https://doi.org/10.1038/s41467-020-19706-9
SARS-CoV-2 Induced CYP19A1 Expression in the Lung Correlates with Increased Aromatization of Testosterone-to-Estradiol in Male Golden Hamsters Stanelle-Bertram, S.; Schaumburg, B. et al. preprint; In Review 2020 https://doi.org/10.21203/rs.3.rs-107474/v1
Transcriptional and Proteomic Insights into the Host Response in Fatal COVID-19 Cases Wu, M.; Chen, Y. et al. Proc Natl Acad Sci USA 2020, 117 (45), 28336–28343 https://doi.org/10.1073/pnas.2018030117
Serum Proteomics in COVID-19 Patients: Altered Coagulation and Complement Status as a Function of IL-6 Level D’Alessandro, A.; Thomas, T. et al. Proteome Res. 2020, 19 (11), 4417–4427 https://doi.org/10.1021/acs.jproteome.0c00365

Biology – timsTOF Pro

Biology – timsTOF Pro  

Title Authors Publication Link
Integration of Transcriptomic And Proteomic Analyses Reveals Several Levels of Metabolic Regulation In The Excess Starch And Early Senescent Leaf Mutant lses1 In Rice Chen, Z., Wang, Y. et al. preprint; In Review 2021 https://doi.org/10.21203/rs.3.rs-805903/v1
Ecological Adaptation and Succession of Human Fecal Microbial Communities in an Automated In Vitro Fermentation System Gnanasekaran, T., Assis Geraldo, J. et al. mSystems 6 2021 https://doi.org/10.1128/mSystems.00232-21
Spectrum graph-based de-novo sequencing algorithm MaxNovo achieves high peptide identification rates in collisional dissociation MS/MS spectra Gutenbrunner, P., Kyriakidou, P. et al. preprint; Bioinformatics 2021 https://doi.org/10.1101/2021.09.04.458985
Upregulation of α enolase (ENO1) crotonylation in colorectal cancer and its promoting effect on cancer cell metastasis Hou, J.-Y., Cao, J. et al. Biochemical and Biophysical Research Communications 2021, 578, 77–83 https://doi.org/10.1016/j.bbrc.2021.09.027
Characterization of the microRNA Transcriptomes and Proteomics of Cochlea Tissue-derived Small Extracellular Vesicles From Different Age of Mice After Birth Jiang, P., Ma, X. et al. preprint; In Review 2021 https://doi.org/10.21203/rs.3.rs-823336/v1
Drone honey bees (Apis mellifera ) are disproportionately sensitive to abiotic stressors despite expressing high levels of stress response proteins McAfee, A., Metz, B. et al. preprint; Cell Biology 2021 https://doi.org/10.1101/2021.08.28.456261
Evaluation of a Bruker timsTOF Pro for Native Mass Spectrometry Panczyk, E., Snyder, D. et al. preprint; Chemistry 2021 https://doi.org/10.33774/chemrxiv-2021-qr78t
Identification of potential autoantigens in anti-CCP-positive and anti-CCP-negative rheumatoid arthritis using citrulline-specific protein arrays Poulsen, T.B.G., Damgaard, D., Stensballe, A. et al. Sci Rep 2021, 11, 17300 https://doi.org/10.1038/s41598-021-96675-z
Thiol and Disulfide Containing Vancomycin Derivatives Against Bacterial Resistance and Biofilm Formation Shchelik, I.S., Gademann, K. preprint; Microbiology 2021 https://doi.org/10.1101/2021.08.23.457343
Use of PASEF for Accelerated Protein and De Novo Sequencing with High Data Quality Suckau, D., Evers, W., Beck, A. et al. 2022, In: Houen, G. (Ed.), Therapeutic Antibodies, Methods in Molecular Biology. Springer US, New York, NY, pp. 207–217 https://doi.org/10.1007/978-1-0716-1450-1_12
Accurate and automated high-coverage identification of chemically cross-linked peptides with MaxLynx Yılmaz, Ş., Busch, F., Cox, J. et al. preprint; Bioinformatics 2021 https://doi.org/10.1101/2021.08.26.457759
A Multi-omics Method Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem Cell-derived Cardiomyocytes Bayne, E.F., Simmons, A.D., Ge, Y. et al. preprint; Systems Biology 2021 https://doi.org/10.1101/2021.06.23.449630
Synthetic antigen-presenting cells reveal the diversity and functional specialisation of extracellular vesicles composing the fourth signal of T cell immunological synapses Céspedes, P.F., Jainarayanan, A., Fischer, R. et al. preprint; Immunology 2021 https://doi.org/10.1101/2021.05.29.445691
Ecological Adaptation and Succession of Human Fecal Microbial Communities in an Automated In Vitro Fermentation System Gnanasekaran, T., Assis Geraldo, J. et al. mSystems 2021 https://doi.org/10.1128/mSystems.00232-21
Complementing Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry Imaging with Chromatography Data for Improved Assignment of Isobaric and Isomeric Phospholipids Utilizing Trapped Ion Mobility-Mass Spectrometry Helmer, P.O., Nordhorn, I.D., Zubeil, F. et al. Anal. Chem. 2021, 93, 2135–2143 https://doi.org/10.1021/acs.analchem.0c03942
Salivary proteome of aphthous stomatitis reveals the participation of vitamin metabolism, nutrients, and bacteria Hernández-Olivos, R., Muñoz, M. et al. preprint; Dentistry and Oral Medicine 2021 https://doi.org/10.1101/2021.08.01.21261411
Darwin’s bark spider shares a spidroin repertoire with Caerostris extrusa but achieves extraordinary silk toughness through gene expression Kono, N., Ohtoshi, R. et al. preprint; Molecular Biology 2021 https://doi.org/10.1101/2021.07.16.452619
High-Throughput Multi-attribute Analysis of Antibody-Drug Conjugates Enabled by Trapped Ion Mobility Spectrometry and Top-Down Mass Spectrometry Larson, E.J., Roberts, D.S., Ge, Y. et al. Anal. Chem. 2021, 93, 10013–10021 https://doi.org/10.1021/acs.analchem.1c00150
Comparative Proteomic Analysis to Investigate the Pathogenesis of Oral Adenoid Cystic Carcinoma Li, W., Zhang, Q. et al. ACS Omega 2021, 6, 18623–18634 https://doi.org/10.1021/acsomega.1c01270
Mode of action of Elasnin as biofilm-formation eradicator of Methicillin-Resistant Staphylococcus aureus Long, L., Sulaiman, J.E. et al. preprint; In Review 2021 https://doi.org/10.21203/rs.3.rs-752510/v1
Trapped Ion Mobility Spectrometry (TIMS) and Parallel Accumulation – Serial Fragmentation (PASEF) in Proteomics Meier, F., Park, M.A., Mann, M. Molecular & Cellular Proteomics 2021, 100138 https://doi.org/10.1016/j.mcpro.2021.100138
Investigating Closed Room Conspirators of Posttraumatic Inflammatory Response: Multi- Omics Profiles of Exosomes Derived from Intestinal Epithelial Cells Under Ischemia Reperfusion Injury Senda, A., Kojima, M. et al. preprint; In Review 2021 https://doi.org/10.21203/rs.3.rs-792334/v1
Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows Van Den Bossche, T., Kunath, B.J. et al. preprint; Microbiology 2021 https://doi.org/10.1101/2021.03.05.433915
AlphaTims: Indexing trapped ion mobility spectrometry – time of flight data for fast and easy accession and visualization Willems, S., Voytik, E., Mann, M. et al. preprint; Bioinformatics 2021 https://doi.org/10.1101/2021.07.27.453933
Integrative proteomics and phosphoproteomics reveals phosphorylation networks involved in the maintenance and expression of embryogenic competence in sugarcane callus Xavier, L.R., Almeida, F.A. et al. preprint; Plant Biology 2021 https://doi.org/10.1101/2021.07.22.453415
Integrative proteomic and metabolomic analyses reveal the mechanism by which bismuth enables Helicobacter pylori eradication Yao, X., Xiao, S., Zhou, L. Helicobacter 2021 https://doi.org/10.1111/hel.12846
Comparative analyses of the venom components in the salivary gland transcriptomes and saliva proteomes of some heteropteran insects Yoon, K.A., Kim, W. et al. Insect Science 2021, 1744-7917.12955 https://doi.org/10.1111/1744-7917.12955
MaxDIA enables library-based and library-free data-independent acquisition proteomics Sinitcyn, P.; Hamzeiy, H.; Cox, J. et al. Nat Biotechnol, 2021 https://doi.org/10.1038/s41587-021-00968-7
A Multi-omics Strategy Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem Cell-derived Cardiomyocytes Bayne, E.F.; Simmons, A.D.; Ge, Y. et al. preprint; Systems Biology, 2021 https://doi.org/10.1101/2021.06.23.449630
Locality-sensitive hashing enables signal classification in high-throughput mass spectrometry raw data at scale Bob, K.; Teschner, D.; Tenzer, S. et al. preprint; Bioinformatics, 2021 https://doi.org/10.1101/2021.07.01.450702
Fragmentation and Mobility Separation of Peptide and Protein Ions in a Trapped-Ion Mobility Device Borotto, N.B.; Graham, K.A. Anal. Chem., 2021 https://doi.org/10.1021/acs.analchem.1c01188
Metabolomic Profiling of Human Urine Samples Using LC-TIMS-QTOF Mass Spectrometry Di Poto, C.; Tian, X. et al. J. Am. Soc. Mass Spectrom., 2021 https://doi.org/10.1021/jasms.0c00467
BCAR1 plays critical roles in the formation and immunoevasion of invasive circulating tumor cells in lung adenocarcinoma Mao, C.-G.; Jiang, S. et al. Int. J. Biol. Sci., 2021, 17, 2461–2475 https://doi.org/10.7150/ijbs.61790
Insight into the collagen-degrading activity of a serine protease in the latex of Ficus carica cultivar Masui Dauphine Nishimura, K.; Higashiya, K. et al. Bioscience, Biotechnology, and Biochemistry, 2021, 85, 1147–1156 https://doi.org/10.1093/bbb/zbab025
The differences of muscle proteins between neon flying squid (Ommastrephes bartramii) and jumbo squid (Dosidicus gigas) mantles via physicochemical and proteomic analyses Shui, S.; Yao, H. et al. Food Chemistry, 2021, 364, 130374 https://doi.org/10.1016/j.foodchem.2021.130374
Global profiling of RNA-binding protein target sites by LACE-seq Su, R.; Fan, L.-H.; Wong, C.C.L et al. Nat Cell Biol, 2021, 23, 664–675 https://doi.org/10.1038/s41556-021-00696-9
Physiological and Proteomic Responses of Pitaya to PEG-Induced Drought Stress Wang, A.; Ma, C. et al. Agriculture, 2021, 11, 632 https://doi.org/10.3390/agriculture11070632
A cell-sorting-based nano-scale pipeline for cell-type specific proteomics in plants Wang, H.; Li, R. et al. preprint; Plant Biology, 2021 https://doi.org/10.1101/2021.07.06.451220
Proteomics and bioinformatics reveal insights into neuroinflammation in the acute to subacute phases in rat models of spinal cord contusion injury Yao, X.; Liu, Z. et al. FASEB, 2021, 35 https://doi.org/10.1096/fj.202100081RR
Nuclear receptors NHR-49 and NHR-79 promote peroxisome proliferation to compensate for aldehyde dehydrogenase deficiency in C. elegans Zeng, L.; Li, X. et al. PLoS Genet, 2021, 17 https://doi.org/10.1371/journal.pgen.1009635
Multi-omics analyses of human colorectal cancer revealed three mitochondrial genes potentially associated with poor outcomes of patients Zhang, W.; Lin, L. et al. J Transl Med, 2021, 19, 273 https://doi.org/10.1186/s12967-021-02939-7
Integrative multiplatform-based molecular profiling of human colorectal cancer reveals proteogenomic alterations underlying mitochondrial inactivation Zhang, W.; Tang, D. et al. Am J Cancer Res, 2021, 11, 2893–2910 https://pubmed.ncbi.nlm.nih.gov/34249434
Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro Aballo, T.J.; Roberts, D.S.; Ge, Y. et al. preprint; Systems Biology, 2021 https://doi.org/10.1101/2021.05.24.445470
DeGlyPHER: an ultrasensitive method for analysis of viral spike N-glycoforms Baboo, S.; Diedrich, J.K.; Yates, J.R. et al. preprint; Biochemistry, 2021 https://doi.org/10.1101/2021.05.13.444041
Identification of proximal SUMO-dependent interactors using SUMO-ID Barroso-Gomila, O.; Trulsson, F.; Azkargorta, M. et al. preprint; Biochemistry, 2020 https://doi.org/10.1101/2020.12.28.424528
Synthetic Antigen Presenting cells reveal the diversity and functional specialisation of extracellular vesicles composing the fourth signal of T cell immunological synapses Céspedes, P.F.; Jainarayanan, A.; Fischer, R. et al. preprint; Immunology, 2021 https://doi.org/10.1101/2021.05.29.445691
Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles De Vrieze, J.; Heyer, R. et al. preprint; Bioengineering, 2021 https://doi.org/10.1101/2021.05.28.446109
A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines Feola, S.; Chiaro, J.; Lehtiö, J. et al. preprint; Cancer Biology, 2021 https://doi.org/10.1101/2021.06.08.447483
PeptiCHIP: a novel microfluidic-based chip platform for tumour antigen landscape identification Feola, S.; Haapala, M.; Lehtiö, J. et al. preprint; In Review, 2021 https://doi.org/10.21203/rs.3.rs-156531/v1
Immunomodulation of T Helper Cells by Tumor Microenvironment in Oral Cancer Is Associated With CCR8 Expression and Rapid Membrane Vitamin D Signaling Pathway Fraga, M.; Yáñez, M. et al. Front. Immunol., 2021, 12 https://doi.org/10.3389/fimmu.2021.643298
Two-dimensional guanidinium-based covalent organic nanosheets for controllable recognition and specific enrichment of global/multi-phosphopeptides He, Y.; Huang, W. et al. Talanta, 2021, 233 https://doi.org/10.1016/j.talanta.2021.122497
A ciliopathy complex builds distal appendages to initiate ciliogenesis Kumar, D.; Rains, A. et al. preprint; Cell Biology, 2021 https://doi.org/10.1101/2021.03.01.433418
High resolution analysis of proteome dynamics during Bacillus subtilis sporulation Tu, Z.; Dekker, H.L.; Kramer, G. et al. preprint; Microbiology, 2021 https://doi.org/10.1101/2021.05.20.445030
LRRC23 is a conserved component of the radial spoke that is necessary for sperm motility and male fertility in mice Zhang, X.; Sun, J. et al. preprint; Cell Biology, 2021 https://doi.org/10.1101/2021.06.01.446532
Ribosome-Inactivating Proteins of Bougainvillea Glabra Uncovered Polymorphism and Active Site Divergence Lin, Y.; Xu, L. et al. Toxins 2021, 13 (5), 331 https://doi.org/10.3390/toxins13050331
Integrated Phospho-Proteogenomic and Single-Cell Transcriptomic Analysis of Meningiomas Establishes Robust Subtyping and Reveals Subtype-Specific Immune Invasion Blume, C.; Dogan, H.; Mann, M. et al. preprint; Genomics, 2021 https://doi.org/10.1101/2021.05.11.443369
Tetrahydrocurcumin Ameliorates Alzheimer’s Pathological Phenotypes by Inhibition of Microglial Cell Cycle Arrest and Apoptosis via Ras/ERK Signaling Xiao, Y.; Dai, Y. et al. Biomedicine & Pharmacotherapy 2021, 139 https://doi.org/10.1016/j.biopha.2021.111651
Hypoxic Acclimation Improves Cardiac Redox Homeostasis and Protects Heart against Ischemia-Reperfusion Injury through Upregulation of O-GlcNAcylation Ou, W.; Liang, Y et al. Redox Biology 2021, 101994 https://doi.org/10.1016/j.redox.2021.101994
DNA Binding Mode, Photophysical Properties and Recommendations for Use of SYBR Gold Kolbeck, P. J.; Vanderlinden, W. et al. Molecular Structure, Nucleic Acids Research 2021, gkab265 https://doi.org/10.1093/nar/gkab265
Comprehensive Plasma Proteomics by Orthogonal Protease Digestion Fossati, A.; Richards, A. L. et al. preprint; Systems Biology, 2021 https://doi.org/10.1101/2021.04.28.441706
Multicomponent Nature Underlies the Extraordinary Mechanical Properties of Spider Dragline Silk Kono, N.; Nakamura, H. et al. preprint; Molecular Biology, 2021 https://doi.org/10.1101/2021.04.22.441049
MiRNAs and Their Gene Targets—A Clue to Differentiate Pregnancies with Small for Gestational Age Newborns, Intrauterine Growth Restriction, and Preeclampsia Timofeeva, A. V.; Fedorov, I. S. et al. Diagnostics 2021, 11 (4), 729 https://doi.org/10.3390/diagnostics11040729
The Autophagy Receptor TAX1BP1 (T6BP) Is a Novel Player in Antigen Presentation by MHC-II Molecules Pereira, M.; Richetta, C.; Pionneau, C. et al. preprint; Immunology, 2021 https://doi.org/10.1101/2021.04.21.440798
Conformational Interconversion of MLKL and Disengagement from RIPK3 Precede Cell Death by Necroptosis Garnish, S. E.; Meng, Y. et al. Nat Commun 2021, 12 (1), 2211 https://doi.org/10.1038/s41467-021-22400-z
Comprehensive Analysis of Lysine Succinylation in Paper Mulberry (Broussonetia Papyrifera) Dong, Y.; Li, P. et al. First BMC Genomics 2021, 22 (1), 255 https://doi.org/10.1186/s12864-021-07567-5
Benefits of Ion Mobility Separation and Parallel Accumulation–Serial Fragmentation Technology on TimsTOF Pro for the Needs of Fast Photochemical Oxidation of Protein Analysis Loginov, D. S.; Fiala, J. et al. ACS Omega 2021, 6 (15), 10352–10361 https://doi.org/10.1021/acsomega.1c00732
SLPI Is a Critical Mediator That Controls PTH-Induced Bone Formation Morimoto, A.; Kikuta, J. et al. Nat Commun 2021, 12 (1), 2136 https://doi.org/10.1038/s41467-021-22402-x
Analysis of Peptide Stereochemistry in Single Cells by Capillary Electrophoresis–Trapped Ion Mobility Spectrometry Mass Spectrometry Mast, D. H.; Liao, H.-W.; Sweedler, J. V. et al. Anal. Chem. 2021, 93 (15), 6205–6213 https://doi.org/10.1021/acs.analchem.1c00445
Simplified High-Throughput Methods for Deep Proteome Analysis on the TimsTOF Pro Sandow, J. J.; Infusini, G.; Webb, A. I. et al. preprint; Biochemistry, 2019 https://doi.org/10.1101/657908
Ti4+-Immobilized Hierarchically Porous Zirconium-Organic Frameworks for Highly Efficient Enrichment of Phosphopeptides He, Y.; Zheng, Q. et al. Microchim Acta 2021, 188 (5), 150 https://doi.org/10.1007/s00604-021-04760-x
Trapped Ion Mobility Spectrometry Reduces Spectral Complexity in Mass Spectrometry Based Workflow Charkow, J.; Röst, H. L. preprint; Bioinformatics, 2021 https://doi.org/10.1101/2021.04.01.438072
Elongation Factor EEF2 Kinase and Autophagy Jointly Promote Survival of Cancer Cells Lenchine, R. V.; Rao, S. R. et al. Biochemical Journal 2021, 478 (8), 1547–1569 https://doi.org/10.1042/BCJ20210126
Proteome-Scale Endogenous Tagging Enables the Cartography of Human Cellular Organization Cho, N. H.; Cheveralls, K. C.; Mann, M. et al. OpenCell; preprint; Cell Biology, 2021 https://doi.org/10.1101/2021.03.29.437450
Hippocampal Proteomic Analysis Reveals Activation of Necroptosis and Ferroptosis in a Mouse Model of Chronic Unpredictable Mild Stress-Induced Depression Huang, Y.; Zhu, L. et al. Behavioural Brain Research 2021, 407, 113261 https://doi.org/10.1016/j.bbr.2021.113261
Developing a Multivariable Prediction Model for Functional Outcome after Reperfusion Therapy for Acute Ischaemic Stroke: Study Protocol for the Targeting Optimal Thrombolysis Outcomes (TOTO) Multicentre Cohort Study Holliday, E.; Lillicrap, T. et al. BMJ Open 2020, 10 (4), e038180 https://doi.org/10.1136/bmjopen-2020-038180
Cross-Linking/Mass Spectrometry Combined with Ion Mobility on a TimsTOF Pro Instrument for Structural Proteomics Ihling, C. H.; Piersimoni, L. et al. preprint; Biochemistry, 2021 https://doi.org/10.1101/2021.03.26.437136
Temporarily Epigenetic Repression in Bergmann Glia Regulates the Migration of Granule Cells Chen, S.; Zhang, K. et al. Adv. Sci. 2021, 2003164 https://doi.org/10.1002/advs.202003164
Ubiquitin Specific Peptidase 32 Acts as an Oncogene in Epithelial Ovarian Cancer by Deubiquitylating Farnesyl-Diphosphate Farnesyltransferase 1 Nakae, A.; Kodama, M. et al. Biochemical and Biophysical Research Communications 2021, 552, 120–127 https://doi.org/10.1016/j.bbrc.2021.03.049
Open and Easy Access to TimsTOF Raw Data Łącki, M. K.; Startek, M. P. et al. OpenTIMS, TimsPy, and TimsR: J. Proteome Res. 2021, 20 (4), 2122–2129 https://doi.org/10.1021/acs.jproteome.0c00962
High Sensitivity Dia-PASEF Proteomics with DIA-NN and FragPipe Demichev, V.; Yu, F. et al. preprint; Bioinformatics, 2021 https://doi.org/10.1101/2021.03.08.434385
Packed Red Blood Cells Inhibit T-Cell Activation via ROS-Dependent Signaling Pathways Gerner, M. C.; Bileck, A. et al. Journal of Biological Chemistry 2021, 296, 100487 https://doi.org/10.1016/j.jbc.2021.100487
Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows Van Den Bossche, T.; Kunath, B. J. et al. preprint; Microbiology, 2021 https://doi.org/10.1101/2021.03.05.433915
A Ciliopathy Complex Builds Distal Appendages to Initiate Ciliogenesis Kumar, D.; Rains, A. et al. preprint; Cell Biology, 2021 https://doi.org/10.1101/2021.03.01.433418
Global Proteomic Analysis of Extracellular Matrix in Mouse and Human Brain Highlights Relevance to Cerebrovascular Disease Pokhilko, A.; Brezzo, G. et al. Cereb Blood Flow Metab 2021, 0271678X2110043 https://doi.org/10.1177/0271678X211004307
Deep Learning the Collisional Cross Sections of the Peptide Universe from a Million Experimental Values Meier, F.; Köhler, N. D. et al. Nat Commun 2021, 12 (1), 1185 https://doi.org/10.1038/s41467-021-21352-8
Comparison of Lipidome Profiles of Caenorhabditis Elegans—Results from an Inter-Laboratory Ring Trial Spanier, B.; Laurençon, A. et al. Metabolomics 2021, 17 (3), 25 https://doi.org/10.1007/s11306-021-01775-6
Insight into the Collagen-Degrading Activity of a Serine Protease in the Latex of Ficus Carica Cultivar Masui Dauphine Nishimura, K.; Higashiya, K. et al. Bioscience, Biotechnology, and Biochemistry 2021, 85 (5), 1147–1156 https://doi.org/10.1093/bbb/zbab025
Genome-Wide CRISPRi Screening Identifies OCIAD1 as a Prohibitin Client and Regulatory Determinant of Mitochondrial Complex III Assembly in Human Cells Vasseur, M. L.; Friedman, J. R. et al. preprint; Cell Biology, 2021 https://doi.org/10.1101/2021.02.16.431450
KCTD19 Associates with ZFP541 and HDAC1 and Is Required for Meiotic Exit in Male Mice Oura, S.; Koyano, T. et al. preprint; Developmental Biology, 2021 https://doi.org/10.1101/2021.02.12.430913
Methylation of KRAS at Lysine 182 and 184 by SETD7 Promotes KRAS Degradation Chiang, C.; Xiao, T. et al. preprint; Cancer Biology, 2021 https://doi.org/10.1101/2021.02.10.429309
A Simple and Robust SDS-Aided Sample Preparation Method for Proteomic Research Gan, G.; Xu, X. et al. SCASP: Molecular & Cellular Proteomics 2021, 20, 100051 https://doi.org/10.1016/j.mcpro.2021.100051
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Acute Post-Injury Blockade of Α2δ-1 Calcium Channel Subunits Prevents Pathological Autonomic Plasticity after Spinal Cord Injury Brennan, F. H.; Noble, B. T. et al. Cell Reports 2021, 34 (4), 108667 https://doi.org/10.1016/j.celrep.2020.108667
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Crystal Structure of Bacterial Cytotoxic Necrotizing Factor CNF Y Reveals Molecular Building Blocks for Intoxication Chaoprasid, P.; Lukat, P. et al. EMBO J 2021, 40 (4) https://doi.org/10.15252/embj.2020105202
Water-Soluble Alkaloids Extracted from Aconiti Radix Lateralis Praeparata Protect against Chronic Heart Failure in Rats via a Calcium Signaling Pathway Xu, X.; Xie, X. et al. Biomedicine & Pharmacotherapy 2021, 135, 111184 https://doi.org/10.1016/j.biopha.2020.111184
Ultra-High Sensitivity Mass Spectrometry Quantifies Single-Cell Proteome Changes upon Perturbation Brunner, A.-D.; Thielert, M. et al. preprint; Systems Biology, 2020 https://doi.org/10.1101/2020.12.22.423933
Structure of the Neurotensin Receptor 1 in Complex with β-Arrestin 1 Huang, W.; Masureel, M. et al. Nature 2020, 579 (7798), 303–308 https://doi.org/10.1038/s41586-020-1953-1
A CRISPR-Based Genome-Wide Screen for Adipogenesis Reveals New Insights into Mitotic Expansion and Lipogenesis Hilgendorf, K. I.; Johnson, C. T. et al. preprint; Molecular Biology, 2020 https://doi.org/10.1101/2020.07.13.201038
Divergent Molecular Signatures of Regeneration and Fibrosis during Wound Repair Mascharak, S.; desJardins-Park, H. E. et al. preprint; Cell Biology, 2020 https://doi.org/10.1101/2020.12.17.423181
DiaPASEF: Parallel Accumulation–Serial Fragmentation Combined with Data-Independent Acquisition Meier, F.; Brunner, A.-D. et al. Nat Methods 2020, 17 (12), 1229–1236 https://doi.org/10.1038/s41592-020-00998-0
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In-Depth Proteomic Analysis of Plasmodium Berghei Sporozoites Using Trapped Ion Mobility Spectrometry with Parallel Accumulation-Serial Fragmentation Hamada, S.; Pionneau, C. et al. preprint; Microbiology, 2020 https://doi.org/10.1101/2020.11.26.400192
Licorice Ameliorates Cisplatin-Induced Hepatotoxicity Through Antiapoptosis, Antioxidative Stress, Anti-Inflammation, and Acceleration of Metabolism Man, Q.; Deng, Y. et al. Front. Pharmacol. 2020, 11, 563750 https://doi.org/10.3389/fphar.2020.563750
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Nuclear Receptor NHR-49 Promotes Peroxisome Proliferation to Compensate for Aldehyde Dehydrogenase Deficiency in C. Elegans Zeng, L.; Li, X. et al. preprint; Cell Biology, 2020 https://doi.org/10.1101/2020.12.04.411637
O-Acetylated Chemical Reporters of Glycosylation Can Display Metabolism-Dependent Background Labeling of Proteins but Are Generally Reliable Tools for the Identification of Glycoproteins Darabedian, N.; Yang, B. et al. Front. Chem. 2020, 8, 318 https://doi.org/10.3389/fchem.2020.00318
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The MPK 8‐ TCP 14 Pathway Promotes Seed Germination in Arabidopsis Zhang, W.; Cochet, F. et al. Plant J 2019, 100 (4), 677–692 https://doi.org/10.1111/tpj.14461
The Marine Bivalve Molluscs Pathogen Vibrio Neptunius Produces the Siderophore Amphibactin Which Is Widespread in Molluscs Microbiota Galvis, F.; Ageitos, L. et al. Environ Microbiol 2020, 1462-2920.15312 https://doi.org/10.1111/1462-2920.15312
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LUZP1, a Novel Regulator of Primary Cilia and the Actin Cytoskeleton, Is a Contributing Factor in Townes-Brocks Syndrome Bozal-Basterra, L.; Gonzalez-Santamarta, M. et al. eLife 2020, 9, e55957 https://doi.org/10.7554/eLife.55957
Ectosomal PKM2 Promotes HCC by Inducing Macrophage Differentiation and Remodeling the Tumor Microenvironment Hou, P.; Luo, L. et al. Molecular Cell 2020, 78 (6), 1192-1206.e10 https://doi.org/10.1016/j.molcel.2020.05.004
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Arachidyl Amido Cholanoic Acid Improves Liver Glucose and Lipid Homeostasis in Nonalcoholic Steatohepatitis via AMPK and MTOR Regulation Fernández-Ramos, D.; Lopitz-Otsoa, F. et al. MWJG 2020, 26 (34), 5101–5117 https://doi.org/10.3748/wjg.v26.i34.5101
Semiquantitative Proteomic Research of Protein Plasma Profile of Volunteers in 21-Day Head-Down Bed Rest Kashirina, D. N.; Brzhozovskiy, A. G. et al. Front. Physiol. 2020, 11, 678 https://doi.org/10.3389/fphys.2020.00678
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Prenatal Endotoxin Exposure Induces Fetal and Neonatal Renal Inflammation via Innate and Th1 Immune Activation in Preterm Pigs Muk, T.; Jiang, P.-P. et al. Front. Immunol. 2020, 11, 565484 https://doi.org/10.3389/fimmu.2020.565484
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Identification of Modified Peptides Using Localization-Aware Open Search Yu, F.; Teo, G. C. et al. INat Commun 2020, 11 (1), 4065 https://doi.org/10.1038/s41467-020-17921-y
Connecting the Dots on Vertical Transmission of SARS-CoV-2 Using Protein-Protein Interaction Network Analysis – Potential Roles of Placental ACE2 and ENDOU Jing, H.; Ackerman, W. E. et al. Placenta 2021, 104, 16–19 https://doi.org/10.1016/j.placenta.2020.11.001
Arachidyl Amido Cholanoic Acid Improves Liver Glucose and Lipid Homeostasis in Nonalcoholic Steatohepatitis via AMPK and MTOR Regulation Fernández-Ramos, D.; Lopitz-Otsoa, F. et al. WJG 2020, 26 (34), 5101–5117 https://doi.org/10.3748/wjg.v26.i34.5101
Deep learning the collisional cross sections of the peptide universe from a million training samples (preprint) Meier, F., Köhler, N.D. et al. Systems Biology, 2021 https://doi.org/10.1101/2020.05.19.102285
Benefits of Collisional Cross Section Assisted Precursor Selection (Caps-PASEF) for Cross-Linking Mass Spectrometry Steigenberger, B.; van den Toorn, H. et al. Mol Cell Proteomics 2020, mcp https://doi.org/10.1074/mcp.RA120.002094
Ethanolamine Phosphate on the Second Mannose as Bridge in GPI Anchored Proteins: Towards Understanding Inherited PIGG Deficiency Ishida, M.; Maki, Y. et al. preprint; Molecular Biology, 2020 https://doi.org/10.1101/2020.11.26.399477
Phosphorylation profile of human AQP2 in urinary exosomes by LC–MS/MS phosphoproteomic analysis Sakai, M., Yamamoto, K. et al. Clin Exp Nephrol, 2020 https://doi.org/10.1007/s10157-020-01899-4
Enrichment-Free Identification of Native Definitive (EnFIND) O-glycoproteome of antibodies in autoimmune diseases (preprint) Sun, X., Cheng, J. et al. Systems Biology, 2020 https://doi.org/10.1101/2020.07.15.204511
Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant (preprint) Yu, F., Haynes, S.E. et al. Bioinformatics, 2020 https://doi.org/10.1101/2020.03.19.999334
Cytoplasmic MRNA Recapping Has Limited Impact on Proteome Complexity Agana, B. A.; Wysocki, V. H. et al. Open Biol. 2020, 10 (11), 200313 https://doi.org/10.1098/rsob.200313
Proteomic profiling of mitochondrial-derived vesicles in brain reveals enrichment of respiratory complex sub-assemblies and small TIM chaperones (preprint) Roberts, R.F., Bayne, A.N. et al. Biochemistry, 2020 https://doi.org/10.1101/2020.07.06.189993
c-Src Promotes Tumorigenesis and Tumor Progression by Activating PFKFB3 Ma, H., Zhang, J. et al. Cell Reports 2020, 30, 4235-4249.e6 https://doi.org/10.1016/j.celrep.2020.03.005
Dephosphorylation of cGAS by PPP6C impairs its substrate binding activity and innate antiviral response Li, M., Shu, H.-B. Protein Cell 2020, 11, 584–599 https://doi.org/10.1007/s13238-020-00729-3
An intracellular membrane protein GEP1 regulates xanthurenic acid induced gametogenesis of malaria parasites Jiang, Y., Wei, J. et al. Nat Commun 2020, 11, 1764 https://doi.org/10.1038/s41467-020-15479-3
Quantitatively profiling acetylome of DNA repair proteins in early DNA damage (preprint) Li, S., Zhou, L. et al. In Review, 2020 https://doi.org/10.21203/rs.3.rs-44043/v1
MaxQuant software for ion mobility enhanced shotgun proteomics Prianichnikov, N., Koch, H. et al. Mol Cell Proteomics, 2020 https://doi.org/10.1074/mcp.TIR119.001720
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Characterization and regulation of extracellular vesicles in the lumen of the ovine uterus O’Neil, E.V., Burns, G.W. et al. Biology of Reproduction 2020, 102, 1020–1032 https://doi.org/10.1093/biolre/ioaa019
Low collision energy fragmentation in structure-specific glycoproteomics analysis Sanda, M., Benicky, J. et al. Anal. Chem. 2020 https://doi.org/10.1021/acs.analchem.0c00519
Spatial Metabolomics of the Human Kidney using MALDI Trapped Ion Mobility Imaging Neumann, E.K., Migas, L.G. et al. Mass Spectrometry n.d., 9
Extending the Separation Space with Trapped Ion Mobility Spectrometry Improves the Accuracy of Isobaric Tag-based Quantitation in Proteomic LC/MS/MS Ogata, K., Ishihama, Y. Anal. Chem. 2020 https://doi.org/10.1021/acs.analchem.0c01695
An effector caspase Sp-caspase first identified in mud crab Scylla paramamosain exhibiting immune response and cell apoptosis Li, J., Dong, L. et al. Fish & Shellfish Immunology 2020, S1050464820303715 https://doi.org/10.1016/j.fsi.2020.05.045
Exploration of human cerebrospinal fluid: A large proteome dataset revealed by trapped ion mobility time-of-flight mass spectrometry Macron, C., Lavigne, R. et al. Data in Brief 2020, 31, 105704 https://doi.org/10.1016/j.dib.2020.105704
Developing a multivariable prediction model for functional outcome after reperfusion therapy for acute ischaemic stroke: study protocol for the Targeting Optimal Thrombolysis Outcomes (TOTO) multicentre cohort study Holliday, E., Lillicrap, T. et al. BMJ Open 2020, 10, e038180 https://doi.org/10.1136/bmjopen-2020-038180
Biallelic variants in SLC35C1 as a cause of isolated short stature with intellectual disability Knapp, K.M., Luu, R. et al. J Hum Genet, 2020 https://doi.org/10.1038/s10038-020-0764-4
Quantitative Proteomic Analysis of Chikungunya Virus-Infected Aedes aegypti Reveals Proteome Modulations Indicative of Persistent Infection Cui, Y., Liu, P. et al. J. Proteome Res. 2020 https://doi.org/10.1021/acs.jproteome.0c00173
Relative Quantitation of Subclass-Specific Murine IgG Fc N -Glycoforms by Multiple Reaction Monitoring Han, J., Liu, Q. et al. ACS Omega 2020, 5, 8564–8571 https://doi.org/10.1021/acsomega.9b04412
Trapped ion mobility spectrometry and PASEF enable in-depth lipidomics from minimal sample amounts Vasilopoulou, C.G., Sulek, K. et al. Nat Commun 2020, 11, 331 https://doi.org/10.1038/s41467-019-14044-x
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Simplified high-throughput methods for deep proteome analysis on the timsTOF Pro Sandow, J. J, Infusini, G. et al. Biochemistry, 2019, doi:10.1101/657908
Cathepsin B/ SAPC inhibition deregulates apoptosis-related proteins in neuronal cells exposed to supernatants from HIV-infected macrophages Melendez L, PhD , Zenon-Melendez C, et al. J Biomol Tech. 2020, 31(Suppl):S19
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Chemistry (timsTOF Pro / timsTOF)

Chemistry (timsTOF Pro / timsTOF)

Title Authors Publication Link
Facile synthesis of Ti4+-immobilized magnetic covalent organic frameworks for enhanced phosphopeptide enrichment He, Y., Zhang, S. et al. Talanta 2021, 235, 122789 https://doi.org/10.1016/j.talanta.2021.122789
Thiol and Disulfide Containing Vancomycin Derivatives Against Bacterial Resistance and Biofilm Formation Shchelik, I.S., Gademann, K. preprint; Microbiology 2021 https://doi.org/10.1101/2021.08.23.457343
Automated Chiral Analysis of Amino Acids Based on Chiral Derivatization and Trapped Ion Mobility–Mass Spectrometry Will, J. M.; Behrens, A. et al. Anal. Chem. 2020, acs.analchem.0c03481 https://doi.org/10.1021/acs.analchem.0c03481
Evaluation of Trapped Ion Mobility Spectrometry Source Conditions Using Benzylammonium Thermometer Ions Naylor, C.N., Ridgeway, M.E. et al. J. Am. Soc. Mass Spectrom. 2021, 31, 1593–1602 https://doi.org/10.1021/jasms.0c00151
Fast Online Separation and Identification of Electrochemically Generated Isomeric Oxidation Products by Trapped Ion Mobility-Mass Spectrometry Fangmeyer, J., Scheeren, S. et al. Anal. Chem. 2019, acs.analchem.9b04337 https://doi.org/10.1021/acs.analchem.9b04337
Solvent Adducts in Ion Mobility Spectrometry: Toward an Alternative Reaction Probe for Thermometer Ions Morsa, D., Hanozin, E. et al. J. Am. Soc. Mass Spectrom. 2020, jasms.0c00108 https://doi.org/10.1021/jasms.0c00108
Integration of •SO4−-based AOP mediated by reusable iron particles and a sulfidogenic process to degrade and detoxify Orange II Yu, X., Sun, J. et al. Water Research 2020, 174, 115622 https://doi.org/10.1016/j.watres.2020.115622
Trends in trapped ion mobility – Mass spectrometry instrumentation Ridgeway, M.E., Bleiholder, C. et al. TrAC Trends in Analytical Chemistry 2019, 116, 324–331 https://doi.org/10.1016/j.trac.2019.03.030
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