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Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

by Meier, Florian, Brunner, Andreas-David, Koch, Scarlet, Koch, Heiner, Lubeck, Markus, Krause, Michael, Goedecke, Niels, Decker, Jens, Kosinski, Thomas, Park, Melvin A., Bache, Nicolai, Hoerning, Ole, Cox, Jürgen, Räther, Oliver, Mann, Matthias
Published in Molecular & cellular proteomics (01.12.2018)

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Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF

by Skowronek, Patricia, Thielert, Marvin, Voytik, Eugenia, Tanzer, Maria C., Hansen, Fynn M., Willems, Sander, Karayel, Özge, Brunner, Andreas-David, Meier, Florian, Mann, Matthias
Published in Molecular & cellular proteomics (01.09.2022)

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dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts

by Demichev, Vadim, Szyrwiel, Lukasz, Yu, Fengchao, Teo, Guo Ci, Rosenberger, George, Niewienda, Agathe, Ludwig, Daniela, Decker, Jens, Kaspar-Schoenefeld, Stephanie, Lilley, Kathryn S., Mülleder, Michael, Nesvizhskii, Alexey I., Ralser, Markus
Published in Nature communications (08.07.2022)

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Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant

by Yu, Fengchao, Haynes, Sarah E., Teo, Guo Ci, Avtonomov, Dmitry M., Polasky, Daniel A., Nesvizhskii, Alexey I.
Published in Molecular & cellular proteomics (01.09.2020)

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Ion mobility‐resolved phosphoproteomics with dia‐PASEF and short gradients

by Oliinyk, Denys, Meier, Florian
Published in Proteomics (Weinheim) (01.04.2023)

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Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography

by Szyrwiel, Lukasz, Gille, Christoph, Mülleder, Michael, Demichev, Vadim, Ralser, Markus
Published in Proteomics (Weinheim) (01.01.2024)

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Parallel Accumulation–Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device

by Meier, Florian, Beck, Scarlet, Grassl, Niklas, Lubeck, Markus, Park, Melvin A, Raether, Oliver, Mann, Matthias
Published in Journal of proteome research (04.12.2015)

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Trapped ion mobility spectrometry and PASEF enable in-depth lipidomics from minimal sample amounts

by Vasilopoulou, Catherine G., Sulek, Karolina, Brunner, Andreas-David, Meitei, Ningombam Sanjib, Schweiger-Hufnagel, Ulrike, Meyer, Sven W., Barsch, Aiko, Mann, Matthias, Meier, Florian
Published in Nature communications (16.01.2020)

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An accessible workflow for high-sensitivity proteomics using parallel accumulation–serial fragmentation (PASEF)

by Skowronek, Patricia, Wallmann, Georg, Wahle, Maria, Willems, Sander, Mann, Matthias
Published in Nature protocols (01.06.2025)

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The Parallel Reaction Monitoring-Parallel Accumulation–Serial Fragmentation (prm-PASEF) Approach for Multiplexed Absolute Quantitation of Proteins in Human Plasma

by Brzhozovskiy, Alexander, Kononikhin, Alexey, Bugrova, Anna E, Kovalev, Grigoriy I, Schmit, Pierre-Olivier, Kruppa, Gary, Nikolaev, Evgeny N, Borchers, Christoph H
Published in Analytical chemistry (Washington) (01.02.2022)

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Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition

by Skowronek, Patricia, Krohs, Florian, Lubeck, Markus, Wallmann, Georg, Itang, Ericka C.M., Koval, Polina, Wahle, Maria, Thielert, Marvin, Meier, Florian, Willems, Sander, Raether, Oliver, Mann, Matthias
Published in Molecular & cellular proteomics (01.02.2023)

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Enhancement of Proteome Coverage by Ion Mobility Fractionation Coupled to PASEF on a TIMS–QTOF Instrument

by Guergues, Jennifer, Wohlfahrt, Jessica
Published in Journal of proteome research (05.08.2022)

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Human amygdala involvement in Alzheimer's disease revealed by stereological and dia‐PASEF analysis

by Gonzalez‐Rodriguez, Melania, Villar‐Conde, Sandra, Astillero‐Lopez, Veronica, Villanueva‐Anguita, Patricia, Ubeda‐Banon, Isabel, Flores‐Cuadrado, Alicia, Martinez‐Marcos, Alino, Saiz‐Sanchez, Daniel
Published in Brain pathology (Zurich, Switzerland) (01.09.2023)

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Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

by Mun, Dong‐Gi, Budhraja, Rohit, Bhat, Firdous A., Zenka, Roman M., Johnson, Kenneth L., Moghekar, Abhay, Pandey, Akhilesh
Published in Proteomics (Weinheim) (01.05.2023)

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Extended coverage of human serum glycosphingolipidome by 4D-RP-LC TIMS-PASEF unravels association with Parkinson’s disease

by Vo, Huong Giang, Gonzalez-Escamilla, Gabriel, Mirzac, Daniela, Rotaru, Lilia, Herz, Damian, Groppa, Sergiu, Bindila, Laura
Published in Nature communications (16.05.2025)

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Increasing taxonomic and functional characterization of host-microbiome interactions by DIA-PASEF metaproteomics

by Gómez-Varela, David, Xian, Feng, Grundtner, Sabrina, Sondermann, Julia Regina, Carta, Giacomo, Schmidt, Manuela
Published in Frontiers in microbiology (16.10.2023)

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Comparative Cross-Kingdom DDA- and DIA-PASEF Proteomic Profiling Reveals Novel Determinants of Fungal Virulence and a Putative Druggable Target

by Ball, Brianna, Sukumaran, Arjun, Krieger, Jonathan R., Geddes-McAlister, Jennifer
Published in Journal of proteome research (06.09.2024)

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Top-Down Protein Analysis by Tandem-Trapped Ion Mobility Spectrometry/Mass Spectrometry (Tandem-TIMS/MS) Coupled with Ultraviolet Photodissociation (UVPD) and Parallel Accumulation/Serial Fragmentation (PASEF) MS/MS Analysis

by Liu, Fanny C., Ridgeway, Mark E., Wootton, Christopher A., Theisen, Alina, Panczyk, Erin M., Meier, Florian, Park, Melvin A., Bleiholder, Christian
Published in Journal of the American Society for Mass Spectrometry (04.10.2023)

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Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model

by Gomez-Zepeda, David, Arnold-Schild, Danielle, Beyrle, Julian, Declercq, Arthur, Gabriels, Ralf, Kumm, Elena, Preikschat, Annica, Łącki, Mateusz Krzysztof, Hirschler, Aurélie, Rijal, Jeewan Babu, Carapito, Christine, Martens, Lennart, Distler, Ute, Schild, Hansjörg, Tenzer, Stefan
Published in Nature communications (13.03.2024)

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Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package

by Langella, Olivier, Renne, Thomas, Balliau, Thierry, Davanture, Marlène, Brehmer, Sven, Zivy, Michel, Blein-Nicolas, Mélisande, Rusconi, Filippo
Published in Journal of proteome research (02.08.2024)

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