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Search life-sciences literature (45,103,589 articles, preprints and more)

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TIMS²Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS²Rescore
Declercq A, Devreese R, Scheid J, Jachmann C, Den Bossche TV, Preikschat A, Gomez-Zepeda D, Rijal JB, Hirschler A, Krieger JR, Srikumar T, Rosenberger G, Trede D, Carapito C, Tenzer S, Walz JS, Degroeve S, Bouwmeester R, Martens L, Gabriels R
bioRxiv, 02 Jun 2024
Cited by: 0 articles | PPR: PPR860700
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An automated workflow based on data independent acquisition for practical and high-throughput personalized assay development and minimal residual disease monitoring in multiple myeloma patients.
Wijnands C, Armony G, Noori S, Gloerich J, Bonifay V, Caillon H, Luider TM, Brehmer S, Pfennig L, Srikumar T, Trede D, Kruppa G, Dejoie T, van Duijn MM, van Gool AJ, Jacobs JFM, Wessels HJCT
Clin Chem Lab Med, 62(12):2507-2518, 17 Jun 2024
Cited by: 0 articles | PMID: 38872409
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The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform.
Armony G, Brehmer S, Srikumar T, Pfennig L, Zijlstra F, Trede D, Kruppa G, Lefeber DJ, van Gool AJ, Wessels HJCT
Int J Mol Sci, 24(9):7869, 26 Apr 2023
Cited by: 2 articles | PMID: 37175577 | PMCID: PMC10178020
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The GlycoPaSER prototype as a real-time N-glycopeptide identification tool based on the PaSER parallel computing platform
Armony G, Brehmer S, Srikumar T, Pfennig L, Zijlstra F, Trede D, Kruppa G, Lefeber DJ, van Gool AJ, Wessels HJ
bioRxiv, 12 Mar 2023
Cited by: 0 articles | PPR: PPR629345
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Transcriptomic, peptidomic, and mass spectrometry imaging analysis of the brain in the ant Cataglyphis nodus.
Habenstein J, Schmitt F, Liessem S, Ly A, Trede D, Wegener C, Predel R, Rössler W, Neupert S
J Neurochem, 158(2):391-412, 25 Mar 2021
Cited by: 12 articles | PMID: 33704768
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Spatial segmentation and metabolite annotation involved in sperm maturation in the rat epididymis by MALDI imaging mass spectrometry.
Lagarrigue M, Lavigne R, Guével B, Palmer A, Rondel K, Guillot L, Kobarg JH, Trede D, Pineau C
J Mass Spectrom, 55(12):e4633, 01 Dec 2020
Cited by: 6 articles | PMID: 33043525
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Detection of small molecule concentration gradients in ocular tissues and humours.
Boughton BA, Thomas ORB, Demarais NJ, Trede D, Swearer SE, Grey AC
J Mass Spectrom, 55(4):e4460, 25 Nov 2019
Cited by: 6 articles | PMID: 31654531
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Three-Dimensional Mass Spectrometry Imaging Identifies Lipid Markers of Medulloblastoma Metastasis.
Paine MRL, Liu J, Huang D, Ellis SR, Trede D, Kobarg JH, Heeren RMA, Fernández FM, MacDonald TJ
Sci Rep, 9(1):2205, 18 Feb 2019
Cited by: 37 articles | PMID: 30778099 | PMCID: PMC6379434
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Lipid Changes Associated with Traumatic Brain Injury Revealed by 3D MALDI-MSI.
Mallah K, Quanico J, Trede D, Kobeissy F, Zibara K, Salzet M, Fournier I
Anal Chem, 90(17):10568-10576, 16 Aug 2018
Cited by: 28 articles | PMID: 30070841
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Targeted Feature Extraction in MALDI Mass Spectrometry Imaging to Discriminate Proteomic Profiles of Breast and Ovarian Cancer.
Cordero Hernandez Y, Boskamp T, Casadonte R, Hauberg-Lotte L, Oetjen J, Lachmund D, Peter A, Trede D, Kriegsmann K, Kriegsmann M, Kriegsmann J, Maass P
Proteomics Clin Appl, 13(1):e1700168, 19 Dec 2018
Cited by: 12 articles | PMID: 30520240
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Unraveling local tissue changes within severely injured skeletal muscles in response to MSC-based intervention using MALDI Imaging mass spectrometry.
Klein O, Strohschein K, Nebrich G, Fuchs M, Thiele H, Giavalisco P, Duda GN, Winkler T, Kobarg JH, Trede D, Geissler S
Sci Rep, 8(1):12677, 23 Aug 2018
Cited by: 8 articles | PMID: 30140012 | PMCID: PMC6107672
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A new classification method for MALDI imaging mass spectrometry data acquired on formalin-fixed paraffin-embedded tissue samples.
Boskamp T, Lachmund D, Oetjen J, Cordero Hernandez Y, Trede D, Maass P, Casadonte R, Kriegsmann J, Warth A, Dienemann H, Weichert W, Kriegsmann M
Biochim Biophys Acta Proteins Proteom, 1865(7):916-926, 09 Nov 2016
Cited by: 14 articles | PMID: 27836618
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Integration of 3D multimodal imaging data of a head and neck cancer and advanced feature recognition.
Lotz JM, Hoffmann F, Lotz J, Heldmann S, Trede D, Oetjen J, Becker M, Ernst G, Maas P, Alexandrov T, Guntinas-Lichius O, Thiele H, von Eggeling F
Biochim Biophys Acta Proteins Proteom, 1865(7):946-956, 01 Sep 2016
Cited by: 12 articles | PMID: 27594533
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Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry.
Oetjen J, Veselkov K, Watrous J, McKenzie JS, Becker M, Hauberg-Lotte L, Kobarg JH, Strittmatter N, Mróz AK, Hoffmann F, Trede D, Palmer A, Schiffler S, Steinhorst K, Aichler M, Goldin R, Guntinas-Lichius O, von Eggeling F, Thiele H, [...] Alexandrov T
Gigascience, 4:20, 04 May 2015
Cited by: 30 articles | PMID: 25941567 | PMCID: PMC4418095
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The challenge of on-tissue digestion for MALDI MSI- a comparison of different protocols to improve imaging experiments.
Diehl HC, Beine B, Elm J, Trede D, Ahrens M, Eisenacher M, Marcus K, Meyer HE, Henkel C
Anal Bioanal Chem, 407(8):2223-2243, 17 Feb 2015
Cited by: 24 articles | PMID: 25687681
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Spatial segmentation of MALDI FT-ICR MSI data: a powerful tool to explore the head and neck tumor in situ lipidome.
Krasny L, Hoffmann F, Ernst G, Trede D, Alexandrov T, Havlicek V, Guntinas-Lichius O, von Eggeling F, Crecelius AC
J Am Soc Mass Spectrom, 26(1):36-43, 06 Nov 2014
Cited by: 14 articles | PMID: 25374335
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MALDI imaging mass spectrometry: discrimination of pathophysiological regions in traumatized skeletal muscle by characteristic peptide signatures.
Klein O, Strohschein K, Nebrich G, Oetjen J, Trede D, Thiele H, Alexandrov T, Giavalisco P, Duda GN, von Roth P, Geissler S, Klose J, Winkler T
Proteomics, 14(20):2249-2260, 21 Aug 2014
Cited by: 27 articles | PMID: 25056804
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Histomolecular interpretation of pleomorphic adenomas of the salivary gland by matrix-assisted laser desorption ionization imaging and spatial segmentation.
Ernst G, Guntinas-Lichius O, Hauberg-Lotte L, Trede D, Becker M, Alexandrov T, von Eggeling F
Head Neck, 37(7):1014-1021, 11 Jul 2014
Cited by: 2 articles | PMID: 24942285
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MRI-compatible pipeline for three-dimensional MALDI imaging mass spectrometry using PAXgene fixation.
Oetjen J, Aichler M, Trede D, Strehlow J, Berger J, Heldmann S, Becker M, Gottschalk M, Kobarg JH, Wirtz S, Schiffler S, Thiele H, Walch A, Maass P, Alexandrov T
J Proteomics, 90:52-60, 02 Apr 2013
Cited by: 30 articles | PMID: 23558029
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MALDI mass spectrometric imaging based identification of clinically relevant signals in prostate cancer using large-scale tissue microarrays.
Steurer S, Borkowski C, Odinga S, Buchholz M, Koop C, Huland H, Becker M, Witt M, Trede D, Omidi M, Kraus O, Bahar AS, Seddiqi AS, Singer JM, Kwiatkowski M, Trusch M, Simon R, Wurlitzer M, Minner S, [...] Schlüter H
Int J Cancer, 133(4):920-928, 04 Mar 2013
Cited by: 26 articles | PMID: 23381989
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2D and 3D MALDI-imaging: conceptual strategies for visualization and data mining.
Thiele H, Heldmann S, Trede D, Strehlow J, Wirtz S, Dreher W, Berger J, Oetjen J, Kobarg JH, Fischer B, Maass P
Biochim Biophys Acta, 1844(1 pt a):117-137, 04 Mar 2013
Cited by: 38 articles | PMID: 23467008
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On the importance of mathematical methods for analysis of MALDI-imaging mass spectrometry data.
Trede D, Kobarg JH, Oetjen J, Thiele H, Maass P, Alexandrov T
J Integr Bioinform, 9(1):189, 21 Mar 2012
Cited by: 15 articles | PMID: 22433312
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Magnification of label maps with a topology-preserving level-set method.
Trede D, Alexandrov T, Sagiv C, Maass P
IEEE Trans Image Process, 21(9):4040-4053, 15 May 2012
Cited by: 2 articles | PMID: 22614645
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Exploring three-dimensional matrix-assisted laser desorption/ionization imaging mass spectrometry data: three-dimensional spatial segmentation of mouse kidney.
Trede D, Schiffler S, Becker M, Wirtz S, Steinhorst K, Strehlow J, Aichler M, Kobarg JH, Oetjen J, Dyatlov A, Heldmann S, Walch A, Thiele H, Maass P, Alexandrov T
Anal Chem, 84(14):6079-6087, 05 Jul 2012
Cited by: 71 articles | PMID: 22720760
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Super-resolution segmentation of imaging mass spectrometry data: Solving the issue of low lateral resolution.
Alexandrov T, Meding S, Trede D, Kobarg JH, Balluff B, Walch A, Thiele H, Maass P
J Proteomics, 75(1):237-245, 11 Aug 2011
Cited by: 19 articles | PMID: 21854879
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