Firas Hamood

SIMSI-Transfer: MaxQuant output files

Firas Hamood, Matthew The

Dataset 1 for the publication "SIMSI-Transfer: Software-assisted reduction of missing values in phosphoproteomic and proteomic isobaric labeling data using tandem mass spectrum clustering". This dataset contains all files generated by MaxQuant from database searches of the studies used for assessment of SIMSI-Transfer …

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TOPAS: phosphoproteome data analysis and decision support platform for molecular tumor boards

Cecilia Bang Jensen, Amirhossein Sakhteman, Firas Hamood, Annika Schneider et autres

Abstract The molecular tumor board (MTB) is central to precision oncology, providing personalized treatment recommendations based on molecular profiles of patient tumors. Genomics is instrumental for MTBs but often fails to identify clinically actionable targets, a gap that phosphoproteomics can fill. We …

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Prospective pan-cancer phosphoproteomics at clinical scale extends therapeutic options in precision oncology

Annika Schneider, Julia Wortmann, Cecilia Bang Jensen, Leonardo Estrada Duenas et autres

SUMMARY Genomics-guided precision oncology has improved survival in cancer entities with actionable mutations but cannot capture oncogenic signaling that manifests at the protein level. Here, we report a prospective, real-world pan-cancer study profiling proteomes and phosphoproteomes of 1,998 tumor samples from adults …

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Erhöhen von Identifizierungen und Reduzieren fehlende Werte bei Proteomik-Experimenten

Firas Hamood

Isobaric labeling experiments in proteomics suffer from missing values that hinder data analysis. This thesis developed the SIMSI-Toolkit with two tools: SIMSI-Transfer uses spectrum clustering to transfer peptide IDs between measurements, reducing missing values by up to 21%. ProSIMSIt adds FDR control …

Chemical proteomics decrypts the kinases that shape the dynamic human phosphoproteome

Florian Bayer, Julian Müller, Nicole Kabella, Miriam Abele et autres

Abstract Mass-spectrometry-based phosphoproteomics enables the analysis of thousands of protein phosphorylation events across the human proteome. However, there is a lack of scalable, hypothesis-free, and statistically sound approaches for discovering, evaluating, and falsifying kinase::substrate relationships (KSRs). Here, we developed a new concept …

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Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale

Mario Picciani, Armin Soleymaniniya, Julian Müller, Amirhossein Sakhteman et autres

Proteomic and phenotypic cell sensitivity datasets are increasingly important for understanding chemoproteomics and the underlying drug mechanisms of action. Yet, integrating such heterogeneous datasets remains challenging due to inconsistent annotations, incompatible IDs, and variable data processing methods. Here, a major update to …

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ProSIMSIt: The Best of Both Worlds in Data-Driven Rescoring and Identification Transfer

Firas Hamood, Wassim Gabriel, Bernhard Küster, Mathias Wilhelm et autres

Multibatch isobaric labeling experiments are frequently applied for clinical and pharmaceutical studies of large sample cohorts. To tackle the critical issue of missing values in such studies, we introduce the ProSIMSIt pipeline. It combines the advantages of tandem mass spectrum clustering via …

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Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response

Stefanie Höfer, Larissa Frasch, Sarah Brajkovic, Kerstin Putzker et autres

The DNA-damaging agent Gemcitabine (GEM) is a first-line treatment for pancreatic cancer, but chemoresistance is frequently observed. Several clinical trials investigate the efficacy of GEM in combination with targeted drugs, including kinase inhibitors, but the experimental evidence for such rationale is often …

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Increasing Identifications and Reducing Missing Values in Proteomics Experiments

Firas Hamood, Bernhard Küster, Technische Universität München

210P Therapeutic implications of phosphoproteomics in molecular cancer diagnostics

Annika Schneider, Camilla Bjørn Jensen, Amirhossein Sakhteman, Firas Hamood et autres

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1772P Phosphoproteomic biomarker for afatinib response stratification in advanced chordoma

Claudia Stange, Agata Schneider, Camilla Bjørn Jensen, Amirhossein Sakhteman et autres

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Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response

Stefanie Höfer, Larissa Frasch, Kerstin Putzker, Joe Lewis et autres

Abstract The DNA-damaging agent gemcitabine (GEM) is a first-line treatment for pancreatic cancer but chemoresistance is frequently observed. Several clinical trials investigate the efficacy of GEM in combination with targeted drugs including kinase inhibitors but the experimental evidence for such rational is …

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