An automated pipeline for high-throughput label-free quantitative proteomics
Weisser, Hendrik, Nahnsen, Sven, Grossmann, Jonas, Nilse, Lars, Quandt, Andreas, Brauer, Hendrik, Sturm, Marc, Kenar, Erhan +3 more·2013·Journal of Proteome Research
Cited by (159)
Items 101–159 of 159
- Prediction and Consequences of Cofragmentation in MetaproteomicsJ. Scott P. McCain, Erin M. Bertrand · 2019 · Journal of Proteome Research
- Tag-Count Analysis of Large-Scale Proteomic DataOwen E. Branson, Michael A. Freitas · 2016 · Journal of Proteome Research
- Contemporary Network Proteomics and Its RequirementsWilson Wen Bin Goh, Limsoon Wong, Judy Sng · 2013 · Biology
- An automated workflow for MALDI-ToF mass spectra pattern identification on large data sets: An application to detect aneuploidies from pregnancy urineRicardo Jorge Pais, Raminta Zmuidinaite, S.A. Butler, Ray K. Iles · 2019 · Informatics in Medicine Unlocked
- ProtyQuant: Comparing label-free shotgun proteomics datasets using accumulated peptide probabilitiesRobert Winkler · 2020 · Journal of Proteomics
- MZDASoft: a software architecture that enables large‐scale comparison of protein expression levels over multiple samples based on liquid chromatography/tandem mass spectrometryMehrab Ghanat Bari, Nelson Ramirez, Zhiwei Wang, Jianqiu Zhang · 2015 · Rapid Communications in Mass Spectrometry
- Novel Endogenous, Insulin-Stimulated Akt2 Protein Interaction Partners in L6 MyoblastsMichael A. Caruso, Xiangmin Zhang, Danjun Ma, Zhao Yang, Yue Andy Qi, Zhengping Yi · 2015 · PLoS ONE
- Examination and characterisation of the effect of amitriptyline therapy for chronic neuropathic pain on neuropeptide and proteomic constituents of human cerebrospinal fluidJonathan Royds, Hilary Cassidy, Melissa Jane Conroy, Margaret R. Dunne, Joanne Lysaght, Connail R. McCrory · 2020 · Brain Behavior & Immunity - Health
- Autonomous Science: Big Data Tools for Small Data Problems in ChemistryAndreas C. Geiger, Ziyi Cao, Zhengtian Song, James R. W. Ulcickas, Garth J. Simpson · 2020 · Royal Society of Chemistry eBooks
- Standard Flow Multiplexed Proteomics (SFloMPro)—An Accessible Alternative to NanoFlow Based Shotgun ProteomicsBenjamin C. Orsburn, Sierra D. Miller, Conor Jenkins · 2022 · Proteomes
- Functional and Structural Properties of a Novel Protein and Virulence Factor (Protein sHIP) in Streptococcus pyogenesM. Wisniewska, Lotta Happonen, Fredrik Kahn, Markku T Varjosalo, Lars Malmström, George Rosenberger, Christofer A. Q. Karlsson, Giuseppe Cazzamali, Irina Pozdnyakova, Inga-Maria Frick et al. · 2014 · Journal of Biological Chemistry
- Assessing a commercial capillary electrophoresis interface (ZipChip) for shotgun proteomic applicationsAimee Rinas, Conor Jenkins, Benjamin C. Orsburn · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- pyBinder: Quantitation to Advance Affinity Selection-Mass SpectrometryJoseph S. Brown, Michael A. Lee, Wayne Vuong, Andrei Loas, Bradley L. Pentelute · 2025 · Analytical Chemistry
- Disease phenotype prediction in multiple sclerosisStephanie Herman, Staffan Arvidsson, Christina Zjukovskaja, Payam Emami Khoonsari, Anders Svenningsson, Joachim Burman, Ola Spjuth, Kim Kultima · 2023 · iScience
- IQMMA: Efficient MS1 Intensity Extraction Pipeline Using Multiple Feature Detection Algorithms for DDA ProteomicsValeriy I. Postoenko, Leyla A. Garibova, Lev I. Levitsky, Julia A. Bubis, Mikhail V. Gorshkov, Mark V. Ivanov · 2023 · Journal of Proteome Research
- Proteomics as a tool to understand Leptospira physiology and virulence: Recent advances, challenges and clinical implicationsEdson G. Nascimento Filho, Mônica L. Vieira, Aline F. Teixeira, Jademilson C. Santos, Luis G. V. Fernandes, Felipe José Passalia, Brenda B. Daroz, Amanda Diaz Rossini, Leandro T. Kochi, Maria F. Cavenague et al. · 2018 · Journal of Proteomics
- An Investigation into Proteomic Constituents of Cerebrospinal Fluid in Patients with Chronic Peripheral Neuropathic Pain Medicated with Opioids- a Pilot StudyJonathan Royds, Hilary Cassidy, Melissa Jane Conroy, Margaret R. Dunne, David Matallanas, Joanne Lysaght, Connail R. McCrory · 2020 · Journal of Neuroimmune Pharmacology
- Profiling the Skeletal Muscle Proteome in Patients on Atypical Antipsychotics and Mood StabilizersKyle Jon Burghardt, Griffin Calme, Michael A. Caruso, Bradley H. Howlett, Elani Sanders, Zaher Msallaty, Abdullah Mallisho, Berhane Seyoum, Yue Andy Qi, Xiangmin Zhang et al. · 2022 · Brain Sciences
- Observations from the Proteomics Bench2024
- Identification of Altered Proteins in the Plasma of Rats With Chronic Prostatic Inflammation Induced by Estradiol Benzoate and Sex HormonesZhijun Cao, Daniel T. Sloper, Noriko Nakamura · 2021 · ACS Omega
- Detection of Unknown Amino Acid Substitutions Using Error-Tolerant Database SearchSven H. Giese, Franziska Zickmann, Bernhard Y. Renard · 2015 · Methods in molecular biology
- qpMerge: Merging different peptide isoforms using a motif centric strategyMatthew Hindle, Thierry Le Bihan, Johanna Krahmer, Sarah F. Martin, Zeenat B. Noordally, T. Ian Simpson, Andrew John Millar · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
- OpenMS: A Modular, Open-Source Workflow System for the Analysis of Quantitative Proteomics DataLars Nilse · 2016 · Royal Society of Chemistry eBooks
- Quantitative proteomic analysis of cerebrospinal fluid from patients with diffuse large B‑cell lymphoma with central nervous system involvement: A novel approach to diagnosisXiaobei Liu, Fei Mo, Hao Zeng, Sha Zhu, Xuelei Ma · 2019 · Biomedical Reports
- Python workflow for the selection and identification of marker peptides—proof-of-principle study with heated milkGesine Kuhnen, Lisa‐Carina Class, Svenja Badekow, Kim Lara Hanisch, Sascha Rohn, Jürgen Kuballa · 2024 · Analytical and Bioanalytical Chemistry
- A coherent mathematical characterization of isotope trace extraction, isotopic envelope extraction, and LC-MS correspondenceRob Smith, John T. Prince, Dan A. Ventura · 2015 · BMC Bioinformatics
- A hybrid method for identification of structural domainsYongpan Hua, Min Zhu, Yuelong Wang, Zhaoyang Xie, Menglong Li · 2014 · Scientific Reports
- Analysis of Bacterial Surface Interactions with Mass Spectrometry-Based ProteomicsChristofer A. Q. Karlsson, Johan Teleman, Johan A. Malmström · 2016 · Methods in molecular biology
- A state-of-art review on the agility of quantitative proteomics in tuberculosis researchManikandan Muthu, Anbarasu Deenadayalan, D. Ramachandran, DIBY ZAMBLE PAUL, Judy Gopal, Sechul Chun · 2018 · TrAC Trends in Analytical Chemistry
- UmetaFlow: An untargeted metabolomics workflow for high-throughput data processing and analysisEftychia Eva Kontou, Axel Walter, Timo T. Sachsenberg, Tilmann Weber, Oliver Alka, Julianus Pfeuffer, Matin Nuhamunada, Omkar S. Mohite, Oliver Kohlbacher · 2022 · ChemRxiv
- Superoxide dismutases shape manganese stoichiometry in Southern Ocean diatomsJ. Scott P. McCain, Loay J. Jabre, Elden E. Rowland, Jinyoung Jung, Youngju Lee, Tae‐Wan Kim, Corina P. D. Brussaard, Rob Middag, Erin M. Bertrand · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- ProFormer: generalizable classification of single-cell and plasma proteomes using deep learningKarl Kristian Krull, Arlene Kühn, Julia Höhn, Syed Azmal Ali, Martin H. Otterbein, Titus J. Brinker, Jeroen Krijgsveld · 2026 · Nature Communications
- Bioinformatics for Proteomics: Opportunities at the Interface Between the Scientists, Their Experiments, and the CommunityMarc Vaudel, Harald Barsnes, Lennart Martens, Frode S. Berven · 2014 · Methods in molecular biology
- Spectral entropy as a measure of the metaproteome complexityHaonan Duan, Zhibin Ning, Ailing Zhang, Daniel Figeys · 2024 · PROTEOMICS
- Mass spectrometric analysis of plant protein concentratesO. L. Meshcheryakova, Anna E. Bugrova, Alexey S. Kononikhin, Oksana A. Kartashova, Olga Sergeevna Korneeva, Л. Э. Глаголева, Vladimir I. Korchagin · 2024 · Сорбционные и хроматографические процессы
- Advantages and Applications of Gel-Free Proteomic Approaches in the Study of ProkaryotesJohn Phillip Bowman · 2014 · Comprehensive analytical chemistry
- Kinase Assay-Linked PhosphoproteomicsJustine V. Arrington, Chuan‐Chih Hsu, W. Andy Tao · 2016 · Methods in enzymology on CD-ROM/Methods in enzymology
- Comparison of early- and late-senescence near-isogenic barley germplasm : proteomics and biochemistry shed new light on an old problemKatelyn E. Mason · 2015 · Montana State University ScholarWorks (Montana State University)
- Improved LC-MS chromatographic alignment increases the accuracy of label-free quantitative proteomics: Comparison of spectral counting versus ion intensity-based proteomic quantification strategiesDaniel Ng, Jonathan D. Humphries, Julian N. Selley, Stacey Warwood, David Knight, Adam Byron, Martin James Humphries · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- KubeNow: an On-Demand Cloud-Agnostic Platform for Microservices-Based Research Environments.Marco Capuccini, Anders O. Larsson, Matteo Carone, Jon Ander Novella, Noureddin Sadawi, Jianliang Gao, Salman Zubair TOOR, Ola Spjuth · 2018 · arXiv (Cornell University)
- Elemental allocation to molecular drivers of biogeochemistry in the Southern OceanLoay J. Jabre, Elden E. Rowland, Charlotte Eich, Mathijs van Manen, Corina P. D. Brussaard, Rob Middag, Erin M. Bertrand · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- PEAKS - A Software Tool for Shotgun Label Free Proteomics with High Sensitivity and High AccuracyXin Lei, Geoff Lumby, Hao Lin, M. Ziaur Rahman, Weiwu Chen, Baozhen Shan, Bin Ma · 2013
- Methods of processing mass spectrometry data to identify peptides and proteinsE. I. Berizovskaya, A. A. Ichalaynen, A. M. Antochin, В. Ф. Таранченко, Valerii M. Goncharov, Д. А. Митрофанов, А. В. Удинцев, A. V. Aksenov, O. A. Shevlyakova, Игорь Александрович Родин et al. · 2015 · Moscow University Chemistry Bulletin
- Labeling and Label-Free Shotgun Proteomics Quantification in the Research of Cardiovascular DiseasesXiaomeng Shen, Shichen Shen, Jun Qu · 2016 · Springer eBooks
- Data Analysis for Data Independent AcquisitionPedro Navarro, Marco Trevisán-Herraz, Hannes Luc Röst · 2016 · Royal Society of Chemistry eBooks
- From the desktop to the grid and cloud: conversion of KNIME workflows to WS-PGRADELuis de la Garza, Fabian Aicheler, Oliver Kohlbacher · 2017
- Ecological Metabolomics: Challenges and PerspectivesSumira Jan, Parvaiz Ahmad · 2019 · Elsevier eBooks
- Benchmarking accuracy and precision of intensity‐based absolute quantification of protein abundances in Saccharomyces cerevisiaeBenjamín J. Sánchez, Petri‐Jaan Lahtvee, Kate Campbell, Sergo Kasvandik, Rosemary Yu, Iván Domenzain, Aleksej Zelezniak, Jens Nielsen · 2021 · PROTEOMICS
- Full Issue PDF2021 · Molecular Plant-Microbe Interactions
- UmetaFlow: An untargeted metabolomics workflow for high-throughput data processing and analysisEftychia Eva Kontou, Axel Walter, Oliver Alka, Julianus Pfeuffer, Timo T. Sachsenberg, Omkar S. Mohite, Matin Nuhamunada, Oliver Kohlbacher, Tilmann Weber · 2022 · ChemRxiv
- UmetaFlow: An untargeted metabolomics workflow for high-throughput data processing and analysisEftychia Eva Kontou, Axel Walter, Oliver Alka, Julianus Pfeuffer, Timo T. Sachsenberg, Omkar S. Mohite, Matin Nuhamunada, Oliver Kohlbacher, Tilmann Weber · 2023 · ChemRxiv
- Chromatography–Mass Spectrometry Analysis of Plant Protein ConcentratesO. L. Meshcheryakova, А. Е. Бугрова, Alexey S. Kononikhin, Oksana A. Kartashova, Olga Sergeevna Korneeva, Л. Э. Глаголева, Vladimir I. Korchagin · 2024 · Journal of Analytical Chemistry
- On the question of correct use of replicates in quantitative label-free proteomicsLeyla A. Garibova, Mikhail V. Gorshkov, Mark V. Ivanov · 2025 · Analytical and Bioanalytical Chemistry
- Additional file 1 of UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysisEftychia Eva Kontou, Axel Walter, Oliver Alka, Julianus Pfeuffer, Timo T. Sachsenberg, Omkar S. Mohite, Matin Nuhamunada, Oliver Kohlbacher, Tilmann Weber · 2023 · Figshare
- Colorectal cancer: Notch signaling dysregulation, potential proteomic techniques, therapeutic strategies, and future perspectivesTabasum Ali, Ifat Jan, Rabiah Bashir, Ghulam Nabi Bader · 2026 · Elsevier eBooks
- Progress towards a better proteome characterization by quantitative mass spectrometry method development and proteogenomicsAlvaro Sebastian Vaca Jácome · 2016 · theses.fr (ABES)
- MassGAT: a graph-based collective learning approach for untargeted detection and annotation of LC-MS dataPaul-Henri Pinart, Annelaure Damont, Sylvain Déchaumet, Etienne Thévenot · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- LC–MS Data Processing Using OpenMSAxel Walter, Eftychia Eva Kontou, Payam Emami, Oliver Kohlbacher · 2026 · Methods in molecular biology
- Elucidation and Improvement of Algorithms for Mass Spectrometry Isotope Trace DetectionRobert Allen Smith · 2014 · ScholarsArchive (Brigham Young University)