algorithms.bib

@article{samanipour2021,
  title={From centroided to profile mode: machine learning for prediction of peak width in HRMS data},
  author={Samanipour, Saer and Choi, Phil and O’Brien, Jake W and Pirok, Bob WJ and Reid, Malcolm J and Thomas, Kevin V},
  journal={Anal. Chem.},
  volume={93},
  number={49},
  pages={16562--16570},
  year={2021},
  publisher={ACS Publications},
  doi={10.1021/acs.analchem.1c03755}
}

@article{reuschenbach2022,
  title={Development of a scoring parameter to characterize data quality of centroids in high-resolution mass spectra},
  author={Reuschenbach, Max and Hohrenk-Danzouma, Lotta L and Schmidt, Torsten C and Renner, Gerrit},
  journal={Anal. Bioanal. Chem.},
  volume={414},
  number={22},
  pages={6635--6645},
  year={2022},
  publisher={Springer},
  doi={10.1007/s00216-022-04224-y}
}

@article{sanchez2021,
  title={Pipelines and Systems for Threshold-Avoiding Quantification of LC--MS/MS Data},
  author={Sanchez Brotons, Alejandro and Eriksson, Jonatan O and Kwiatkowski, Marcel and Wolters, Justina C and Kema, Ido P and Barcaru, Andrei and Kuipers, Folkert and Bakker, Stephan JL and Bischoff, Rainer and Suits, Frank and others},
  journal={Anal. Chem.},
  volume={93},
  number={32},
  pages={11215--11224},
  year={2021},
  publisher={ACS Publications},
  doi={10.1021/acs.analchem.1c01892}
}

@article{gorrochategui2019,
  title={ROIMCR: a powerful analysis strategy for LC-MS metabolomic datasets},
  author={Gorrochategui, Eva and Jaumot, Joaquim and Tauler, Rom{\`a}},
  journal={BMC Bioinf.},
  volume={20},
  number={1},
  pages={1--17},
  year={2019},
  publisher={Springer},
  doi={10.1186/s12859-019-2848-8}
}

@article{purschke2020,
  title={Identification of unknowns in industrial wastewater using offline 2D chromatography and non-target screening},
  author={Purschke, Kirsten and Zoell, Christian and Leonhardt, Juri and Weber, Markus and Schmidt, Torsten C},
  journal={Sci. Tot. Environ.},
  volume={706},
  pages={135835},
  year={2020},
  publisher={Elsevier},
  doi={10.1016/j.scitotenv.2019.135835}
}

@article{boulet2021,
  title={High-resolution mass spectrometry (HRMS): Focus on the m/z values estimated by the Savitzky--Golay first derivative},
  author={Boulet, Jean-Claude and Meudec, Emmanuelle and Vallverdu-Queralt, Anna and Cheynier, V{\'e}ronique},
  journal={Rapid Communications in Mass Spectrometry},
  volume={35},
  number={6},
  pages={e9036},
  year={2021},
  publisher={Wiley Online Library},
  doi={10.1002/rcm.9036}
}

@article{du2006,
  title={Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching},
  author={Du, Pan and Kibbe, Warren A and Lin, Simon M},
  journal={bioinformatics},
  volume={22},
  number={17},
  pages={2059--2065},
  year={2006},
  publisher={Oxford University Press},
  doi={10.1093/bioinformatics/btl355}
}

@article{vergeynst2013,
  title={Accurate mass determination, quantification and determination of detection limits in liquid chromatography--high-resolution time-of-flight mass spectrometry: Challenges and practical solutions},
  author={Vergeynst, Leendert and Van Langenhove, Herman and Joos, Pieter and Demeestere, Kristof},
  journal={Analytica Chimica Acta},
  volume={789},
  pages={74--82},
  year={2013},
  publisher={Elsevier},
  doi={10.1016/j.aca.2013.06.024}
}

@article{tautenhahn2008highly,
  title={Highly sensitive feature detection for high resolution LC/MS},
  author={Tautenhahn, Ralf and B{\"o}ttcher, Christoph and Neumann, Steffen},
  journal={BMC bioinformatics},
  volume={9},
  number={1},
  pages={1--16},
  year={2008},
  publisher={BioMed Central},
  doi={10.1186/1471-2105-9-504}
}

@article{myers2017one,
  title={One step forward for reducing false positive and false negative compound identifications from mass spectrometry metabolomics data: new algorithms for constructing extracted ion chromatograms and detecting chromatographic peaks},
  author={Myers, Owen D and Sumner, Susan J and Li, Shuzhao and Barnes, Stephen and Du, Xiuxia},
  journal={Analytical chemistry},
  volume={89},
  number={17},
  pages={8696--8703},
  year={2017},
  publisher={ACS Publications},
  doi={10.1021/acs.analchem.7b00947}
}

@article{dietrich2022open,
  title={Open-source feature detection for non-target LC--MS analytics},
  author={Dietrich, Christian and Wick, Arne and Ternes, Thomas A},
  journal={Rapid Communications in Mass Spectrometry},
  volume={36},
  number={2},
  pages={e9206},
  year={2022},
  publisher={Wiley Online Library},
  doi={10.1002/rcm.9206}
}

@article{zhu2019feature,
  title={Feature Extraction for LC--MS via Hierarchical Density Clustering},
  author={Zhu, Huimin and Chen, Yi and Liu, Cha and Wang, Rong and Zhao, Gaokun and Hu, Binbin and Ji, Hongchao and Zhang, Zhi-Min and Lu, Hongmei},
  journal={Chromatographia},
  volume={82},
  number={10},
  pages={1449--1457},
  year={2019},
  publisher={Springer},
  doi={10.1007/s10337-019-03766-1}
}

@article{wei2014data,
  title={Data dependent peak model based spectrum deconvolution for analysis of high resolution LC-MS data},
  author={Wei, Xiaoli and Shi, Xue and Kim, Seongho and Patrick, Jeffrey S and Binkley, Joe and Kong, Maiying and McClain, Craig and Zhang, Xiang},
  journal={Analytical chemistry},
  volume={86},
  number={4},
  pages={2156--2165},
  year={2014},
  publisher={ACS Publications},
  doi={10.1021/ac403803a}
}

@article{isaacman2017automated,
  title={Automated single-ion peak fitting as an efficient approach for analyzing complex chromatographic data},
  author={Isaacman-VanWertz, Gabriel and Sueper, Donna T and Aikin, Kenneth C and Lerner, Brian M and Gilman, Jessica B and de Gouw, Joost A and Worsnop, Douglas R and Goldstein, Allen H},
  journal={Journal of Chromatography A},
  volume={1529},
  pages={81--92},
  year={2017},
  publisher={Elsevier},
  doi={10.1016/j.chroma.2017.11.005}
}

@article{kuhl2012camera,
  title={CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets},
  author={Kuhl, Carsten and Tautenhahn, Ralf and Bottcher, Christoph and Larson, Tony R and Neumann, Steffen},
  journal={Analytical chemistry},
  volume={84},
  number={1},
  pages={283--289},
  year={2012},
  publisher={ACS Publications},
  doi={10.1021/ac202450g}
}

@article{permiakova2021chickn,
  title={CHICKN: extraction of peptide chromatographic elution profiles from large scale mass spectrometry data by means of Wasserstein compressive hierarchical cluster analysis},
  author={Permiakova, Olga and Guibert, Romain and Kraut, Alexandra and Fortin, Thomas and Hesse, Anne-Marie and Burger, Thomas},
  journal={BMC bioinformatics},
  volume={22},
  number={1},
  pages={1--30},
  year={2021},
  publisher={Springer},
  doi={10.1186/s12859-021-03969-0}
}

@inproceedings{wei2012novel,
  title={A Novel Two-Stage Alignment Method for Liquid Chromatography Mass Spectrometry-Based Metabolomics},
  author={Wei, Xiaoli and Shi, Xue and Kim, Seongho and McClain, Craig and Zhang, Xiang},
  booktitle={International Conference on Intelligent Computing},
  pages={152--159},
  year={2012},
  organization={Springer},
  doi={10.1007/978-3-642-31588-6_20}
}

@article{prince2006chromatographic,
  title={Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping},
  author={Prince, John T and Marcotte, Edward M},
  journal={Analytical chemistry},
  volume={78},
  number={17},
  pages={6140--6152},
  year={2006},
  publisher={ACS Publications},
  doi={10.1021/ac0605344}
}

@article{gorrochategui2019roimcr,
  title={ROIMCR: a powerful analysis strategy for LC-MS metabolomic datasets},
  author={Gorrochategui, Eva and Jaumot, Joaquim and Tauler, Rom{\`a}},
  journal={BMC bioinformatics},
  volume={20},
  number={1},
  pages={1--17},
  year={2019},
  publisher={Springer},
  doi={10.1186/s12859-019-2848-8}
}

@article{schollee2016statistical,
  title={Statistical approaches for LC-HRMS data to characterize, prioritize, and identify transformation products from water treatment processes},
  author={Scholl{\'e}e, Jennifer E and Schymanski, Emma L and Hollender, Juliane},
  journal={Assessing Transformation Products of Chemicals by Non-Target and Suspect Screening- Strategies and Workflows Volume 1},
  pages={45--65},
  year={2016},
  publisher={ACS Publications},
  doi={10.1021/bk-2016-1241.ch004}
}

@article{hohrenk2022non,
  title={Non-target Analysis and Chemometric Evaluation of a Passive Sampler Monitoring of Small Streams},
  author={Hohrenk-Danzouma, Lotta L and Vosough, Maryam and Merkus, Valentina I and Drees, Felix and Schmidt, Torsten C},
  journal={Environmental Science \& Technology},
  volume={56},
  number={9},
  pages={5466--5477},
  year={2022},
  publisher={ACS Publications},
  doi={10.1021/acs.est.1c08014}
}

@article{koppe2020application,
  title={Application of a non-target workflow for the identification of specific contaminants using the example of the Nidda river basin},
  author={K{\"o}ppe, Toni and Jewell, Kevin S and Dietrich, Christian and Wick, Arne and Ternes, Thomas A},
  journal={Water Research},
  volume={178},
  pages={115703},
  year={2020},
  publisher={Elsevier},
  doi={10.1016/j.watres.2020.115703}
}