
@article{langella_xtandempipeline:_2017,
	title = {X!{TandemPipeline}: {A} {Tool} to {Manage} {Sequence} {Redundancy} for {Protein} {Inference} and {Phosphosite} {Identification}},
	volume = {16},
	issn = {1535-3907},
	shorttitle = {X!{TandemPipeline}},
	doi = {10.1021/acs.jproteome.6b00632},
	abstract = {X!TandemPipeline is a software designed to perform protein inference and to manage redundancy in the results of phosphosite identification by database search. It provides the minimal list of proteins or phosphosites that are present in a set of samples using grouping algorithms based on the principle of parsimony. Regarding proteins, a two-level classification is performed, where groups gather proteins sharing at least one peptide and subgroups gather proteins that are not distinguishable according to the identified peptides. Regarding phosphosites, an innovative approach based on the concept of phosphoisland is used to gather overlapping phosphopeptides. The graphical interface of X!TandemPipeline allows the users to launch X!tandem identification, to inspect spectra and to manually validate their assignment to peptides, to launch the grouping program, and to visualize elementary data as well as grouping and redundancy information. Identification results obtained from other search engines can also be processed. X!TandemPipeline results can be exported as ready-to-use tabulated files or as XML files that can be directly used by the PROTICdb database or by the MassChroQ quantification software. X!TandemPipeline runs fast, is easy to use, and can process hundreds of samples simultaneously. It is freely available under the GNU General Public License v3.0 at http://pappso.inra.fr/bioinfo/xtandempipeline/ .},
	language = {eng},
	number = {2},
	journal = {Journal of Proteome Research},
	author = {Langella, Olivier and Valot, Benoît and Balliau, Thierry and Blein-Nicolas, Mélisande and Bonhomme, Ludovic and Zivy, Michel},
	year = {2017},
	pmid = {27990826},
	keywords = {Proteomics, Tandem Mass Spectrometry, Software, Humans, Phosphopeptides, Algorithms, Amino Acid Sequence, Benchmarking, Bioinformatics, database search, Databases, Protein, Mass Spectrometry, phosphopeptide, protein inference, Proteins, Search Engine, User-Computer Interface, software, mass spectrometry, pappso, bioinformatics},
	pages = {494--503},
	file = {ACS Full Text Snapshot:/home/langella/Zotero/storage/9456NYWM/acs.jproteome.html:text/html;Snapshot:/home/langella/Zotero/storage/PNMZ9JE9/acs.jproteome.html:text/html},
}


@article{langella_full_2024,
	title = {Full {Native} {timsTOF} {PASEF}-{Enabled} {Quantitative} {Proteomics} with the {i2MassChroQ} {Software} {Package}},
	volume = {23},
	copyright = {https://doi.org/10.15223/policy-029},
	issn = {1535-3893, 1535-3907},
	url = {https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00732},
	doi = {10.1021/acs.jproteome.3c00732},
	language = {en},
	number = {8},
	urldate = {2024-09-06},
	journal = {Journal of Proteome Research},
	author = {Langella, Olivier and Renne, Thomas and Balliau, Thierry and Davanture, Marlène and Brehmer, Sven and Zivy, Michel and Blein-Nicolas, Mélisande and Rusconi, Filippo},
	month = aug,
	year = {2024},
	keywords = {gqe-pappso, Free Software, quantitative proteomics, Mass spectrometry, gqe-mdavanture-pappso, gqe-mblein-pappso, gqe-mzivy-pappso, gqe-tballiau-pappso, gqe-olangella-pappso, gqe-frusconi-pappso, DDA bottom-up proteomics, Mass spectrometry DDA bottom-up proteomics quantitative proteomics Free Software},
	pages = {3353--3366},
}


@article{rusconi_massxpert_2009,
	title = {{massXpert} 2 : a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data},
	volume = {25},
	issn = {1367-4811, 1367-4803},
	shorttitle = {\textit{{massXpert} 2}},
	url = {https://academic.oup.com/bioinformatics/article/25/20/2741/194220},
	doi = {10.1093/bioinformatics/btp504},
	abstract = {Abstract
            Summary: Since the middle of the 90s, mass spectrometry has evolved into an almost indispensable tool in structural studies on an ever-growing variety of (bio-)polymers, of which proteins, sugars and nucleic acids are the most prominent. Since the first public release of massXpert, the advances of mass spectrometry have motivated continuous and thorough maintenance of that software, in the form of two full software rewrites, culminating with massXpert 2, which we describe in this report. We shall describe the profound changes in massXpert that were performed so as to keep up with the technical advances in mass spectrometry since a decade.
            Availability: The massXpert 2 software is an open source and free software project hosted at http://www.massxpert.org.
            Contact:  rusconi@mnhn.fr
            Supplementary information:  Supplementary data are available at Bioinformatics online.},
	language = {en},
	number = {20},
	urldate = {2025-03-16},
	journal = {Bioinformatics},
	author = {Rusconi, Filippo},
	month = oct,
	year = {2009},
	pages = {2741--2742},
	file = {Texte intégral:/home/langella/Zotero/storage/ASMU67LG/Rusconi - 2009 - massXpert 2  a cross-platform software environment for polymer chemistry modelling and simul.pdf:application/pdf},
}
