@ARTICLE{Breitwieser_Colinge2011-JPR,
  author = {Florian P Breitwieser and André Müller and Loïc Dayon and Thomas
	Köcher and Alexandre Hainard and Peter Pichler and Ursula Schmidt-Erfurth
	and Giulio Superti-Furga and Jean-Charles Sanchez and Karl Mechtler
	and Keiryn L Bennett and Jacques Colinge},
  title = {General statistical modeling of data from protein relative expression
	isobaric tags.},
  journal = {J Proteome Res},
  year = {2011},
  volume = {10},
  pages = {2758--2766},
  number = {6},
  month = {Jun},
  abstract = {Quantitative comparison of the protein content of biological samples
	is a fundamental tool of research. The TMT and iTRAQ isobaric labeling
	technologies allow the comparison of 2, 4, 6, or 8 samples in one
	mass spectrometric analysis. Sound statistical models that scale
	with the most advanced mass spectrometry (MS) instruments are essential
	for their efficient use. Through the application of robust statistical
	methods, we developed models that capture variability from individual
	spectra to biological samples. Classical experimental designs with
	a distinct sample in each channel as well as the use of replicates
	in multiple channels are integrated into a single statistical framework.
	We have prepared complex test samples including controlled ratios
	ranging from 100:1 to 1:100 to characterize the performance of our
	method. We demonstrate its application to actual biological data
	sets originating from three different laboratories and MS platforms.
	Finally, test data and an R package, named isobar, which can read
	Mascot, Phenyx, and mzIdentML files, are made available. The isobar
	package can also be used as an independent software that requires
	very little or no R programming skills.},
  doi = {10.1021/pr1012784},
  file = {Breitwieser_Colinge2011-JPR.pdf:Quant/Breitwieser_Colinge2011-JPR.pdf:PDF},
  institution = {CeMM , Center for Molecular Medicine of the Austrian Academy of Sciences,
	Vienna, Austria.},
  language = {eng},
  medline-pst = {ppublish},
  owner = {fbreitwieser},
  pmid = {21526793},
  timestamp = {2011.08.09},
  url = {http://dx.doi.org/10.1021/pr1012784}
}


@ARTICLE{Taus_Mechtler2011-JPR,
  author = {Taus, Thomas and Köcher, Thomas and Pichler, Peter and Paschke, Carmen
	and Schmidt, Andreas and Henrich, Christoph and Mechtler, Karl},
  title = {Universal and Confident Phosphorylation Site Localization Using phosphoRS.},
  journal = {J Proteome Res},
  year = {2011},
  month = {Nov},
  abstract = {An algorithm for the assignment of phosphorylation sites in peptides
	is described. The program uses tandem mass spectrometry data in conjunction
	with the respective peptide sequences to calculate site probabilities
	for all potential phosphorylation sites. Tandem mass spectra from
	synthetic phosphopeptides were used for optimization of the scoring
	parameters employing all commonly used fragmentation techniques.
	Calculation of probabilities was adapted to the different fragmentation
	methods and to the maximum mass deviation of the analysis. The software
	includes a novel approach to peak extraction, required for matching
	experimental data to the theoretical values of all isoforms, by defining
	individual peak depths for the different regions of the tandem mass
	spectrum. Mixtures of synthetic phosphopeptides were used to validate
	the program by calculation of its false localization rate versus
	site probability cutoff characteristic. Notably, the empirical obtained
	precision was higher than indicated by the applied probability cutoff.
	In addition, the performance of the algorithm was compared to existing
	approaches to site localization such as Ascore. In order to assess
	the practical applicability of the algorithm to large data sets,
	phosphopeptides from a biological sample were analyzed, localizing
	more than 3000 nonredundant phosphorylation sites. Finally, the results
	obtained for the different fragmentation methods and localization
	tools were compared and discussed.},
  doi = {10.1021/pr200611n},
  file = {Taus_Mechtler2011-JPR.pdf:Phospho_report/Taus_Mechtler2011-JPR.pdf:PDF},
  institution = {Research Institute of Molecular Pathology (IMP) , Dr. Bohrgasse 7,
	A-1030 Vienna, Austria.},
  keywords = {sitelocalization},
  language = {eng},
  medline-pst = {aheadofprint},
  owner = {fbreitwieser},
  pmid = {22073976},
  timestamp = {2011.11.16},
  url = {http://dx.doi.org/10.1021/pr200611n}
}

@ARTICLE{Savitski_Kuster2011-MCP,
  author = {Savitski, Mikhail M. and Lemeer, Simone and Boesche, Markus and Lang,
	Manja and Mathieson, Toby and Bantscheff, Marcus and Kuster, Bernhard},
  title = {Confident phosphorylation site localization using the Mascot Delta
	Score.},
  journal = {Mol Cell Proteomics},
  year = {2011},
  volume = {10},
  pages = {M110.003830},
  number = {2},
  month = {Feb},
  abstract = {Large scale phosphorylation analysis is more and more getting into
	focus of proteomic research. Although it is now possible to identify
	thousands of phosphorylated peptides in a biological system, confident
	site localization remains challenging. Here we validate the Mascot
	Delta Score (MD-score) as a simple method that achieves similar sensitivity
	and specificity for phosphosite localization as the published Ascore,
	which is mainly used in conjunction with Sequest. The MD-score was
	evaluated using liquid chromatography-tandem MS data of 180 individually
	synthesized phosphopeptides with precisely known phosphorylation
	sites. We tested the MD-score for a wide range of commonly available
	fragmentation methods and found it to be applicable throughout with
	high statistical significance. However, the different fragmentation
	techniques differ strongly in their ability to localize phosphorylation
	sites. At 1\% false localization rate, the highest number of correctly
	assigned phosphopeptides was achieved by higher energy collision
	induced dissociation in combination with an Orbitrap mass analyzer
	followed very closely by low resolution ion trap spectra obtained
	after electron transfer dissociation. Both these methods are significantly
	better than low resolution spectra acquired after collision induced
	dissociation and multi stage activation. Score thresholds determined
	from simple calibration functions for each fragmentation method were
	stable over replicate analyses of the phosphopeptide set. The MD-score
	outperforms the Ascore for tyrosine phosphorylated peptides and we
	further show that the ability to call sites correctly increases with
	increasing distance of two candidate sites within a peptide sequence.
	The MD-score does not require complex computational steps which makes
	it attractive in terms of practical utility. We provide all mass
	spectra and the synthetic peptides to the community so that the development
	of present and future localization software can be benchmarked and
	any laboratory can determine MD-scores and localization probabilities
	for their individual analytical set up.},
  doi = {10.1074/mcp.M110.003830},
  file = {Savitski_Kuster2011-MCP.pdf:Phospho/Savitski_Kuster2011-MCP.pdf:PDF;Savitski_Kuster2011-MCP:Phospho/Savitski_Kuster2011-MCP:},
  institution = {Cellzome AG, Heidelberg, Germany.},
  keywords = {Algorithms; Binding Sites; Chromatography, Liquid, methods; Computational
	Biology, methods; Humans; Ions; Mass Spectrometry, methods; Peptides,
	chemistry; Phosphopeptides, chemistry; Phosphorylation; Protein Processing,
	Post-Translational; Proteome; Proteomics, methods; Reproducibility
	of Results; Software, sitelocalization},
  language = {eng},
  medline-pst = {ppublish},
  owner = {fbreitwieser},
  pii = {M110.003830},
  pmid = {21057138},
  timestamp = {2011.12.07},
  url = {http://dx.doi.org/10.1074/mcp.M110.003830}
}


@ARTICLE{Wu_Gygi2011-MCP,
  author = {Ronghu Wu and Noah Dephoure and Wilhelm Haas and Edward L Huttlin
	and Bo Zhai and Mathew E Sowa and Steven P Gygi},
  title = {Correct interpretation of comprehensive phosphorylation dynamics
	requires normalization by protein expression changes.},
  journal = {Mol Cell Proteomics},
  year = {2011},
  volume = {10},
  pages = {M111.009654},
  number = {8},
  month = {Aug},
  abstract = {The interpretation of quantitative phosphoproteomics studies is complicated
	because each differential phosphorylation event integrates both changes
	in protein expression and phosphorylation. Here we investigated this
	phenomenon by performing parallel comparisons of protein expression
	and phosphorylation in S. cerevisiae. In each of two experiments
	comparing yeast mutants bearing deletions in FUS3 or STE7 with their
	wild-type counterparts, we quantified over 4100 proteins, including
	all members of the yeast mating pathway. We also identified 12,499
	unique phosphorylation sites in this work. We demonstrate the critical
	importance of controlling the protein-level false-discovery rate
	and provide a novel method to assess the accuracy of protein false-discovery
	rate estimates. For the first time, 96\% of nonredundant phosphopeptide
	ratios could be calibrated by protein levels, allowing truly differential
	phosphorylation to be distinguished from altered protein expression.
	This revealed a starkly different view, with 25\% of seemingly differential
	phosphopeptides now attributed to changes in protein expression.
	Combined protein expression and phosphorylation surveys uncovered
	both independent and concerted changes in protein expression and
	phosphorylation, while highlighting the partially redundant role
	of a second MAPK (Kss1) in the mating pathway.},
  doi = {10.1074/mcp.M111.009654},
  file = {Wu_Gygi2011-MCP.pdf:Phospho/Wu_Gygi2011-MCP.pdf:PDF;Wu_Gygi2011-MCP:Phospho/Wu_Gygi2011-MCP:},
  institution = {Department of Cell Biology, Harvard Medical School, Boston, MA 02115.},
  language = {eng},
  medline-pst = {ppublish},
  owner = {fbreitwieser},
  pii = {M111.009654},
  pmid = {21551504},
  timestamp = {2011.08.09},
  url = {http://dx.doi.org/10.1074/mcp.M111.009654}
}

@ARTICLE{Lane_Bairoch2012-NAR,
  author = {Lane, Lydie and Argoud-Puy, Ghislaine and Britan, Aurore and Cusin,
	Isabelle and Duek, Paula D. and Evalet, Olivier and Gateau, Alain
	and Gaudet, Pascale and Gleizes, Anne and Masselot, Alexandre and
	Zwahlen, Catherine and Bairoch, Amos},
  title = {neXtProt: a knowledge platform for human proteins.},
  journal = {Nucleic Acids Res},
  year = {2012},
  volume = {40},
  pages = {D76--D83},
  number = {Database issue},
  month = {Jan},
  abstract = {neXtProt (http://www.nextprot.org/) is a new human protein-centric
	knowledge platform. Developed at the Swiss Institute of Bioinformatics
	(SIB), it aims to help researchers answer questions relevant to human
	proteins. To achieve this goal, neXtProt is built on a corpus containing
	both curated knowledge originating from the UniProtKB/Swiss-Prot
	knowledgebase and carefully selected and filtered high-throughput
	data pertinent to human proteins. This article presents an overview
	of the database and the data integration process. We also lay out
	the key future directions of neXtProt that we consider the necessary
	steps to make neXtProt the one-stop-shop for all research projects
	focusing on human proteins.},
  doi = {10.1093/nar/gkr1179},
  file = {Lane_Bairoch2012-NAR.pdf:Proteomics/Lane_Bairoch2012-NAR.pdf:PDF;Lane_Bairoch2012-NAR-neXtProt.pdf:Phospho_report/Lane_Bairoch2012-NAR-neXtProt.pdf:PDF},
  institution = {CALIPHO Group, Swiss Institute of Bioinformatics, CMU - 1, Rue Michel
	Servet 1211 Geneva 4, Switzerland.},
  keywords = {Databases, Protein; Humans; Knowledge Bases; Proteins, genetics/metabolism;
	User-Computer Interface},
  language = {eng},
  medline-pst = {ppublish},
  owner = {fbreitwieser},
  pii = {gkr1179},
  pmid = {22139911},
  timestamp = {2012.10.15},
  url = {http://dx.doi.org/10.1093/nar/gkr1179}
}

@ARTICLE{Hornbeck_Sullivan2012-NAR,
  author = {Hornbeck, Peter V. and Kornhauser, Jon M. and Tkachev, Sasha and
	Zhang, Bin and Skrzypek, Elzbieta and Murray, Beth and Latham, Vaughan
	and Sullivan, Michael},
  title = {PhosphoSitePlus: a comprehensive resource for investigating the structure
	and function of experimentally determined post-translational modifications
	in man and mouse.},
  journal = {Nucleic Acids Res},
  year = {2012},
  volume = {40},
  pages = {D261--D270},
  number = {Database issue},
  month = {Jan},
  abstract = {PhosphoSitePlus (http://www.phosphosite.org) is an open, comprehensive,
	manually curated and interactive resource for studying experimentally
	observed post-translational modifications, primarily of human and
	mouse proteins. It encompasses 1,30,000 non-redundant modification
	sites, primarily phosphorylation, ubiquitinylation and acetylation.
	The interface is designed for clarity and ease of navigation. From
	the home page, users can launch simple or complex searches and browse
	high-throughput data sets by disease, tissue or cell line. Searches
	can be restricted by specific treatments, protein types, domains,
	cellular components, disease, cell types, cell lines, tissue and
	sequences or motifs. A few clicks of the mouse will take users to
	substrate pages or protein pages with sites, sequences, domain diagrams
	and molecular visualization of side-chains known to be modified;
	to site pages with information about how the modified site relates
	to the functions of specific proteins and cellular processes and
	to curated information pages summarizing the details from one record.
	PyMOL and Chimera scripts that colorize reactive groups on residues
	that are modified can be downloaded. Features designed to facilitate
	proteomic analyses include downloads of modification sites, kinase-substrate
	data sets, sequence logo generators, a Cytoscape plugin and BioPAX
	download to enable pathway visualization of the kinase-substrate
	interactions in PhosphoSitePlus®.},
  doi = {10.1093/nar/gkr1122},
  file = {Hornbeck_Sullivan2012-NAR.pdf:Phospho_report\\Hornbeck_Sullivan2012-NAR.pdf:PDF},
  institution = {Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923, USA.
	phornbeck@cellsignal.com},
  keywords = {Acetylation; Amino Acid Sequence; Animals; Cattle; Databases, Protein;
	Humans; Mice; Phosphorylation; Protein Processing, Post-Translational;
	Proteins, chemistry/genetics/metabolism; Rats; Ubiquitination},
  language = {eng},
  medline-pst = {ppublish},
  owner = {fbreitwieser},
  pii = {gkr1122},
  pmid = {22135298},
  timestamp = {2012.10.09},
  url = {http://dx.doi.org/10.1093/nar/gkr1122}
}


