NEWS

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isobar 1.19.1

• Fix error in subsetIBSpectra and exclude and namespace imports (Laurent Gatto <2016-10-07 Fri>)

isobar 1.17.1

• Fixed critical bug in isotope impurity correction method. Isobar used a transposed matrix for isotope impurity correction prior to this fix. Quantification results will change when isotope impurity correction is performed Bug discovered by Dario Strbenac https://support.bioconductor.org/p/74301/#79900).

isobar 1.16.0

• Bioconductor release 3.2

isobar 1.14.0

• Bioconductor release 3.1

isobar 1.13.0

• calcCumulativeProbXGreaterThanY() contributed by A. Stukalov, for calculating cummulative p-values with replicates
• Bioconductor version increment

isobar 1.12.0

• Bioconductor release 3.0

isobar 1.10.0

• Bioconductor release 2.9

isobar 1.9.5

• FIX FOR TMT-10plex tags: previous version had wrong annotation of N and C for 127,128,129,130
• Speed improvements for p-value calculation by vectorization, contributed by A. Stukalov

isobar 1.9.3

• allow the use of a combination matrix in NoiseModel reporterTagNames
• added function getProteinInfoFromTheInternet which automatically recognizes Uniprot and Entrez ACs. Set now as default 'protein.info.f' in the report configuration.
• Overhauled isobar-analysis.Rnw
• use of ltxtables to allow optimal column widths (longer runtime, however)
• use [[ instead of $ for accession of lists
• better column and grouping description
• allow report generation without a proteinInfo object
• set report cache directory to 'cache' (instead of '.') by default
• 1.9.3.2:
• mascotParser2.pl: allow to skip modif-conversion with -no-modiconv
• mascotParser2.pl: set --lightXML as default
• report generation: set combn.method="versus.channel", which computes the ratios against the first channel
• various PDF report improvements
• 1.9.3.3:
• report tables are written into tables which are loaded with LTxtable report generation takes longer now
• fixes in correct.peptide.ratios
• use combined protein group for peptide-protein mapping
• use only reporter proteins for mapping
• fix in creation of protein groups from template, subset by peptide _and_ modif

isobar 1.9.2

• fix issue of NA in 'n.spectra' when calculating summarized ratios
• various report improvements:
• use column of variable width to display class labels
• add attributes of quant table to summarized result table
• improved placement of tikz peptide group pictures

isobar 1.7.6

• added TMT 10plex (contribution from Florent Gluck)
• fixed bugs with system.file not working on R < 2.11 (contribution from Florent Gluck)
• fixed bug in isobar-qc which was not working without normalize=TRUE
• added writeHscoreData for usage with Hscorer.py (MM Savitski, 2010)
• shQuote commands correctly - should fix issues running report generation on Windows
• added calculations and XLS tab for peptides with unsure localization of the modification site
• updated scripts for creating multi-sample reports (create.meta.reports)

isobar 1.7.5

• fixed critical bugs: Excel report output had wrong ordering, ie ratios did not correspond to the meta information [introduced in version 1.7.3].
• fix of real peptide names: Reexport I/L peptides in reports

isobar 1.7.4

• improved MSGF+ search result import
• refactored report properties: all properties can now be defined in in the properties.R
• speed and memory usage improvements when creating wide XLS report
• ratio p-value adjustment now works per comparision instead of globally

isobar 1.7.3

• fix wide XLS report format
• novel plot for ratio combinations in QC report showing individual ratio distributions and significant ratios

isobar 1.7.2

• added TMT 6plex masses to phosphoRS export script
• fixed mascot parsers
• MzIdentML version 1.1.0 support implemented [not fully tested]

isobar 1.7.1

• fixed import of MzIdentML files from Mascot and ProteomeDiscoverer

isobar 1.6.0

• added modules and functions for PTM quantification

isobar 1.5.3

• parallelization support! Set options(isobar.parallel=TRUE) and register a cluster using registerDoMC or registerDoSNOW. Used when creating ratio tables.

isobar 1.5.2

• added MSGF+ tsv import [one-line-per-psm format]
• refactored various parts of the code (proteinRatios, report-utils, isobar-import)
• PTM XLS report: report significance for protein ratio, and peptide ratio

isobar 1.5.1

• added molecular weight correction to emPAI and dNSAF
• added property 'ratiodistr.class.labels': biological variability can be calculated in the report with other labels
• improved PDF analysis report: added number of proteins in each section
• added location scale family T distribution as biological variability distribution (distr class) and fitTlsd.
• better protein PDF analysis report layout.

isobar 1.5

• Added modules for PTM validation and quantification
• Validation
• PhosphoRS XML import writers and outpout readers
• DeltaScore calculation when the data is provided
• Quantification
• All quantifications can be done now either on the protein level, peptide level, or modified peptide level. For modified peptide level, supply a matrix with a 'peptide' and 'modif' column to the appropriate functions.
• Correction of peptide ratios with protein ratios is possible. Also the variance can be adjusted (assuming no or full correlation)
• Report generation
• Import PhosphoSitePlus or neXtProt information on modification sites

isobar 1.3.0

• Rockerbox import (just define the XXX.dat.peptides.csv as identifications)
• possibility to define columns for XLS report in properties.R. e.g. xls.report.columns <- c("ratio","is.significant", "ratio.minus.sd","ratio.plus.sd", "p.value.ratio","p.value.sample", "log2.ratio","log2.variance")

isobar 1.1.3

• better matching of file patterns of peaklist and id in report
• tab2xls improvements:
• fix when there are cells with preceeding colons - would think they are cell properties
• fix row limitation of 65536 - add new worksheet with remaining lines
• re-added ibspiked_set2 dataset as the xz requirement allows for additional data

isobar 1.1.2

• fixed handling of divergent identifications in one search engine
• fixed number of spectra in isobar-analysis report
• fixed recently introduced error when reading mgf file
• identifications tab in XLS report is now in concise format
• shared peptides are colored in gray
• added xls report format = wide

isobar 1.1.1

NEW FEATURES

• normalization can now be performed on individual channels (and channel pairs)
• added semi-quantitative Quantitation with emPAI, dNSAF and spectral count
• proteinInfo can now be gathered from Uniprot directly
• added reporter intensity plot shpwing effect of normalization
• added linear regression as ratio estimator
• improved MA plot: added 'Infinity' on the axis

isobar 1.0.0

• first Bioconductor version (version bump to 1.0.0)!
• slot name reporterMasses is renamed to reporterTagMasses to fix clash with method reporterMasses which fetches assayData(ibspectra)[["mass"]]
• slot name reporterNames is renamed to reporterTagNames to distinguish from deprecated Biobase::reporterNames
• added option 'scan.lines' to readIBSpectra: read mgf files in parts for large MGF files
• use a function for protein reporting: create.reports.R properties.conf will be replaced by properties.R

isobar 0.2.5

• MSnbase support: Added functions to coerce from MSnSet to IBSpectra and vice versa. Added Msnbase to Suggests.
• support for multiple classes added
• updated Perl parsers: mascotParser2.pl and pidresParser2.pl instead of isobarXParser.pl resulting XML files can be converted to id.csv using psx2tab2.pl
• prob otion for readIBSpectra worked errornous - fixed (thanks to Xavier Robin)
• added property use.na: Use NA values for quantification
• various Analysis Report beautifications (thanks to Xavier Robin)
• varous bug fixes

isobar 0.2.4

• improved Vignette descriptions, added CITATION (still UTF-8 error)
• added possibility to revert Mascot escaped TITLEs
• if proteins are excluded w/ subsetIBSpectra, exclude all it's peptides, not only reporter-specific ones
• fix error introduced in 0.2.3: When multiple MGFs were read, an false error occured that not all id spectra could be matched
• add property 'author' for LaTeX reports
• section 'Significantly regulated proteins' not shown anymore by default added property show.significant.proteins to reenable
• added properties isotope.impurities and fragment.outlier.prob
• bug fixes:
• naming not correct when class labels contain NAs
• numeric class labels are not handled correctly
• added naRegion to noise model
• data is now stored before normalization. Those values are then used to normalize. (Thanks to observation of Chris Bielow)

isobar 0.2.3

• specify combination matrix for proteinRatios and in properties.conf
• improved logging of IBSpectra creation and normalization
• fix: maplot crashed on all NA channels
• NA names in PDF report section 'Not quantified proteins' removed
• allow for NA class labels - they are ignored in the comuptation of ratios

isobar 0.2.2

• re-added ratio vs intensity plot in QC report
• issue warning when summarize property is incorrectly defined
• create cachedir if it does not exist
• estimateRatio.group_specific_proteins renamed to quant.w.grouppeptides
• sanitize analysisname, uniprotlink, and subsection names for LaTeX
• use fancyhdr instead of fanctheadings
• added argument require.reporter.specific to reporterProteins

isobar 0.2.1

• Bug fix: as.data.frame generated ions/mass colnames with a 'X' in front

isobar 0.2

• Published online with JPR Publication