Version 2.3.3

Fixes a quantitation bug when launching from a dataset on which a ‘Retrieve Protein Sequences’ has been executed.

Version 2.3.2

This new release focuses mainly on Isobaric labelling quantification in particular by taking into account purity correction matrices and Precursor Ion Fraction (PIF) information. Works was also carried out on the overall pipeline by developing mzdbConverter, a new tool for converting raw data to mzDB, and MGFBoost to generate more accurate peaklists.

Server Features and Bug Fixes

• Quantification
  • In all Quantification, (Label Free, Isobaric …) sum is the default abundance aggregation method. (Peptide ions to peptides, peptides to proteins sets…)
  • Label free Quantification: some improvement to ensure repeatability of RT alignment
  • Isobaric labelling quantitation aggregation
    • The type of the aggregated quantitation is “isobaric labelling quantitation” if all child are “isobaric labelling quantitation”, even if they don’t have exactly the same quantitation method (TMT16plex vs TMT10plex…)
    • The quantitation method will be set using the first quantitation channel “isobaric method”. If no method is found (could happen in previous Proline version) the Dataset quantitation type will be identified as “generic”.

• Isobaric labelling Post-Processing
  • Possibility to define a “purity correction Matrix” for abundance correction in post processing parameters
  • Define aggregation summarizing method for abundances aggregation from PSM to Peptide Ions
  • Allow PIF (Precursor Ion Fraction) filtering of PSMs. This value will be available if mgfBoost has been used to generate the MGF file.

• Other Post-Processing
  • Use Abundance instead of Raw Abundance for normalisation and further process
  • Do some tests on quantification method: verify that quant labels are consistent with method

• Other changes
  • Performance issue during validation to update Spectral Count values.
  • Export : Add some columns
    • Razor status: peptide is valid for some protein and invalid for others …
    • Specific Isobaric information: PIF value…
    • General information: Proline version…
  • Upgrade to Java 17
• Bug Fixes
  • PTMs: NTerm clusters error: some peptides were missing due to the fact that “any Nterm” position was not correctly considered.
  • X!Tandem invalid date error: Use specific date format to parse search date.
  • Validation : use 256 decimal math precision instead of unlimited (unlimited causes performance issues)
  • Other :
    • Peptide : take into account ‘no enzyme’ in Missed Cleavages count
    • Peptide : sequence AA substitution improved
    • Quantification: initialize “best Peptide Match” , none was specified when score was 0
  • Administration: Fix project change owner error

ProlineStudio

• Retrieve Bio Sequence
  • At start-up, test if Sequence Repository module is reachable. If not, disable the associated tasks
    • No need of timeout, Retrieve Sequence tasks should not generate “Message has expired” errors any more
  • Only one task at a time for “Retrieve Sequence”? If a task is already running, the action is disabled until the task is completed.
• Isobaric labelling quantitation – TMT
  • Add a specific view for isobaric labelling quantitation and add “psm table” below peptide ion in protein set view.
  • Create Quantification dialog: Adapt display for Isobaric labelling Quantitation
    • Allow to drag and drop multiple identification datasets to create multiple quantitation at once.
    • Save Isobaric Method parameters in Preferences and between next/previous views.
  • Aggregation : use quantitation labels information to define default quant channels mapping
• Post Processing
  • In case of Isobaric labelling quantitation, add purity matrix option and file selection. Verify quant labels are consistent to quant method before enabling this option.
  • Reorganized post processing dialog
  • Summarizing method option added to aggregate from PSM to PepIon
  • Dialog to edit Purity Correction Matrix added, using a generic format or “Thermo like” matrix.
  • Post-Processing PSM filter on PIF value added (the information is read from the spectrum title)
• Display
  • A filter to search a String in all Proteins not only typical has been added…
  • DataAnalyzer CSV Exporter error: takes null cells into account
  • Optimize load quantitation peptide performance
  • Bugs fixes
    • Display of values is incorrect if the user change the column ordering or hide a column.
    • Fixe quantitation peptide ions display error in some DataAnalyzer views
    • Fix error in Aggregation Dialog when channel names where to large
    • Error In Admin/User Account view
    • Add warning if no item found using Search button
    • Add simple filter on PTM (as string)
• Quantification
  • Change Quantification Drop-Zone behaviour to consider only mzdb files.
  • Bugs fixes
    • Define best columns for Quant Peptide Linear Plot
• Other
  • Allow batch export of mzIdentML
  • PTM
    • Recommend to run new Identify PtmSites Task version
    • Allow to display multiple PTM at one location( NTerm & AA for example)
    • N/CTerm is now located on first/last peptide AA (not before/after)

mzDB Tools

mzScope

• MGF generation added
• MGF Panel refactoring
• Allow mirror display of reference spectra thanks to a scaling factor
• MGF MS2 can be displayed as reference spectrum to be compared with MS2 scans
• Batch extraction improvements : allow extraction of MS2 fragments from PRM/DIA files
• isotopic prediction use an additional (not used in proline server) refinement step
• isotopic pattern shape prediction based on formula or atomic composition or AA sequence

mzDB-Wizard

• “Split mzDB” added
  • For FAIMS data, this task split mzdb files into 2 or more files using CV information in spectra.
• Add read-only option in configuration to lock a given configuration and so preventing unexpected change. This is useful on computer shared between many users.
• Create MGF command added to use mgfBoost to generate MGF
• Now use the new mzdbConverter for raw file conversion.
• Bug fixes :
  • No more multiple uploads of the same file (due to monitoring on directory)
  • Uploaded mzdb files must always have the extension .mzdb (and not mzDB)
  • mzDB-Wizard do no longer wait for all conversions to be completed before uploading mzdb.
  • Mount point on server side are now updated when the host is modified
  • A patch has been added to generating mzdb for old DIA/PRM data

mzDBConverter – NEW 

• New converter to mzdb files
• Support Bruker and Thermo Fischer raw files. Conversion is done using manufacturer libraries.

mgfBoost – NEW

• New MGF generation tools
• Add some selection window statistics
• Enable header comments in MGF files
• Bug Fixes
  • Fix error when spectrum header precursor is null
  • Fix m/z values ordering problem
  • 0+ charge precursor of MS2 spectrum from PRM acquisition is now properly handled.
• use “Ion Mobility Mode” to configure “Create MGF” command

Version 2.2.0

This new release improves the PTMs oriented functionalities. The previous version introduced a clear distinction between modification sites and clusters of modifications .A significant work has been done on the visualisation and exploitation of these two concepts.

The 2.2.0 version also includes several improvements and fixes detailed here after.

Server Features and Bug Fixes

• Some label free quantitation improvement
  • Ensure repeatability of RT alignment
  • Peakels slicing improved
  • Bug fixes in peakel smoothing and isomeric peptides computation.
• Identifications merges
  • Merged peptide matches will reference child’s ‘spectrum matches’ in order to display spectrum annotation.
  • Add Fragmentation Rule Set information in merged dataset, if same value in all children
• Result files Imports
  • Add Peptide Match disambiguated sequence properties (where corresponding AA replaces X/J). Export this property as new column.
  • Multi thread import service. First version to allow multiple imports at the same time, one per group of projects in the limit of the maximum number of allowed thread
  • Support no enzyme result
  • Variable PTM was lost when at the same position on the peptide sequence than fixed PTM
• Validation
  • New PSM filter: Single Sequence per Pretty Rank. This filter keeps the best PSM for a specific query’s pretty rank, using the same rules as Single PSM per Pretty Rank Once the PSM is identified it also keeps all PSMs with the same sequence (without considering PTMs)
• Export
  • “Quantified Peptide” export sheet added for MS1 quantification datasets

• Other Bugs fixes
  • Generate Spectrum matches : was long + failed in specific case
  • Peptide raw abundance was modified during Post Processing
  • Error in Spectral count that could occur in some very specific conditions.
  • X!Tandem import failed due to duplicate in databases.
  • Add a low-level configuration mechanism to allow the modification of some “hidden” parameters.

Studio

• Huge refactoring to remove framework dependency
• Modifications process and visualisation
  • Annotated PTM Dataset added:
    • add annotation information to clusters: selection Level, description, notation
    • merge of co-localized cluster.
    • edit cluster: modify annotation or remove peptides from the cluster
  • Fixes error in default value for abundances
  • Identify PTM Dialog
    • Adapt to large number of PTMs (scrollbar, resizable, select/unselect all)
  • View
    • Add Annotated PTM Dataset view
    • Add contextual menu in Cluster table to “view co-localized clusters”
    • Add possibility to navigate from Cluster to Site
  • General display
    • Some changes in Map Alignment
      • Don’t display cross assign PSM by default.
      • Fix error in iterative mode: update both plots when needed.
      • Display adaptive RT tolerance plots, which is a beta feature, not used in cross assignment yet.
      • “Loess smooth curve” display: match the values used on Proline server during processing
    • Add MoZ calibration view
      • Display the moz variation as a function of retention time. This is still a beta feature that is not yet used in cross assignment.
    • Peptide table
      • Add charge and moz columns.
      • Display ambiguous AA in bold (X,J…) and add column to view “None ambiguous sequence”
    • Add PTM and charge in annotated spectrum title
    • In Quantitation peptides view, graphic default columns for axis were incorrect.
  • Identification
    • Add Single Sequence Peptide per Pretty Rank filter
    • Allow to clear validation without clearing merge.
  • Other features/Fixes
    • Make validation dialog resizable
    • Ms Files tab
      • add support of raw2mzdb version 1.1
      • Fixe error when converting without uploading
    • Empty Label Free DropZone when clearing mzdb-sample association
    • Bug Fixes
      • display error in Server Tasks Log History
      • Validation save/load properties error
      • Admin menu was always unable
      • Data Analyzer: error on some CSV import
      • Generate Spectrum Matches Dialog: specified “fragmentation rule set” was always “Unknown”

Version 2.1.2

The main change in this version is the new FDR control procedure

Server Features and Bug Fixes

• FDR control based on Benjamini-Hochberg (BH) method
  • peptide level filtering : BH filter implemented at PSM, peptide and protein set level
  • peptide scoring based on Sidak correction instead of best PSM score.
  • enhanced pValue precision
  • validation properties includes all validation levels (PSM/Peptide/ProteinSet)
• Merge MSI Search information when merging Search Result
• Spectral Count:
  • Try to find corresponding ProteinSet in child dataset using not only Identification Summary reference Typical ProteinMatch but also samesets
• Bugs fixes
  • Modules version were not defined anymore and not well displayed in System Information dialog
  • Isobaric quantification
    • summarize reporter ions to ion abundances by using MEDIAN summarizer
  • Export
    • PTM Cluster export: filter NAN value when summing (to avoid NAN result) and set to NAN if no abundances

Proline Studio

• Benjamini-Hochberg FDR filtering : validation dialog and tasks updated to validation service version 3.0
  • Protein scoring Fisher added
  • BH filter at PSM and Protein levels added
  • Peptide score column added
  • remove score type column in protein set tables
  • filter dialog refactoring
• Graphics :
  • Allow selection for PTM peptides (PTM Quantitation view)
  • Add PTM color in sequence in graphic tootip
• Quantitation Pepitde status
  • Added icons for Quant Peptide Status
  • modification to enhance quant. peptide status display and understanding for the user
• Added Refresh icon for Retry to connect to R Server Panel. This icon was lacking, so the button was not displayed
• Bugs fixes
  • Isobaric quantification
    • isobaric tagging display bug fix
    • enhanced parameter dialog for isobaric tagging
  • Error in create label free quantification panel (due to modification for TMT)
  • Graphics
    • Hide selection button wasn’t displayed any more
    • Set min to 0 for quantitative plot
  • In multi-screen configuration, dialogs are not opened in the right screen
  • Features display not synchronized with selection
  • Identify modification sites should be disabled for dataset without Identification Summary
  • String filters are not identical in all windows
  • Empty trash exception (when windows with data are opened)
  • MsFiles tab
    • Double scrollbar for Ms Files Tab : server part
    • Download mzdb files from server to local file system

Version 2.1

The release 2.1 adds two new interesting features to Proline:

• support of isotopic and isobaric labeling strategies
• quantification of fractionated samples

This release was also the opportunity to improve several existing algorithms (e.g. label free quantitation, post processing … ), as well as visualization interfaces (performance improved and new available views, see below). Additionally, various bugs are now fixed ( see below).

Server Features and Bug Fixes

• PTMs
  • New Modification Site data structure
  • Create Modification Clusters
  • PTM cluster best Peptide Match improved: prefer best identification score in case of probability equality

• Quantitation
  • Add the possibility to retrieve XIC chromatograms  (and to view it in Proline Studio features view)
  • Residue Labelling quantification prototype (SILAC)
  • Isobaric Labelling quantification prototype (iTRAC/TMT)
  • Aggregation of Quantitation result
  • Label Free Quantitation
    • Improve signal detection and PSM matching
    • Reinitialize ion abundances to raw abundances at the beginning of the post processing process
    • Track the list of aggregated Peptide ions for Peptide abundances
  • New Compute Post Processing service :
    • Post Processing:  Add “Razor and Specific” peptide selection method
    • Change “discard oxidated peptides” to “discard modified peptides”
    • Refactor post processing parameters
    • “Compute Post Processing” called from Protein Set view must use previous “Compute Post Processing” parameters
• Identification
  • ‘Single PSM Per Query’ filter : uses also delta mass to choose PSM by query
  • Import MaxQuant Error : change query to get peaklist software without version
  • Import: create new Enzyme in database if necessary
  • Generate fragment match : use only neutral loss evidences while reading Mascot NLString
• Export
  • Export MzIdentML: Add PSI CVParam mapping for immonium fragment
  • PTM cluster export added for identification and quantification datasets
  • Quantitation dataset: Add “#Quant. Peptides” column
  • Remove Pride Export: MzIdentML is used for ProteomXchange
  •  
• Bugs fixes

• • Spectra Library
    • Export Spectra Library export also peptides linked to none validated protein sets.
    • Export Spectra Library error when Generate Spectrum match not run : Add explicit message
    • Make sure always the same bestPSM is used in export library. Compare score, deltaMoz then ID
  • Label Free Quantitation
    • Map Alignment error ignores didn’t work
    • Post Processing error when some peptide ions abundances were null.
    • specify default MissCleavedPeptideFilteringMethod if not specified (default = DISCARD_MISS_CLEAVED_FORMS)
    • When cloning identification summary (for quantification for instance) only one sequence match per peptides was cloned
    • Ensure peptide/PSMs count are correct in the different cases:
    • Update peptide match count when aggregating ions.
  • Identification
    • Fixes Protein FDR calculation for RSM Merged dataset: FDR was calculated using hardcoded decoy/target. Change to use SD/or CD calculation in the same way it’s done in validation
    • Shared peptides between decoy and target results now have same properties
    • X!Tandem merge failure: ion series matches and scores are not available during merge, this must be taken into account in the writer
    • Import mzIdent, error in parsing enzyme description
  • Export
    • Master_elution_time column sometime empty after compute post processing
    • Use initial raw_abundance in export (as it is in Studio GUI).
    • Error in exported value #psm_prot_sets for peptide ions.
    • Export #peptide_match, #sequence etc according to protein match (in case it is subset) + rename #peptide_match, #specific_peptide_match to spectral_count, specific_spectral_count
    • subset columns (accession & number) are specific to peptide in Protein Set and not generic to Protein Set
  • PTMs
    • Peptide “readable PTMs” on merged dataset sometimes differ from same peptide in leaves datasets.

Proline Studio

• Implement Memory Management to free unnecessary memory usage. Clean transient data

• Quantitation
  • New Aggregation interface
  • Modify Peptides / Peptide Ions status lookup and the way to invalidate peptides for quantitation.
  • When running quantitation from identification tree, use identification Summary  of the dataset as identification Summary reference even if leaf Dataset
  • Use quant channel names to display columns in XIC tables
  • No quantitation graphic associated to some quant peptides
  • re-enable raw file opening from XIC features view (raw files searched among workingSets)
• PTMs
  • new Compute Post Processing on Abundances service : add modified peptides filtering method option
  • PTM Site view/PTM Cluster views.
    • Remove duplicate peptide instance
    • New displays
  • add PTM graphic representation
    • with selection management + add a “Hide Selection” button on Graphics Panel
    • Add Tooltips;
    • Enable graphic representation on user Windows
    • Re-order clusters/sites columns and hide confidence column by default
    • PTM column info missing if quantitation dataset not expanded…
  • PTM Site for quantitation data
    • add the “FC dist” column to PTM Site table
    • Modify linear plot (quantitation peptide intensity) to show also protein intensity plot
  • PTM Cluster algorithm
  • configure PTM Clustering method name in Studio & take this parameter into account in Server
• Admin/Project view
  • Display of Project associated raw files added
  • Allow user to view tasks logs from server. This service download the requested log file and presents the tasks information in a tasklog table.

• Aggregation & Residue Labelling
  • Allow aggregated and Labelling (isobaric & residue) prototypes
  • “Properties” view was not updated with post processing parameters until Studio was restarted
  • In Display Exp. Design remove quantitation parameters tab. if aggregation quanti
  • Disable “Discard Peptides sharing Peakels” in Compute PostProcessing for Aggregation

• Map Alignment:
  • show selected map’s alignment curve
  • show peptide cloud with the alignment curve
  • add tolerance edge around the alignment curve
  • fixed: can’t view ‘set range’ panel

• Added the possibility to retrieve XIC chromatograms and display it with dashed lines plot
• Add export dataset protein sequence and description in Fasta files.
• Data Analyser:
  • #19983: if more than one group MV Filter only first group was filtered
  • Add power operator to ExpressionBuilder

• Graphic:
  • Parallel Coordinates:
    • improve values selection on axes
    • manage overlay of labels
    • Do not accept horizontal move of columns when selecting a handle.
  • Zoom/Unzoom error in quantitation peptide graph + fix zoom second Y axis
  • Spectrum view:
    • fixes a bug related to z+1 series display
    • Spectrum view updated after calling Generate Spectrum Match for a specific peptide match
• Others
  • Installation: clean cache folder to prevent error if installation directory has changed
  • MsFile: exception occurs when converting raw file without updating it to server side
  • Studio export table: Add description in export from Studio table
  • Display unknown for fasta file in properties if no value defined for current Search Result
  • Export:  RT now in minute
  • adjacency matrix default cell size is now constant
  • Add filter to column “description” in XIC protein set display.
  • Error in query executed when Clear Trash is called

mzScope

• Features

• • Batch extraction & display enhanced
  • TimsTof: allow open timstof data .d directory as “raw file”
  • Add possibility to have centroid spectrum as reference spectrum

• Bugs Fixes

• • do not crash anymore when scan without data are encountered
  • better error message when parsing CSV files fails

Sequence Repository

• When parsing fasta file use description from fasta, not from protein in Proline database, to create SeqDb Databank Protein. Update description if newer fasta with same identification + sequence
• Add query to get Protein attached to a specific databank (using name & revision). This ensure correct sequence is used to retrieve MSI protein properties and bio Sequence
• Add a command line parameter to specify a RSM to update protein sequence for

Version 2.0.1

• Fixes an error (see this Forum Topic) when accessing new project
• Proline-Zero: Improve memory distribution between PostgreSQL, Proline Server and other components.

Version 2.0

WARNING: If you are doing an upgrade from previous version, be aware that  an important Proline database upgrade is needed. It is highly recommended to make a copy of your databases before the upgrade process (see ProlineSuite Installation Guide).

• New feature in Proline Server:
  • Change management on Instrument and Fractionation Rules: now separated
    • Fragmentation rules can be specified when running “Generate Spectrum Matches”
    • Fragmentation rules set should be specified at import
    • Fragmentation rules set can be configured
  •  Export
    • Spectral libraries could be exported into spectronaut or peakview format.
    • mzIdentML export format is now supported
  • LC-MS quantitation
    • Change the parameter management
    • Some enhancement
      • Be more tolerant to LC-MS alignment outliers
      • log warn if landmarks cannot be smoothed
      • Feature mapping method “PEPTIDE_IDENTITY” now takes into account clusterized features
  • Label Free quantitation
    •  allow quantifier based on quantitative data read from third party software: MaxQuant results
  • Bug Fixes
    • Quantitation: error getting run for quantitation datasets. That was causing wrong assignments in cross assignment within group quantitation algorithm
    • Retrieve Sequence error: When cloning Identification Summary, clone also MSI Search (needed in case of quanti on leaf)
    • Import Mascot with invalid PTM classifier
    • Properties error for Search Result created with separated Decoy mode.
• New feature in Proline Proline Admin
  • User management modified. Allowed operation: create, activate, disable, change password.
  • Project management modified. Allowed operation: create, activate, disable, archive, restore.
  • Database management: initialize, check for update, update ….
• New feature in Proline Studio
  • Graphical
    • Changed PTM Site view
    • Add Information in some display (protein description in quantitation view, …)
    • Copy/Paste of html cell supported for “search” or “filter” in display
    • Show the Merge Mode used when creating merged dataset: union or aggregation
    • PTM display on peptide sequences was missing in some views
    • drag’n’drop from All imported panel takes filters into account fixes
    • Bug fix on filters mapping for join
    • Fixes som bugs in Venn diagram graphics
  • Algorithm
    • Import duration bug (wrong value was displayed)
    • Add validation filter on #C13 (isotope offset)
    • Fix bug in validation with propagate: dataset tree wasn’t refreshed
    • Allow Generate Spectrum Matches even if already defined
  • Admin
    • Fragmentation rules set can be configured in Admin view
    • New view in admin dialog: list of projects/Databases/Databases Size with possibility to filter and export
    • None admin user can see admin info (not modify !)
  •  MzScope
    • a spectrum can now be made ‘persistent’ in the display to be visually compared with current spectrum
    • bug in mzDB QC metrics calculation corrected
    • Display options enhanced
    • Set min/max RT for extracted chromatograms to run duration
    • Bug fix for batch extraction
    • import any CSV file for batch extraction
    • enhanced zoom synchronization
  • LC-MS Quantitation
    • Map alignment display problem fixed
    • show reference dataset in experimental design
• New feature in Proline Zero
  •  Enhanced launcher, now compatible with Windows and Linux

Version 1.6

• New features in Proline Server:
  • Ptm sites identification for identification and merged RSM
  • Improve search result import performance
  • LC-MS quantitation
    • user can choose to not cross align features between groups.
    • user can choose to retain only reliable cross aligned features.
    • Generated quantitation datasets list also subset proteins.
  • Validation
    • Add mudPIT score for protein sets scoring type
    • Allow user to propagate validation parameters from parent to child datasets
  • Export Pride: fixes connection to solve server problem and peptide with ‘X’ in sequence correctly exported
  • Allow SC on merged Search Result if a Validation with propagate on child has been run.
  • Generate sprectrum matches (annotation of spectra): now generates “z+1″ and “z+2″ ion series depending on the instrument config

• New features in Proline Studio 1.6.1:
  • Export Pride needed new JRE to connect to ebi site
• New features in Proline Studio 1.6:
  • Parallel Coordinates first version
  • DataAnalyzer
    • Allow multiples joins
    • Venn diagram available
    • Added adjustP column to Compute FDR Function
  • MsFile
    • Raw to mzDB conversion accessible
    • Upload mzDB files on server side (necessary for LCMS Quantitation)
    • Download of mzDB files from server locally
    • Add Working sets containing set of mzDB files to work on
  • MzScope
    • mzScope module enhanced: better isotopic prediction – MSData in profile mode display
    • First implementation of id free QC metrics
    • Display mzDB file properties (converter version, acquisition date, format version, acquisition mode, data encoding)

• Changes in Proline Web eXtension:
  • MS-Angel
    • New features
      • Integration of the SearchGUI tool
      • Support the import of Comet results in Proline (through the creation of mzIdentML with IdConvert)
      • Support default peak picking with MsConvert
      • New panel allowing to design quantitation ratios and post-processing configuration
    • Improvements
      • GUI: better configuration checks and errors display
    • Fixes
      • Fix files monitoring errors (more tolerant, won’t affect the other tasks)
      • Fix many bugs in GUI and task execution
  • Dataset Explorer
    • New features
      • Link favorite proteins and peptides to volcano plots
      • Add identification/quantitation folders to projects tree
      • React to peptide/peptide ion selection(/deselection) in dataset/in protein
      •  Integration of Lorikeet viewer
    • Improvements
      • Add and re-organize columns in all identification tables
      • Check ratios validity when updating the experimental design
      • Improve tree items manipulation (re-ordering)
    • Fixes
      • Fix link to Uniprot
      • Minor display fixes
  • SpecLight
    • Improve the speed of XICs display and resize
    • Fix some visualization bugs
  • Heatmaps
    • Add module to PWX as a new app, accessible via Proline Web interface
    • Export data as TSV format
    • Add charts for quantitative profiles display
    • Re-arrange main layout
  • Raw File Explorer
    • Externalize view as an application accessible via the Proline Web home page

Version 1.5

• LC-MS quantitation performance optimization and enhancement: lower memory consumption and faster quantitation processing
• Export enhancement
  • Several bugs fixed (order of columns, MW&coverage, fix the computation of #PSMs/#Specific PSMs/#Sequences, support of decimals with comma separator)
  • Quantitative exports: keep sample order (same as specified in GUI)
  • Add some new columns: samesets/subsets accessions, gene name, PTM location on protein, number of observable peptides, observed m/z and corrected RT of each quantified ion.
• Short services are treated separately. This prevent waiting fot connection, server browsing… when server is busy.
• Determination of spectrum retention time
  • Update Spectrum using new Peaklist software: fixes issues in order to get RTInSeconds if no value found for Time
  • Fix a bug: RTINSECONDS was not taken into account when its value was zero

New features in Studio:

• Add Folder in quantitation and identification tree
• XIC dialog bug fixes and enhancement and separate simple vs advanced parameters
• Ability to cancel server running tasks
• DataAnalyzer
  • import CSV: automatic detection of the separator, preview of the file parsing, bug fixes when loading data from CSV
  • Enhancements for ProStar Macro: Graphical Selection of Thresholds, possibility to show Differential Proteins
  • New algorithm for Diff/join: possibility to have 2 keys and one of the keys can be a double value with tolerance.
• Add Admin features (add/modify user; peaklist software…)
• Raw/MzDB: Convert and/or upload on Server side
• Bug fixes for Adjacency Matrices: memory problems, tasks not stopped
• Observable Peptides column for validated proteins (need to potentially retrieve protein sequences)

New features in Web:

• Set/Unset favorites in batch from table content (using table filters)
• Clone a quantitation: open pre-filled form to launch a new quantitation
• Utilities to copy all tables
• Vizualize the parameters used for LFQ and post-processing
• Fix user creation
• Add organization folders in quantitation tree
• Some enhancements in SpecLight XIC visualization

New features in MS-Angel:

• Improve panel for input files
• Add many checks for workflow validity, previous to task launching
• Improve/fix task cancellation

New features in mzDB-Wizard:

• New two-step opening dialog. In step 2 we can now select an existing mounting point based on the server selection done on step 1.
• Possibility to restart failed task.
• Check for corrupted files before running actions.
• Add MGF export from mzDB files.
• Task Manager: sorting is now possible ans more tasks’ details displayed.
• User Interface changed ti be more user friendly
• Documentation is accessible inside the application.
• Logs: in GUI now contain date & time; Refined all messages and changed logfile names

Version 1.4

• New global features (on server):
  • Quantitation Refine: new Abundance Summarizer method, Median Ratio Fitting
  • Filter: add Protein Set score filter
  • Export
    • Quantitation export: elution time and peptide number was wrong
    • Export Pride: explicit error when spectra are missing
  • Spectral Count: Fix error when parent identification summary was added in list of identification summaries to calculate SC for
• New features in Studio:
  • Add a “General Settings” windows
  • Ability to view also Server Tasks Logs and to cancel user pending tasks
  • XIC Quantitation
    • experimental design: Drop Zone to automatically associated mzDB files to Identification Summaries
    • result could be refined by selecting/unselecting quantified peptides
  • New Data Analyzer, finished first integration of DAPAR (ProStar)
  • Navigation facility: added a popup option in all data tables to display complementary information. (Like adjacency matrix for a Protein, Identification data for XIC Protein Set…)
  • Enhanced Adjacency matrices: added selection of Proteins/Peptides
  • Export: change default value for ProteinSet list to export: Only validated by default
• New features in Web:
  • Add a system for favorite entities
  • Add a tool to change sample names in batch using copy/paste from an Excel table
  • Add a tool to create a dataset on 2 or 3 levels using copy/paste from an Excel table
  • Improve information on quantitation result graphics (tooltips)
  • Add tables in quantitation viewers, replacing the protein set grouping system
  • Selection/deselection of a peptide at protein/dataset level
  • Ease the creation of the experimental design (improve drag and drop, display sample name)
  • Fix some display bugs, in particular toward tables rows filtering
• About 50 issues closed…
• New Tools are available in this Release
  • mzDB-Wizard: this tool allow user to easily convert raw files to mzDB (for XIC quantitation) and upload them on server side
  • MS-Angel: Provide a complex workflow, complete data visualization, real time monitoring, submission to many search engines (Mascot, OMSSA, X! Tandem: in progress).

Version 1.3

• New global features (on server):
  • Algorithm and other operation
    • Faster datasets export
    • New service to clean up a project: remove unused identification data (Search Results or Identification Summaries put to trash or no more accessible to user, after re-validation for example)
    • New Quantitation Post-Processing options
    • Import MzIdentML result file
• New features in Studio:
  • Allow to run “XIC” from a merged dataset. The identification summary associated to the dataset will be used as parent identification summary of quantified identification summaries.
  • XIC – experimental design: Change view to associate mzDB files to dataset
  • Simplify Mascot specific parameter in import
  • Integration of R package DAPAR (also interfaced with ProStaR)
• About 40 issues closed…

Version 1.2

• New global features (on server):
  • Algorithm and other operation
    • Fragment Match Generator for XTandem result.
    • FDR change: Use TD competition if rank filtering is used
    • XIC Enhancement
• New features in Studio:
  • Menus’ reorganization (Identification and Quantitation)
  • New display of MsQueries (for a Search Result or an Identification Summary)
  • XIC: New display of experimental design and XIC parameters
  • XIC: New display of alignment map and calculating of predicted elution time
  • MzScope (mzDB file viewer) convert into MGF files, display of multi raw files, LC-MS map viewer
  • Allow Fragment Match Generator to be called from both Identification & Quantitation Trees
  • Add spectra Library generation
• New features in Web:
  • Customizable export of identification and quantification datatsets
  • Enhancement of quantification results visualization
  • Integration of Spectlight, a 3D web-viewer of mzDB files to manually check a peptide environment and its XICs over all input files
• About 150 issues closed…

Version 1.1

• New global features (on server):
  • Algorithm and other operation
    • Spectral Count algorithm modification: Spectral Count Weigth is based on specific PSM count instead of specific peptide count.
    • ProteinSets filtering (independently of validation)
  • Save, import and export ◦Export to PRIDE format
    • Support import of X!Tandem result file
• New features in Studio:
  • Algorithm and other operation
    • Enhancement of data mixer: module to easily do calculations/comparisons on data.
    • Integration of a calculator: it lets you write python scripts to manipulate freely viewed data.
    • Add interface for ProteinSets filtering
  • Save, import and export
    • Customizable export of Identification dataset, or Spectral Count or XIC
    • Add interface for Export to PRIDE format
    • Add interface for import of X!Tandem result file
  • Display
    • Display MzDB Files through mzScope module (directly in Studio)
    • Enhancement of the XIC display and Spectral Count display
• New features in Web:
  • New & improved Interface !
  • New data and chart visualizations for quantitation stats