ProteinCenter User Manual
Table of Contents

Chapter 30. Version History for ProteinCenter

Table of Contents

30.1. Updates in ProteinCenter 3.15
30.2. Updates in ProteinCenter 3.14
30.3. Updates in ProteinCenter 3.13
30.4. Updates in ProteinCenter 3.12
30.5. Updates in ProteinCenter 3.11
30.6. Updates in ProteinCenter 3.10
30.7. Updates in ProteinCenter 3.9
30.8. Updates in ProteinCenter 3.8
30.9. Updates in ProteinCenter 3.7
30.10. Updates in ProteinCenter 3.6
30.11. Updates in ProteinCenter 3.5
30.12. Updates in ProteinCenter 3.4
30.13. Updates in ProteinCenter 3.3
30.14. Updates in ProteinCenter 3.2
30.15. Updates in ProteinCenter 3.1
30.16. Updates in ProteinCenter 3.0
30.17. Updates in ProteinCenter 2.8
30.18. Updates in ProteinCenter 2.7
30.19. Updates in ProteinCenter 2.6
30.20. Updates in ProteinCenter 2.5
30.21. Updates in ProteinCenter 2.2
30.22. Updates in ProteinCenter 2.0
30.23. Updates in ProteinCenter 1.4
30.24. Updates in ProteinCenter 1.3
30.25. Updates in ProteinCenter 1.2
30.26. Updates in ProteinCenter 1.1

These sections list the changes and additions made between consecutive ProteinCenter releases. Users familiar with earlier versions of ProteinCenter can get a quick overview of new features and changes to existing features here.

30.1. Updates in ProteinCenter 3.15

  • ProteinCard has a link to PROTTTER.

  • Reference data sets are no longer limited to a predefined set of taxonomies/sources.

  • Improved comparison clustering speed.

30.2. Updates in ProteinCenter 3.14

  • Incorporated Wiki Pathway data (www.wikipathways.org).

30.3. Updates in ProteinCenter 3.13

  • Information on monoisotopic and average protein masses is now available throughout the application: Proteins View, Protein data View, ProteinCard, Export. The mass derived columns are not on the views by default, as it can be rather expensive memory-wise to complete all the sequences, but these columns can be activated by clicking right mouse over the columns or view, and selecting the columns you want. The masses on the Protein data view also includes any modifications to the peptides of any protein data, while the masses on the Proteins view are without any modifications. On the ProteinCard they are included in the Sequence detail section (click the blue sequence header). Export page let you output your masses for both proteins and protein data.

  • New lookup enables searching for all proteins with a particular taxonomy in the database (see Section 7.4, “Lookup by annotation”).

30.4. Updates in ProteinCenter 3.12

  • It is now possible to select proteins in the similar proteins detail section of the ProteinCard. The selected proteins can then subsequently be turned into a new dataset or used as selection throughout the application tools.

  • We have adopted the newest Blast executables (BLAST+) for improved sequence similarity and sequence alignment execution.

30.5. Updates in ProteinCenter 3.11

  • All CSV importers now support limiting input on taxonomy, i.e. each CSV line can specify a required species (see Section 21.2.5, “Taxonomy limitation”).

  • Importers now have support for attaching generic supplementary data to peptides: GI#, GD#, GS# and L# (see ). Furthermore, the number of generic supplementary data of any type for both proteins and peptides has been extended to 9, i.e. allowed values for the # above are in the range 1-9 (used to be 1-3).

  • The application will now automatically update itself whenever a new version is released (see Section 32.4, “Update”).

30.6. Updates in ProteinCenter 3.10

30.7. Updates in ProteinCenter 3.9

  • By far the biggest change in this version of ProteinCenter is a complete (Tapestry 5) rewrite of the user interface. This has benefitted the application in terms of responsiveness, UI updating (Ajax), and general look and feel.

  • The StatisticsCard has been redesigned to present better and more specific overview and detail sections, and the Gene Ontology statistics have been increased and split into several sections.

  • Interaction exporter now supports limiting output on (STRING) interaction scores (see Section 23.2.6, “Protein interactions format”).

30.8. Updates in ProteinCenter 3.8

30.9. Updates in ProteinCenter 3.7

30.10. Updates in ProteinCenter 3.6

30.11. Updates in ProteinCenter 3.5

  • New lookup enables searching for all proteins in the database with a particular annotation: GO, Enzyme Code, KEGG pathway, PFAM and InterPro domains (see Section 7.4, “Lookup by annotation”).

  • The possibility to filter on GO sources and GO evidence codes has been added to experimental, proteins and clusters view (see Section 11.3.17, “GO Source”).

  • Peptide view has been optimized for much faster load of large datasets.

30.12. Updates in ProteinCenter 3.4

30.13. Updates in ProteinCenter 3.3

  • The Similar Proteins button on the ProteinCard now causes the shown protein to be blasted against the whole ProteinCenter sequence database. This offers better results at the expense of longer run time spent by running the BLAST job, compared to the previous method where a precalculated grouping only offered approximate results.

  • ProtXML-based data importers now support quantitation data from LIBRA, ASAPRatio and ASAPRatio_pvalue analysis results.

  • KEGG pathway maps can now visualize quantitation by coloring its contained elements (see Section 18.1, “Quantitation coloring of KEGG pathway maps”). This is achieved by clicking the appropriate KEGG pathway and supplementary data cell on heat maps, and uses the same value transformation and color coding.

  • Chromosome information has been added to descriptive and significance statistics. Is is also possible to use chromosomes as an aggregation level on profiling and heat maps.

  • Clicking proteins, peptides, clusters, chromosomes or annotation catgories on heat map rows will bring up a filtered view, showing the proteins/peptides/clusters with the corresponding heat map row annotation.

  • Profiling, heat mapping and statistics can now be performed on either entire datasets, or on selected proteins only.

  • The data source CMR has been added as a primary data source, together with the sequences and accessions from the Comprehensive Microbial Resource project (see CMR data source). Pseudomonas Genome database has been upgraded from a secondary to a primary data source, and can now be used in the accession preference order.

  • Many new reference statistics sets have been added for significance analyzes: New database sources include Ensembl, NCBI (GI), TubercuList and CMR (Comprehensive Microbial Resource). Four merged HUPO project datasets have also been added: HUPO Brain, HUPO Liver, HUPO Plasma and HUPO Urinary Proteome project.

  • Direct CSV export added to heatmap view.

30.14. Updates in ProteinCenter 3.2

  • A new page allows for a heat map view of quantitative data, or any type of supplementary data. The color coded values can be displayed for proteins, genes, clusters and peptides, as well as aggregated on annotation categories: GO Slim and GO terms (with and without more general terms), KEGG and UniProt pathways, enzyme codes (with and without more general terms), PFAM and InterPro domains, as well as diseases and keywords. For details on how to use this new feature, see Chapter 18, Heat Maps view.

  • Profiling can now also be carried out on annotation categories: GO Slim and GO terms (with and without more general terms), KEGG and UniProt pathways, enzyme codes (with and without more general terms), PFAM and InterPro domains, as well as diseases and keywords. This enables the analyst to identify e.g. which KEGG pathways or GO terms that share the same quantitative expression and hence could be involved in related processes. Links from the resulting annotation groups to the annotated proteins are provided. See Chapter 17, Profiling View.

  • Support for 3 new types of protXML-based data import: Section 21.4.1.1, “ProteinProphet and iProphet protXML” (Trans-Proteomic Pipeline), Section 21.4.1.1, “ProteinProphet and iProphet protXML” (Trans-Proteomic Pipeline), and Section 21.4.1.2, “Proteome Discoverer protXML” (Thermo Scientific).

  • The data source TBLIST has been added as a primary data source, together with the sequences and accessions from the TubercuList project (see TubercuList data source).

  • CSV export of significance statistics (over- and under-representation) available directly on the tables in statistics page.

  • Peptide modifications on n- and c-terminals are now supported throughout ProteinCenter, and can be imported with all input formats containing this information (e.g. Mascot and CSV files).

  • 5 new types of protein identification data, and 4 new types of peptide identification data. These more detailed supplementary data types supercede the previous generic protein and peptide probabilities in certain importers (e.g. Mascot scores). See Appendix B, Supplementary Data.

  • Many new updates to the data importers:

30.15. Updates in ProteinCenter 3.1

30.16. Updates in ProteinCenter 3.0

  • More data formats supported - ProteinCenter 3.0 supports more data import formats making it easier to get data from other applications into ProteinCenter:

  • Peptides view - A separate view for working with peptide data including sorting and filtering has been added. See Chapter 12, Peptides view.

  • Increased support for quantitative data - Data from user-defined quantitative methods can now be imported from Mascot XML.

  • Advanced export options - Per-column selection avoids unwanted data and results in better performance.

30.17. Updates in ProteinCenter 2.8

  • Profiling now also includes grouping by quantitative data on the peptide level and also across datasets in a comparison. See Chapter 17, Profiling View.

  • A page displaying basic protein sequence and annotation counts for current data release can be opened from the about box. See Section 5.4.2.2, “About”.

  • An "Empty recycle bin" clean-up procedure can be executed from the μLIMS page.

30.18. Updates in ProteinCenter 2.7

30.19. Updates in ProteinCenter 2.6

30.20. Updates in ProteinCenter 2.5

30.21. Updates in ProteinCenter 2.2

  • Batch import - The cumbersome one-file-at-a-time import is no longer required, instead you can add a number of files to the upload queue. See Section 21.1, “How to import data” for more details.

  • PlasmoDB data included - Sequences, protein identifications and descriptions from The Plasmodium Genome Resource (ref_plasmodb) have been included starting from PlasmoDB 5.5.

30.22. Updates in ProteinCenter 2.0

  • Reference statistics - ProteinCenter now includes a number of reference datasets for which statistics have been pre-calculated. These datasets can be for comparative statistics. See Section 25.4, “How to calculate statistics” for more details.

  • Access control on datasets - ProteinCenter 2.0 introduces a mechanism for controlling access to datasets. For example, certain datasets can be set as 'read-only' for some users while other uses will have permissions to change the dataset. For more information about the different permission and how to set them on datasets and categories. See Section 22.2, “Permissions”.

  • Recycle bin - A recycle bin has been included. When deleting a dataset it is now moved to a recycle bin, from which it can be restored or deleted permanently.

  • Peptide export - A new peptide-centric export type has been added, which outputs modified peptides, their protein relations, along with peptide-specific supplementary data (pI, GRAVY, ScorePlusMS3, iTRAQs, SILACs). See Table 23.4, “Data description for peptide-centric CSV export format”.

  • Automatic software update - ProteinCenter 2.0 includes a feature which allows future software updates to be installed simply by clicking a button. See Section 32.4, “Update”.

  • Improved filtering on peptide modifications - It is now not only possible to filter for certain types of peptide modifications, but also to specify the amino acid they modify.

  • Performance improvements - A number of performance enhancing initiatives have been implemented.

30.23. Updates in ProteinCenter 1.4

  • Scaffold import - data from Scaffold can be imported into ProteinCenter as Scaffold protXML files. See Section 21.4.1.3, “Scaffold protXML” for more information

  • Predicted isoelectric point and the GRAVY hydro are calculated for all peptide sequences. EmPAI score is calculated for each imported protein. These values are displayed in the Experimental data view. See Chapter 13, Protein data view for more information. Please note that since these values are calculated during import, they will not be contained in datasets imported in earlier versions of ProteinCenter. Filters have been added for these values as well.

  • Extended exporting facilities (see Chapter 23, Export):

    • The output data can now be limited to include only the cluster anchors, only the selected data, or both limitations in combination.

    • Two new types of CSV exports have been added, which export either on the experimental data or on the protein level (aggregated as lists of unique items).

    • Numeric supplementary data are given with descriptive statistics: mean, standard deviation, minimum, and maximum.

    • For comparison datasets, the descriptive statistics for each numeric supplementary data are specified per dataset to facilitate detailed comparison.

  • 'Indistinguishable Proteins' clustering now considers possible peptides, i.e. (unmodified) peptide sequences that are identified on other proteins, to which they were not assigned.

  • GO cellular components are now also illustrated on a cell image. See Chapter 25, Statistics for more information.

30.24. Updates in ProteinCenter 1.3

  • Gene symbol lookup - The lookup functionality has been expanded to include protein lookup based on gene symbols. See Section 7.3, “Lookup by gene symbol” for details.

  • Peptide view - Sub-view to the experimental data view. See Chapter 13, Protein data view for details.

  • New data sources - ProteinCenter 1.3 provides additional data compared to version 1.2:

    • FlyBase data included - Sequences, protein identifications, descriptions and gene symbols from the FlyBase database (ref_flybase) of the Drosophila genome have been included.

    • TAIR data included - Sequences, protein identifications and descriptions from The Arabidopsis Information Resource (ref_tair) have been included.

  • More data formats supported - ProteinCenter 1.3 supports two more data import formats making it easier to get data from other applications into the application. Also, peptides that do not match the protein sequence are reported:

    • MSQuant import - data from MSQuant can be imported into ProteinCenter. See Section 21.5.1, “MSQuant” for more information

    • X! Tandem import - results from the X! Tandem search engine can now be imported into ProteinCenter. See Section 21.4.3, “X! Tandem XML” for more information

    • Mascot import - quantitative data (iTRAQ & SILAC) is now also imported.

  • Additional statistics are calculated:

    • Venn diagrams showing overlap between proteins in compared datasets.

    • Significance of GO annotation in compared datasets.

30.25. Updates in ProteinCenter 1.2

  • Alignment viewer - An alignment viewer for the protein sequences in a cluster have been included. See Chapter 20, The Alignment Viewer for details.

  • The import functionality has changed such that users can now specify the location of the datasets they are importing. Details are described in Section 21.1, “How to import data”. In addition support for a number of data formats makes it significantly easier to import data from other applications into ProteinCenter:

    In addition a pane has been added which allows users to supply additional information about the datasets they have imported. See Chapter 22, μLIMS for more information.

  • Improved statistics - Statistics are calculated for numerical supplementary data. See Section 25.2.2.3, “Binned histograms and descriptive statistics” for details.

  • More filters - Filters working on PFAM keys and gene symbols have been included. See Chapter 11, Filters for details.

  • New data sources - ProteinCenter 1.2 provides additional data compared to version 1.1:

    • SGD data included - Sequences, protein identifications and descriptions from the Saccharomyces Genome Database (ref_sgd) have been included.

    • MIPS protein data included - Protein protein interactions from The MIPS Mammalian Protein-Protein Interaction Database (ref_mips) have been included.

30.26. Updates in ProteinCenter 1.1

  • Statistics - a module called Statistics have been added to the navigation menu. It can be found by selecting the Statistics pane and contains summary and statistics about one or more datasets. For more information about Statistics see Chapter 25, Statistics.

  • Graphical protein overview - a graphical overview of the protein including mapping of peptides with known modifications, PFAM domains, InterPro domains, etc. More info in Chapter 10, The ProteinCard.

  • Peptide support - From version 1.1 ProteinCenter includes peptide support.

    • It is now possible to import peptides along with the proteins in both the CSV format and the protXML format supported from this version.

    • Peptides are mapped on the protein sequences and displayed in the new graphical overview in the ProteinCard.

    • Peptide clustering groups proteins that share peptides in the experimental data. This gives a better overview of the protein content, by grouping similar isoforms or indistinguishable proteins from the peptide evidence. The clustering algorithm can create more or less cohesive groups by changing how many peptides proteins must share to be grouped. See Section 16.3.2, “Clustering based on peptide sharing” for more information on the peptide clustering.

    • Peptide modifications are stored and can be viewed in the ProteinCard.

    • Peptides are included in the CSV export.

  • Changed data loading patterns - In ProteinCenter 1.0 the entire dataset was loaded when a data folder was selected. In ProteinCenter 1.1 the loading of the data is deferred to time where it is actually needed in the interface. This has reduced the initial loading times significantly.

  • protXML import - protXML files from the TransProteomic Pipeline can now be imported directly into the system. See Section 21.4.1, “ProtXML”.

  • PRIDE import - PRIDE files from the PRoteomics IDEntification database can now be imported directly into the system. See Section 21.4.4, “PRIDE XML”.

  • FASTA export - From version 1.1 it is possible to export lists of proteins in the FASTA format. See Section 23.2.5, “Protein FASTA format” for details about the FASTA export.

  • Ensembl records promoted to primary source - In ProteinCenter 1.0 Ensembl keys where secondary keys. In ProteinCenter 1.1 they have been promoted to primary keys.

  • Gramene data included - Go annotation from the Gramene database (ref_gramene) have been included.