ProteinCenter User Manual
Table of Contents

Chapter 1. Getting Started

Table of Contents

1.1. Login
1.2. Looking up a protein
1.3. Protein neighbors
1.4. Looking up a peptide
1.5. Selecting, saving and deleting within a dataset
1.6. Import a dataset and view experimental data, proteins and groups
1.6.1. Import a dataset
1.6.2. View a dataset in the Protein Data view
1.6.3. View a dataset in the Proteins view
1.6.4. View a dataset in the Clusters view
1.7. Filters
1.8. Reports
1.9. Comparison of datasets
1.10. Context-sensitive online help

This chapter contains a simple tutorial introduction to ProteinCenter.

Several guided examples provide an introduction to the core functionalities of the system in approximately half an hour. The most basic functionality is explained, while details on the different functions can be found in the various chapters of this user manual.

These 10 examples will address:

  1. Login

  2. Looking up a protein and view details in the ProteinCard

  3. Protein neighbors

  4. Looking up a peptide

  5. Selecting, saving and deleting within a dataset

  6. Import a dataset and view it in the data views for

    • Experimental data

    • Proteins

    • Clusters (groups of proteins)

  7. Filters

  8. Reports

  9. Comparison of datasets

  10. Context-sensitive online help

(For installation of the system, please refer to Chapter 31, Installation)

1.1. Login

First, connect to ProteinCenter through a web browser (Internet Explorer or Firefox) using an URL provided by your administrator, and log in using your username and password that has likewise been supplied by your administrator.

Figure 1.1. Login menu

Login menu

  1. Enter you user ID

  2. Enter your password

  3. Press Login

Once logged in the system greets you by the "welcome [User ID]" message, just below the ProteinCenter icon in the upper left corner.

(Details can be found in Chapter 6, Login).

1.2. Looking up a protein

  1. Upon login, the Lookup can be accessed in the left part of the interface. Click the pane with the binoculars.

  2. In the Lookup pane find the text box for entering an accession key.

  3. Type the accession key P13073 into the box (or any of your favourite protein accession codes, GIs or other protein identifier from any of the databases: GenBank, RefSeq, UniProt (Swiss-prot, Trembl), SGD, TAIR, FlyBase, PIR, PDB, Ensembl TPG, TPE, PRF, EMBL, Dbj. )

  4. Press Search

  5. The result view is shown to the right with information about the function, subcellular localization and much more. Note that the system might show another accession key than the one entered. ProteinCenter allows users to define the precedence of different types of accession keys. Depending on your settings, you might see a GI accession referring to the same protein instead of the SwissProt accession key entered in the example. For details on setting the prefered type of accession keys see Section 4.3, “Preferred accession”

  6. Click the accession key link (P13073) to view the ProteinCard with detailed information about the protein, including the graphical representation of the sequence features.

  7. Each of the blue headers of the information frames in the ProteinCard may be clicked to obtain more detailed information. In the figure the Keys header is selected, so the all primary accession keys for this protein is displayed along with the protein descriptions.

(Further details about the lookup functionality can be found in Chapter 7, The Lookup).

1.3. Protein neighbors

An overview of close protein neighbors (based on sequence similarity) is available by a single click. Notice that it may take some minutes to run the BLAST job.

  1. In the ProteinCard, click the Similar proteins pane (1)

  2. This provides a list of protein neighbors (down to 60% sequence similarity) annotated like proteins in the lookup results. In addition, information on percent similarity to the query protein is available.

  3. By clicking on a pct sim link (3), a BLAST alignment to the query protein is shown in a separate window (4):

(Details on the information found in the ProteinCard can be found in Chapter 10, The ProteinCard).

1.4. Looking up a peptide

In Section 1.2, “Looking up a protein”, accession codes were used to lookup proteins. Tryptic peptides can also be used to lookup proteins:

  1. In the Lookup pane find the text box for entering a Tryptic Peptide List.

  2. Type in a peptide (For example: YWTAFAGILK )

  3. Press Search

  4. The result view is shown to the right with information about the function, subcellular localization etc. of all proteins with this tryptic peptide:

Note: If you are still on the ProteinCard view, you will see the ProteinCard for the first protein in the list. Choose the Proteins view to see the list of proteins.

It is also possible to submit a list of peptides - for example:MTSQSR, YWTAFAGILK. All punctuation characters and whitespace can be used as delimiters.

Only proteins containing all of the given tryptic peptides will be returned.

To make more advanced lookups try combining with the filters described in Section 1.7, “Filters” below.

(Details can be found in Chapter 7, The Lookup).

1.5. Selecting, saving and deleting within a dataset

Within a dataset (resulting from a lookup or chosen from the workspace), it is possible to delete or select individual proteins. Moreover it is possible to save data to a new folder - rather than overwriting the original dataset.

  1. Save as - Save the selected data to a new folder

  2. Delete - Delete proteins selected with the checkbox

  3. Check all - Selects all proteins in the current dataset (excluding those that have been filtered out)

  4. Uncheck all - Unselects all proteins in the current dataset (excluding those that have been filtered out)

The colors in the figure reflects the fact that no proteins have been selected (checked). Hence buttons 1,2 and 4 have been disabled. If one or more proteins have been selected these buttons will be enabled and the colors will change as showed below

1.6. Import a dataset and view experimental data, proteins and groups

The import functionality enables the users to get their own protein data into the system. In this example a small dataset is imported and the dataset viewed in the Proteins view and in the Clusters view where similar proteins can be grouped together.

First, an input file must be created. Copy the following four lines into a text file and save it (the numbers are GIs, i.e., protein accession keys from NCBI).

Key
24586663
61212997
55638781

In a text editor the file should look like this. (If using Word or Excel remember to save in txt format).

1.6.1. Import a dataset

Figure 1.2. Import pane

Import pane

To import the dataset into ProteinCenter do the following

  1. In the Workspace select a destination category (blue folder like icon) for the dataset.

  2. In the right menu bar select the Import view.

  3. Select CSV (Comma Separated Values) in the Format dropdown box.

  4. Click Browse to bring up the file browser and select the newly created input file.

  5. Press Import to start the import.

  6. Select the imported dataset.

  7. Once selected, the µLIMS page, containing import information, will be displayed:

    It lists the number of records parsed, the number of proteins found, etc. In this case there were three records each containing a protein. Since the number of unique proteins is also three, the imported dataset was not redundant. The number of rejected records is simply the number of records which ProteinCenter, for whatever reason, cannot use. The number of records that do not comply with the CSV format is also shown.

(More details about importing data into ProteinCenter can be found in Chapter 21, Import).

1.6.2. View a dataset in the Protein Data view

The protein data view displays the data that was imported. This may include a number of experimental measurements (e.g. quantitation, peptides, probabilities) or it can be a simple list of accession keys as in this example.

  1. Select the Protein Data pane

  2. The experimental data is displayed with one line per experimental measurement

  3. A number of columns include imported experimental data and links back to e.g. LIMS system (but in this example none was imported with the accession keys)

  4. Checkboxes for selecting proteins.

  5. At the bottom of this and the subsequent data view is a menu bar for saving dataset to a new folder, saving dataset changes, deleting selected proteins, selecting proteins, un-seleting proteins as described in Section 1.5, “Selecting, saving and deleting within a dataset”

(More details can be found in Chapter 13, Protein data view).

1.6.3. View a dataset in the Proteins view

The Proteins view summarizes experimental measurements for each protein, so that each line corresponds to one protein.

  1. Select the Proteins view.

  2. Each line corresponds to one protein (i.e. one specific protein sequence).

  3. The No column shows the number of experimental data points for the particular protein and can be clicked to see the experimental data for that protein. Click the number again to hide the experimental data.

  4. A number of columns provide information related to the biology of the protein, including subcellular components, molecular function, signal peptide etc.

(More details can be found in Chapter 14, Proteins view).

1.6.4. View a dataset in the Clusters view

In this example the dataset of three proteins from Section 1.6, “Import a dataset and view experimental data, proteins and groups” is clustered at 98% sequence similarity grouping two alleles of the same protein.

  1. Select the Clusters view

  2. Click the cluster all data button

  3. Each line corresponds to a cluster of proteins - in this case we have two clusters. One cluster with one protein and one cluster with two proteins. The number of proteins in the cluster is displayed in the No column

  4. In the Clusters view the annotation is a summary for all members in the cluster

  5. Click the number '2' in the No column for the cluster that has two members to display details. (Details will disappear when clicked again)

  6. The details (protein view) for the cluster is displayed below

  7. The sequence similarity between the anchor protein and the individual members of the cluster is shown - here it is clearly two different alleles of the same protein. Clicking the sim link will display a BLAST alignment.

The clustering can be used to remove redundancy, speed up functional analysis of large datasets and for very powerful comparison of different datasets where one allele is seen in one dataset and another allele in the other.

(More details can be found in Chapter 16, Clusters View).

1.7. Filters

In this example we see how filters can be applied to focus on specific parts of a dataset. This enables the user to focus on the relevant parts of a dataset that may often consist of many proteins. Moreover the filters enable a lot of different specialized data analysis workflows.

  1. Select the example dataset that was imported in Section 1.6, “Import a dataset and view experimental data, proteins and groups”

  2. Select the Proteins view

  3. Click the Edit filter definitions button. A filter pane will appear.

  4. Select 'GO Slim - Cellular Component' in the filter drop down and click reset button to see the values for this dataset. Delete all values in the box except membrane and nucleus

  5. Click the Save and select filter part button

  6. The filter is now on by default (green filterbutton) and the result is shown immediately .

  7. Of the three proteins only the two annotated having cellular components membrane or nucleus are shown

  8. Click the Negated filter button to see all the entry that is not annotated with either membrane or nucleus (the filter icon turns yellow)

  9. Filters can be disabled by clicking the rightmost filter button. This action will return the complete unfiltered dataset.

It is possible to do much more advanced filtering by combining different filters.

(More details can be found in Chapter 11, Filters).

1.8. Reports

The reporting modules allows for creation of printable summary reports as well as detailed reports with list of proteins.

  1. After selection of a dataset (and possibly application of filters, clustering and comparisons), go to the report pane in the navigation menu

  2. A status message of the selected proteins is given

  3. Choose report type. Currently six are available:

    • Proteins - a summary view for each protein

    • GO Slim - a summary view of gene ontology for the chosen dataset

    • GO Slim Cellular Component - a summary view of gene ontology for the chosen dataset limited to the Cellular Component category

    • GO Slim Biological Process - a summary view of gene ontology for the chosen dataset limited to the Biological Process category

    • GO Slim Molecular Function - a summary view of gene ontology for the chosen dataset limited to the Molecular Function category

    • General Info - information on the dataset: path and owner of the dataset, size of the dataset, import type, version identification of the protein database and application version

  4. Choose report format

    • Currently only PDF - Portable Document Format is available

  5. Shows the resulting name of the report file.

  6. Choose rows

    • selected - only includes proteins that has been selected (e.g. after filtering)

    • All - includes all proteins from the datasets)

  7. An optional info page can be included in the generated report.

  8. Click Report to create the report

More details can be found in Chapter 24, Reports.

1.9. Comparison of datasets

In this example we will create a second dataset and compare it to the dataset imported in Section 1.6, “Import a dataset and view experimental data, proteins and groups”.

  1. Select the example dataset that was imported in Section 1.6, “Import a dataset and view experimental data, proteins and groups”

  2. Select the Proteins view

  3. Check the check box of the two first proteins in the list. Note that the order in which the proteins appear in the list may depend on the settings such as the preferred accession key, and the sorting of the columns. However for the purpose of this example it does not matter which two proteins are selected.

  4. Save the two entries to a new dataset using the Save checked proteins in a new folder button.

  5. A new folder appears in the same catagory as the selected dataset. Rename the folder 'example2'. We now have two datasets that can be compared. Click the yellow folder icons of 'example' and 'example2' - and a green check mark will appear on the folder icons.

  6. Click the name of the category that you imported the data into e.g. DataSets to indicate that a new comparison folder should be placed here

  7. Click the Compare the selected folders button to create a comparison folder

  8. A comparison folder with the default name 'Comparison' is created in the DataSets category. This dataset now contains three proteins as indicated by the number in the parenthesis. This is expected since example2 is a subset of example, which contains three proteins. Click the name of the comparison folder to select it and click the Proteins tab to view the list of proteins.

  9. A compare menu is now displayed below the filter menu.

  10. For each protein it is shown which dataset the protein was seen in by displaying either a colored or empty square representing each of the datasets in the comparison.

  11. In the compare menu click the white boxes next to And to specify that only proteins occurring in both datasets are shown.

  12. Two of the three proteins are shown.

  13. Now, click the second box next to Not to display proteins seen in dataset (blue) but not occurring in the example2 dataset (purple)

  14. Only one protein is shown.

For more advanced comparison combine the comparison with the clustering functionality

(More details can be found in Chapter 19, Dataset comparison).

1.10. Context-sensitive online help

For any given component in the interface, there is a context sensitive online help.

Follow this example to access the online help.

  1. In the upper right of the interface click Help

  2. The cursor changes and a question mark appears

  3. Now press any component of the interface for which help is wanted. In this example we press the lookup tab

  4. Now the online help appears in another window - in this case Chapter 7, The Lookup.

  5. Use the PDF version link to obtain the complete printable user manual

  6. Click Prev to go to Previous chapter - and to browse back to main index

  7. Click Next to go to next chapter

  8. Use the index to jump directly to specific sections of the chapters

  9. Below the index, you will find the help for the first section of the given chapter