ProMS: Proteome Analysis using Mass Spectrometry

Account

Open a ProMS account.
You need a personal account (login and password) to access the Proms server.
You can request one by clicking on the corresponding link on the ProMS Welcome page.

Session

Start a ProMS session.
From the ProMS Welcome page, click on to start a ProMS session. Your login and password will be required.
Once open, your session displays your profile information and the list of projects you have access to. If you are a massist, the list of non/partialy-validated analyses is also display.
If you connect to ProMS for the first time, you will be asked to fill out your profile information.

At this stage, you can either edit your profile, create a new project or open one of the projects you have access to.

Close a ProMS session.
To close your session, you can either click on from the session main window (you will need to close your project first), or simply close your browser window.
If you connect to ProMS from a multi-user computer, make sure to close all browser windows as your login and password information remain active after closing the ProMS window. This will prevent someone else from connecting to your account.

User Profile

Edit your profile.
From your session main window, click on user information.

You can edit any items in your profile except your login, password and status.
Click on to save your changes and go back to your session main window.

Project

Create a project.
Click on from your session main window and fill out the corresponding form.

You are asked to provide a name, description, owner and comments.
Click on to create the project.
You automatically become an administrator of the project you have created.

Open a project.
The list of projects you have access to is displayed in your session main window. Click on to access the selected project.
- In the left frame, a navigation window allows you to list any item contained in your project.
You can expand / collapse individual project items by clicking on the

icones of the navigation tree
You can also expand the entire project/item contents by clicking on /
The selected item appears in red.
- In the right top frame, a menu window containing a series of buttons allows you to perform various actions on the selected item.
- The right bottom frame displays the result of the action performed.

Project hierarchy.
A Project is composed of a set of Experiments. Experiments are themselves composed of any number of Samples. Samples contain one or more Analyses.
Experiments and Samples are generic containers and may represent various experimental entities.
For instance :
   - If a project contains data from 1D gels, experiments may represent the different lanes of the gel and samples, the protein bands found in each lane.
   - If a project contains data from 2D gels, experiments may represent the different gels and samples, the protein spots of each gel.
Bands and spots are usually analyzed once by Mass Spectrometry, but they can also contain more than one Analysis.

Edit a project.
If you have write access to a project, you can edit the name, description, owner and comments associated with this project.
To do edit a project, select the project's name in the navigation window and click on in the menu window.
Make the necessary changes and click on to validate your changes.

Set project accessibility.
Massists have full access to all projects.
Biologists can have any of the following read/write/validation access to projects:
   - No access to project,
   - Guest: Read only access to all data,
   - User: Read access to all data + write access to validated data,
   - Administrator: Same as User + ability to give access to other biologists,
   - Power user/administrator: Same as user/administrator + ability to exclude non-validated proteins,
   - Super user/administrator: Same as power user/administrator + ability to select/reject non-validated peptides.

To edit the project accessibility, select the project's name from the navigation window and click on in the menu window.
A form allows you to set the desired access priviledges for each biologist with a ProMS account.

Click on to record the changes made, then on to go back to your project's main window.

Close project.
To close a project and go back to your session main window, click on located at the top of navigation window.

Experiment

Add experiments.
To add an experiment to a project, you must have write access to the project.
First select the project's name in the navigation window and click on in the menu window.
A form is displayed that allows you to give a name, description and to write comments to the new experiment.
You can also add several experiments at once by filling out the "Multiple entries labels" field. The experiments will then be numbered according to the numbers (or range of numbers) you input.

Click on to create the new experiment(s).

Edit an experiment.
If you have write access to the project, you can edit the name, description and comments of any experiment.
To do so, select the experiment in the navigation window. Then click on in the menu window.
Click on to record your changes.

Sort experiments.
By default, experiments are displayed in the order they were created, but you can sort them differently if you wish to.
To move an experiment up or down the list, select it in the navigation window and click on the

arrows until the desired position is reached.

Delete an experiment.
An experiment can be deleted only if it does not contain any samples.
Select the experiment in the navigation window and click on in the menu window.
You will be asked for confirmation before deletion occurs.

Sample

Add samples.
To add a sample to an experiment, you must have write access to the project.
First select the experiment to which to wish to add a new sample in the navigation window. Then click on in the menu window.
A form is displayed that allows you to give a name, description and write comments to the new sample.
You can also add several samples at once by filling out the "Multiple entries labels" field. The samples will then be numbered according to the numbers (or range of numbers) you input.

Click on to create the new sample(s).

Edit a sample.
If you have write access to the project, you can edit the name, description and comments of any sample.
To do so, select the sample in the navigation window. Then, click on in the menu window.
Click on to record your changes.

Sort samples.
By default, samples are displayed in the order they were created, but you can sort them differently if you wish to.
To move a sample up or down the list, select it in the navigation window and click on the

arrows until the desired position is reached.

Delete a sample.
A sample can be deleted only if it does not contain any analyses.
Select the sample in the navigation window and click on in the menu window.
You will be asked for confirmation before deletion occurs.

Analysis

An Analysis corresponds to the search results data obtained by Mascot analysis of either a 'Peptide Mass Fingerprint' (PMF) or a 'Peptide Fragmentation' (MS/MS) experiment performed on a Sample.

Add/Import an analysis.
You must be a massist to add an analysis to a sample.
First, select the sample to which you want to add the analysis, then click on in the menu window.

In addition of filling out the classical name, description and comments fields, you need to :
   - Provide the MASCOT data file corresponding to the analysis performed on the sample. The data file can be in DAT or XML format for a search performed locally or on MASCOT's web site respectively.
This file will be uploaded on to the server where the data will be extracted and imported in the database.
   - Choose to import the data immediately (this takes a few minutes) or later. In the later case, the user can edit the analysis at any time during the same day to import the data. Otherwise, an automatic importation will occur overnight.
   - Specify the sequence databank used to generate the MASCOT data file.
Click on to create the analysis.

Edit an analysis.
You must be a massist or a super user/administrator to edit an analysis.
You can edit the name, description and comments of any analysis. To do so, select the analysis in the navigation window. Then, click on in the menu window.
If you are a massist and a delayed import of the Mascot data was chosen when the analysis was created, you are able to change this option to 'Now' for immediate import.
Click on to validate your changes.

Delete an analysis.
You must be a massist to delete an analysis.
An analysis can be deleted at any time independently of its state of validation.
Be careful when deleting a validated analysis since all associated peptides and proteins will be also deleted. This could affect multiple clusters and classifications.
Select the analysis in the navigation window and click on in the menu window. You will be asked for confirmation before deletion occurs.

Sort analyses.
By default, analyses belonging to the same sample are displayed in the order they were created. You can sort them differently if you wish to.
To move an analysis up or down the list, select it in the navigation window and click on the

arrows until the desired position is reached.

Combine several analyses.
Multiple non-validated analyses can be pooled into a single combined analysis to improve protein identification and reduce validation time.
Only analyses in DAT format can be combined. Furthermore, combined analyses must be of homogeneous type (either 'PFM' or 'MS/MS') to be combined.
You must be a massist or a super user/administrator to combine analyses.
From the navigation window, select the project's item (experiment or sample) containing the analyses to be combined. Then click in the menu window.

Select the type ('PMF' or 'MS/MS') and set of analyses you wish to combine from the list, give a name and description to the new analysis. If you are combining analyses from an experiment, you need to choose which sample will house the new analysis. You can also choose to delete the old analyses after they have been combined.
Click on to combine the analyses.

Duplicate one or more analyses.
You can duplicate any number of non-validated analyses together with their corresponding sample(s) and/or experiment if necessary.
You must be a massist or a super user/administrator to duplicate analyses.
To do so, proceed as if you wanted to apply a filter on the analyses. Do not select any filters and check the 'Duplicate item' box in the form.

Apply a filter on one or more analyses.
Non-validated analyses can be filtered to select or reject only a subset of the proteins identified.
This is particularly useful to compare the protein contents of different items or reject recurrent contaminants before validation.
You must be a massist or a super user/administrator to filter analyses.
From the navigation window, select the item (experiment or sample) containing at least one analysis to be filtered. Then click in the menu window.

3 types of filters can be applied to the selected analyses:
   - You can use a list of proteins generated from any item in the project including other validated and/or non-validated analyses.
If proteins from non-validated analyses are used, you can apply restriction rules such as 'ignore already rejected proteins' or 'ignore proteins with score below a certain threshold'.
   - You can use a list of proteins from a file. This file must contain 1 protein/line in fasta format (>protein_name) or not (protein_name).
   - Proteins can also be filtered based on the species they belong to.
You can provide a name and comments to the filter. They will be added to the corresponding attributes of the selected item.
Click on to start the filtering process.

Reversibly, filter(s) applied on one or more analyses can a removed by clicking on in the menu window.

Validation of an analysis

Validation Mode.
Analyses must be validated before the corresponding proteomic data can be accessed and used by biologists.
Only massists can validate analyses. However, other users may also contribute to the validation process depending of their access right to the corresponding project.
To enter validation mode, select the analysis you want to validate, then click on in the menu window.

Validation windows:
   - The top left frame contains a series of global action buttons and a summary of the validation process.
   - In the lower left frame, the user can switch views to display the list of proteins or queries.
By default, Proteins are combined in match groups corresponding to groups of proteins matched by the same set or subset of peptides. Within a match group, proteins are sorted by decreasing number of peptide matches.
Various sort options are available for both views: match groups, score (descending or ascending), peptide matches, protein identifier, query number, etc...
The user can select an item of the list to display all corresponding information in the right-hand frames.
Each item of the list has a color-code reflecting its validation status. The meaning of each color is described at the bottom of the list.
   - The top right frame displays the list of matching peptides (query interpretations) and associated query number, masses, sequence, number of proteins containing this peptide, etc...
   - The lower right frame display more detailed information about the parameter selected in the top right frame (fragmentation spectrum, list of proteins matched by the selected peptide, etc...).

Manual validation of an analysis.
Based on the information displayed in all frames, the user can manually select and/or reject the query interpretations listed in the matching peptides window. In addition, the a confidence level can be set for the validation performed. This selection must then be saved by clicking on .
Exclude/Include proteins:
The user can manually exclude (and reversely include) the protein displayed from the list of selectable protein by clicking on . Alternatively, the user can exclude multiple proteins at once: First list the proteins matching the corresponding (set of) query(ies) (click on the title/values of the 'Proteins' column in displayed the matching peptides window). Then, select the proteins to be excluded (checkboxes) and click on .
Excluded proteins can only be re-included one by one.
Excluded proteins will not be sent to biologists even if they contain validated peptides.
Reference spectrum (MS/MS only):
During manual validation of an MS/MS analysis, any fragmentation spectrum displayed in the spectrum window can be saved as a reference by clicking on .
This spectrum will be automatically displayed each time an MS/MS query with the same interpretation, charge and post-tranlational modifications will be selected.
Match group validation (MS/MS only):
All peptides corresponding to a match group can be validated at once. From the matching peptides window, select the peptide score thresehold at the end of peptide list and click on .
Reversibly, the match group peptide velidation can be cleared by clicking on
Cross-analysis validation (MS/MS only):
A given MS/MS spectrum interpretation (peptide + charge + post-translational modifications) can be validated across multiple analyses at once.
From the matching peptides window, click on the corresponding number in the Analyses column to display detailed information corresponding to all occurences of the peptide (works only if the peptide is found in at least 2 MS/MS analyses).
The user can easily display all corresponding fragmentation spectra and ions tables and thus quickly select or reject the interpretations proposed.

Automated validation of analyses.
One or more analyses can be automatically validated according to criteria selected from a predefined list by the user.
- Either select the project item containing the list of analysi(e)s to be validated from the navigation window and click on in the menu window.
If the item selected contains more than 1 type of analysis (both PMF and MS/MS), you must specify to which type the automated validation must be applied.
- or enter validation mode and click on .
The following autovalidation form will then be displayed:

The form is composed of 2 sections:
   + The 1st one to set peptide selection/rejection rules. Define :
        - whether to use these rules to select and/or reject interpretations;
        - the minimum score(s) for peptide selection (MS/MS only);
        - the peptide length range if any;
        - the maximum acceptable mass error;
        - the maximum peptide rank (MS/MS only);
        - whether to select only 1 interpretation per query;
        - and whether to overwrite previous validation if any.
   + The 2nd one to set protein selection/rejection rules. Define :
        - whether to apply any additional protein selection rules;
        - the minimum number of peptides per protein;
        - the minimum protein score (MS/MS only);
        - the minimum peptide coverage allowed.
        - whether to select only the best matched protein(s) of each match group;
        - and whether to overwrite previous protein exclusion(s).
Click on to perform the automated validation.
Automated validations can be cumulated with different parameters.
The user can then enter validation mode to display the list of selected/rejected peptides and proteins.

Clear validation.
If the current validation state of an analysis does not correspond to your expectations, you can clear all peptide and protein selections/rejections.
From within the validation mode and click on .
WARNING: Protein filtering and/or exclusion are not affected.

Send data to biologists.
At any time during the validation process, the user can make the validated data public (visible by all users) by clicking on from within the validation mode. Only the currently selected peptides and matched proteins (except those excluded or filtered out of the list) become accessible to all users.
WARNING: Peptides/proteins previously made public but subsequently deselected, excluded or filtered later during the validation process will be deleted from the valid data after the next data transfer.

Restore validation.
The last transferred validation state (sent to biologists) of a partially validated analysis can be restored if necessary. This is useful for instance after restarting a validation process.
From within the validation mode and click on .
WARNING: If no longer applied, previous protein filtering will not be restored. However, proteins matched by previously validated peptides but missing in the list of transferred proteins will be considered as excluded.

Close validation:
At any time, the user can exit the validation mode to go back to the project main window by clicking on . All the selections/rejections performed will be recovered the next time the user reenters the validation mode.
Other options such as adding new interpretations for a query, recording a spectrum to be used as a reference or cross-MS/MS analysis validation of a peptide sequence are also available.

End validation.
When the user juges that there are no more data to be validated, he must enter validation mode and click on to terminate the current analysis validation. The user will have the option to send the validated data to biologists beforehand.
All temporary data will be deleted from the database and the selected analysis will no longer be accessible for further validation unless the entire validation process is restarted.

Restart validation.
If a previously terminated analysis validation must be modified/performed again, the user as the possibility to restart the validation process.
To do so, first edit the corresponding analysis and click on at the bottom of the edition form.
You will be asked to provide again the corresponding Mascot data file and to choose a new sequence databank if the original one is no longer in use. All search results will be imported again in the database and the analysis will tagged as partially validated. Finally, the last transferred validation state can be restored if necessary.

Proteins

Protein list.
You can display the protein contents of any project item containing at least 1 validated analysis.
To list the proteins contained in an item, select this item in the navigation window and click on in the menu window

The list displayed is subdivided by child items according to the project hierarchy (default). This organisation can be changed to a raw list or to any other classification created by the users.
The name (same as the identifier by default), cluster, number of matching peptides, description and organism are displayed for each protein.
Proteins validated with a low confidence level appear in gray.
In standard view mode, only the visible proteins of each match group are displayed. However, if the expandable mode is selected (available only in Project hierarchy and Raw list views), match groups can be expanded to display hidden proteins.
The proteins in the list can be sorted by name, number of peptides (default) or by organism. This is done by clicking on the corresponding column label. The label used to sort the list appears in red.
From the protein list window, you can:
   - Change the current classification.
   - Display detailed information on a protein.
   - Display a graphical view of the peptide matches for a set of selected proteins.
   - Display the protein contents of a cluster.
   - Add/Remove protein(s) to/from a user-made classification.
   - Edit a match group.

Organize proteins.
The proteins contained in a project can be organized in different groups (categories) based on the user's criteria (classifications). For instance, you may wish to organize the proteins based on their revelance to your research. In this case, you could create a classification called 'Biological interest'. This classification could contain categories such as 'Very interesting', 'Potentially interesting', 'Not interesting', etc...
Multiple classifications can be created for the same project. Other examples of possible classifications are 'Experimentally confirmed proteins', 'Cellular localization', etc...
A given protein can be found in different classifications. However this protein must belong to only 1 category in each classification.
To organize proteins from the protein list window, you must first create at least one classification and its associated categories.
From the protein list window, select (check boxes) the proteins we wish to add to or remove from a category. Then, select the category from the drop-down menu located at the top of the window.

Click on to validate your selection. The protein list window will be then updated to display the corresponding classification contents.

Graphical view of peptide matches.
A graphical view of the peptide matches for selected protein(s) can be displayed.
A set of proteins (from a project item, a cluster or a match group) or a protein entry must be displayed to access to this option.
Depending on the context, click on or to view the matches graphically.
The peptide matches displayed correspond to the project item selected in the navigation window.

Up to 4 graphical views are available depending of the item selected:
   - Standard Expanded (default): Match patterns of a given protein are drawn separately for each selected analysis + Peptides are drawn indivially.
   - Standard Compact: Same as Standard Expanded except that peptides are drawn directly on the protein.
   - Cumulated Expanded: Match patterns for all selected analyses are cumulated + Peptides are drawn indivially.
   - Cumulated Compact: Same as Cumulated Expanded except that peptides are drawn directly on the protein.

The set of selected proteins is displayed with for each of them:
- name, description, size and organism.
- The protein and peptide sequences are drawn as gray (

) and red (

) lines respectively.
Mouse over a peptide to display its sequence, length and position on the protein sequence.
In Expanded views, click on a peptide to highlight all its occurences. Selected occurences appear as blue (

) lines.

Compare two items.
The protein contents of 2 project items can be compared to find proteins that are unique or common to the 2 items.
This can be done by clicking on in the menu window.
Select any 2 items in the project. By default, the last item selected in the navigation window is chosen as first item. Items of different types can be compared (eg: an Experiment versus a Sample). Click on to display the result.

The numbers of proteins unique and common to both items are displayed in a table. Common proteins visible in one item but hidden in the other are also counted. In this case, 2 different values will be displayed: The first one represents the number of proteins proteins visible in both items and the second value, the total number of common proteins, hidden included.
Click on the each item to display the corresponding list of proteins.

Once displayed, the list can be saved in a Classification. To do so, click on . A new form will appear to allow you to select/create the Classification and category that will be used to store the list.

View a detailed protein entry
At any time, you have access to the complete information about a protein by clicking on its name in any list.
The following information is available:
   - Name (same as identifier by default).
   - Identifier (in the sequence databank used for validation).
   - Nominal mass.
   - Organism used.
   - MASCOT score.
   - Comments.
   - List of analyses where the protein is found.
   - Sequence with peptide matches in bold red (overlapping matches are in bold blue).
The peptide matches displayed correspond to the analysis selected in the list above.
   - A peptide match summary displaying information on each peptide identified. Massists and super users/administrators have access to complete PMF or MS/MS information about the peptides (including fragmentation spectra for MS/MS).
   - External links to biological servers, including the possibility to directly blast the protein sequence on the NCBI server.

From this window, you can:
- Display a graphical view of the peptide matching this protein for the analyses selected (checked boxes) by the user.
- Edit the protein entry.

Edit protein.
The protein entry can be edited for the following information: name, description, organism and comments by clicking on

Fill out the form and click on to validate your changes.

Export the protein list.
You can export any item's list of proteins into a MS Excel format and save it on your local computer for further processing. Only visible proteins are exported.
Click on in themenu window. A form will be displayed to allow you to choose between various export options:
   1- The classification.
   2- The project's depth (only if Project Bierarchy is selected as classification): The lowest subitem to be displayed in the exported list.
   3- The sort option.
   4- The proteomic and MS data to be exported.

Select your options and click on

Match group

To minimize data redundancy, proteins matched my the same (sub)sets of peptides are organized into match groups. A given protein belongs to only 1 match group within the same analysis. However, since match groups are computed independantly for each analysis, the same protein can be found in different match groups within a project.
By default, only 1 best matching protein (matched by all the peptides in the set) in each match group is visible to the user (name in 'bold' characters). This protein is also used as an 'alias' for the match group it represents. All the other proteins are hidden. The user can however edit the match groups to show/hide any number of proteins.

Display a match group
Hidden proteins of a match group can be temporarily displayed (name in 'light' characters) when the Run in expandable mode option is checked in the protein list window (only available in Project hierarchy and Raw list views). In this case, a

is displayed in front of each alias. Clicking on this

displays all the proteins of the corresponding match group. Reversely, clicking on the

in front a the alias closes the match group.

Edit a match group
From an expanded match group, the user can click on to access graphical views of the peptide matches within this match group. He can also click on to select a new alias and/or visible proteins.
The match group edition form has 2 different sections:

- The top section allows the user to select the alias (best representative) and any other proteins he wishes to make visible.
- The bottom form allows to define rules to extend the user's settings to match groups of other analyses where the proteins are also found.
If changes are made, secondary visible proteins (non alias) are indicated by

when listed in the protein list window.

Classification

A classification is a convenient way to organize the proteins in a project based on the user's own criteria.

List the classifications.
To display the list of classifications created, select your project's name in the navigation window and click on in the menu window.
From the list window, you can create, edit or delete your classifications.

Create a classification.
To create a new classification, first display the list of classifications, then click on

Provide a name and description and click on to create the new classification.

Edit a classification.
From the list of classifications, click on the button corresponding to the classification to be edited. A form will be displayed to allow you to modify the classification's name, description and to add, edit or delete its categories.

Click again on next to the classification's information to change the name and/or description and save your changes.

Delete a classification.
From the classification list, click on the button corresponding to classification to be deleted. All its categories will also be deleted, but not the proteins contained.

Select a classification.
A given classification can be selected when displaying or exporting a list of proteins contained in a project's item.

Cluster

Protein clustering
Clustering is a useful tool to annotate proteins regarding their sequence similarities. This procedure assigns highly similar proteins to clusters, thus helping the user to deal with the unavoidable protein sequence redundancy.
Clustering can be performed on the whole project or on any item containing validated proteins.
From the navigation window, select the project's item from which you want to perform protein clustering and click on in the menu window. The sequences of the proteins contained are then compared with that of all the proteins in the project using the BLAST algorithm. This process can last several minutes if a large number of sequences are compared. A status window is displayed to inform the user of process progression.

In the mean time, the user can continue using the server for other tasks.
Clicking again on while a clustering has already been launched only brings back the status window and has no damaging effects.

Clustering mode
When the BLAST process is completed, a '*' appears on the clustering button () to invite the user to move to the clustering mode.
In this mode:
- The left window displays a list of temporary groups of similar proteins.
Each group must be manually verified by the user before becoming valid cluster.

- Click on a group number to display the list of pairwise sequence similarities found in this group in the top right window.

From this window, you can select the proteins you want to clusterize together and click on .
- This will display the corresponding multiple sequence alignment in the lower right window.

Based on the quality of the alignment, you will have to decide to validated or not the this cluster by clicking on .

Provide a name and description for the cluster and click on to record the information in the database.

On the other hand, if you decide that some of the aligned proteins should not belong to the same cluster, you can deselect them from the list in the top right window and test the cluster again. You can also ignore the entire candidate group none of the proteins selected You can exit clustering mode at any time by clicking on . In this case, the temporary data are saved, allowing you to re-enter clustering mode and continue cluster validation.
You can also click on to terminate clustering. All clustering data except Validated clusters, will be deleted.

List clusters
To display the list of clusters created, you must exit clustering mode. Click on in the menu window. The clusters' names, descriptions and protein counts are displayed.

View a cluster
To access detailed information about a cluster's protein contents, click the cluster's name where ever it is displayed.
The list of proteins contained and the corresponding alignment will be displayed.

Edit cluster
A cluster's name and description can edited either by clicking on the corresponding button from the Cluster list window, or on from a displayed cluster.

You can modify the name, description and remove protein(s) from the cluster.
Click on to save your changes.

Add protein(s)
Proteins cannot be directly added to a cluster. You must restart a global the clustering process after selecting the project's item containing the proteins you want to clusterize together.
The proteins must share significant sequence similarity to be found in the same cluster.

Remove protein(s)
First, display the cluster's information. Select the protein(s) (checkboxes) you want to remove and click on .
The cluster will be automatically deleted if less than 2 proteins are remaining.

Delete a cluster
A cluster can be directly deleted by clicking on from the cluster list window or on from a displayed cluster.

Databank

List Databanks
The protein sequence databanks used for the MASCOT searches must be imported onto the server in order provide complete protein information to the users.
Only massists are allowed to manage sequence Databanks.
From the session main window, click on .

Add Databanks
Click on at the bottom of the databank list window to add a new one.

Fill out the corresponding form to provide information on the databank you want to add. In particular, you must select the databank type so that the server will know how to extract the protein data from the file and which external links to provide.
the file itself but be in FASTA format and can be either uploaded from your local computer or directly fetched from the internet.

Edit Databanks
From the databank list window, click on the button corresponding to the databank you want to edit.
You can edit all information concerning an existing databank except the type and the sequence file.

Delete Databanks
You should delete a databank if it is no longer in use (outdated) and replace it with a more recent one.
From the databank list window, click on the button corresponding to the databank you want to delete.

Search for proteins

Keyword Search
Click on in the menu window to display the Search form. The Keyword Search is the default search option.

You can perform the search within the whole project or to restrict it to only the item selected in the navigation window. All proteins (visible as well as hidden) will be searched.
Type a list of keywords and check the desired search options and protein attributes to be searched.
Click on to launch the search.

A list of matching proteins is displayed. As in all proteins lists, proteins visible in at least 1 analysis contained in the project's item searched are displayed in 'bold' and hidden ones in 'light'. Corresponding molecular weight, cluster, description and organism are also displayed.
Click on the desired protein's name to display detailed information including the list of items where it was found.

Sequence Search
Click on in the menu window and select Sequence Search to display the proper form.

As for Keyword Search, you can extend/restrict your search to the desired project's item.
You also can extend/restrict the search to all/visible proteins.
Paste the sequence to be searched (non-residue characters are ignored) and define the desired BLAST parameters for the search. Click on to launch the search.

The search result displays the list of the proteins found with associated molecular weight and cluster together with a graphical view of corresponding the query/subject matches. The list is sorted by decreasing percentage of similarity.
If too many hits were found, the list can be further filtered by increasing the similarity thresehold.
Mouseover the protein's name and matches to display more information. Additionaly, you can click on the desired protein's name to display detailed information including the list of items where it was found.