Agilent Spectrum Mill MS Proteomics Workbench

Server Administration


Table of Contents


Read this first!

Before you modify any files on the Spectrum Mill server, be sure to archive the originals so they can be restored if necessary!

The Agilent Software Status Bulletin may help you with any difficulties you encounter with the software. To view this document, click here.


To Add/Change Amino Acid Modifications

See SMCustomModifications.pdf. Read the entire overview (section 1) of the document before you begin, and refer to section 2 for the detailed specification.


To Add/Change VML Score Amino Acid Choices

Before you modify any files, be sure to archive the originals so they can be restored if necessary!

Edit the file: E:\SpectrumMill\millhtml\SM_js\protChem.js.

To add or modify VML score amino acid choices to list in Protein Peptide Summary, in protchem.js edit the displayVariableModificationLocalizationAAChoices() function.

Follow the format used in the file, for example:

document.writeln ("<option>s|t|y<option>"),

which enables you to report the VML score only for peptides containing phosphoryulated serine, phosphorylated threonine or phosphorylated tyrosine.  For more details see Amino Acid Filtering.

The values must be PERL regular expressions.



To change the HTML link from the accession number in the search results

Before you modify any files, be sure to archive the originals so they can be restored if necessary!

Edit the file: E:\SpectrumMill\msparams_mill\urlsAccessionNum.txt.  

Or obtain an updated file from the Agilent Software Status Bulletin and Patches website.  Agilent updates this file periodically when the URLs for external databases change.  If you have customized this file, be sure to save a backup before you install the new file from Agilent.

The database accession number in the search results has an HTML link to retrieve the complete entry, including comments, from a remote database. In order for this link to be created, the programs need to know the URL for the remote database. This is accomplished through parameters contained in the msparams_mill\urlsAccessionNum.txt file. Occasionally the URLs to the remote database may need to be updated, or new ones added for use of a new database. This requires editing of the msparams_mill\urlsAccessionNum.txt file.

Within the msparams_mill\urlsAccessionNum.txt file, an entry for an HTML link from the accession number MUST contain one line:

The line must contain the following information:

  1. The prefix name for the database as listed in the HTML input page for each program. The prefix should be long enough to uniquely identify the database or set of databases you wish to refer to.
  2. The URL to link to if the accession number for the entry is added to the end of the URL. The URL addition is internal to the programs and is expected to retrieve a fully-annotated entry from a remote database.

    Note that this link need not be to to a sequence database. The link could be to whatever a Spectrum Mill server administrator specifies.

Example:
Below is an example of the entries for Genpept in msparams_mill\urlsAccessionNum.txt:

      Genpept http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=n&form=6&dopt=ng&uid=
      gen http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=n&form=6&dopt=ng&uid=

The lowercase prefixes gen, owl, swp, or nr are intended to be used for a second database that is of the same format as the uppercase one. See Linking for creating links into NCBI databases. 

As mentioned above, the prefix name can refer to a single database or a set of databases. For example if you have two user-created databases called PA3_mouse and PA33_mouse, an entry in the acclinks file of the form:

      PA3 some_url_prefix

would give the databases the same accession number link. On the other hand, entries of the following form:

      PA3 some_url_prefix
      PA33 another_url_prefix

would give the databases different accession number links.

Species alias files work on the same principle. The sets of databases with the same accession number link do not have to correspond to the sets of databases with the same species alias file.


To change the HTML link from the MS Digest index number in the search results

Before you modify any files, be sure to archive the originals so they can be restored if necessary!

Edit the file: E:\SpectrumMill\msparams_mill\urlsIndexNum.txt.

The MS Digest index number in the search results has an HTML link to retrieve an MS Digest listing for the matched database entry. In order for this link to be created, the programs need to know the URL to MS Digest and some default parameters. This is accomplished through information contained in the file msparams_mill\urlsIndexNum.txt. A server administrator can customize these parameters by editing the msparams_mill\urlsIndexNum.txt file.

Within the msparams_mill\urlsIndexNum.txt file, an entry for an HTML link from the MS Digest index number MUST contain two lines.

The lines must contain the following information:

  1. The program name for which the specified HTML link will be created from the index number link in the program's output.
  2. The URL to link to if the enzyme, MS Digest index number, and modified AA parameters (from PMF Search only) for the entry are added to the end of the provided URL. The URL addition is internal to the programs and is expected to provide an MS Digest listing for the database entry corresponding to the index number.

    Note that this link need not be the same for each Spectrum Mill program creating the link, and that the MS Digest parameters can be customized. Furthermore, this link need not be to MS Digest at all; the link could be to whatever a Spectrum Mill server administrator specifies.

Example:
Below is an example of the entries for msfit and mstag in msparams_mill\urlsIndexNum.txt:

msfit
../millbin/MSDIGEST?
mstag
../millbin/MSDIGEST?mod_AA=Peptide+N-terminal+Gln+to+pyroGlu&mod_AA=Oxidation+of+M&mod_AA=Protein+N-terminus+Acetylated


To change the HTML link from the peptide sequence in the search results

Before you modify any files, be sure to archive the originals so they can be restored if necessary!

Edit the file: E:\SpectrumMill\msparams_mill\urlsSequence.txt.

The peptide sequence in the search results has an HTML link to retrieve an MS Product listing for the peptide sequence. In order for this link to be created, the programs need to know the URL to MS Product and some default parameters. This is accomplished through information contained in the msparams_mill\urlsSequence.txt file. A server administrator can customize these parameters by editing the msparams_mill\urlsSequence.txt file.

Within the msparams_mill\urlsSequence.txt file, an entry for an HTML link from the peptide sequence MUST contain two lines:

The lines must contain the following information:

  1. The program name for which the specified HTML link will be created from the peptide sequence link in the program's output.
  2. The URL to link to if the peptide sequence is added to the end of the URL. The URL addition is internal to the programs and is expected to provide an MS Product listing for the peptide sequence. Parameters for PSD fragmentation are the defaults specified in msparams_mill\urlsSequence.txt.

    Note that the parameters need not be for PSD and the link need not be to to MS Product. The link could be to whatever a Spectrum Mill server administrator specifies (BLAST or other sequence homology search programs, for example).

Example:
Below is an example of the entry for mstag in msparams_mill\urlsSequence.txt:

mstag
../millbin/MSPROD?parent_mass_convert=average&it=i&it=m&it=a&it=b&it=y&it=I&it=h&it=n&it=B


To Change the HTML link from the elemental composition in the search results

Before you modify any files, be sure to archive the originals so they can be restored if necessary!

Edit the file: E:\SpectrumMill\msparams_mill\urlsElementalComposition.txt.

The elemental composition in the search results has an HTML link to retrieve an MS Isotope listing for the elemental composition. In order for this link to be created, the programs need to know the URL to MS Isotope and some default parameters. This is accomplished through information contained in the msparams_mill\urlsElementalComposition.txt file. A server administrator can customize these parameters by editing the msparams_mill\urlsElementalComposition.txt file.

Within the msparams_mill\urlsElementalComposition.txt file, an entry for an HTML link from the elemental composition MUST contain two lines:

The lines must contain the following information:

  1. The program name for which the specified HTML link will be created from the elemental composition link in the program's output.
  2. The URL to link to if the elemental composition is added to the end of the URL. The URL addition is internal to the programs and is expected to provide an MS Isotope listing for the elemental composition.

    Note that the link need not be to MS Isotope and that further MS Isotope parameters could be specified. The link could be to whatever a Spectrum Mill server administrator specifies.

Example:
Below is an example of the entry for msprod in msparams_mill\urlsElementalComposition.txt:

msprod
../millbin/MSISO?distribution_type=Elemental+Composition


To Enable the HTML link to BLAST search

Before you modify any files, be sure to archive the originals so they can be restored if necessary!

Edit the file: E:\SpectrumMill\millscripts\libspecmill\lsmGlobals.pm.

If you wish to have the amino acid sequence in Protein/Peptide Summary link to BLAST (Basic Local Alignment Search Tool), change the following line (near line 36):

From: $GLOBAL_ADD_BLAST_LINK = 0;

To: $GLOBAL_ADD_BLAST_LINK = 1;

If you enable the BLAST link, be aware that it will take longer to load large data sets in Protein/Peptide Summary.


To Add/Change a Species Filter

Before you modify any files, be sure to archive the originals so they can be restored if necessary!

Edit the file: E:\SpectrumMill\msparams_mill\species.txt.

In order to limit searches to a particular species, or a collection of species, the programs have to correlate the species name selected in the HTML form with the species names in the database entries. This is accomplished through a species alias file species.txt

Click here to view the species definitions that ship with the software (default species.txt).

To add or change a particular species filter you must edit the msparams_mill\species.txt, file and the JavaScript which controls the appearance of the species in the program HTML input files:

  • millhtml\SM_js\species.js
  • Steps to add a species filter

    Caution:  Do not leave blank lines in the file.  You can add comment lines by preceding them with "#". 

    1. If this is the first time you have done this, read the explanation just below.
    2. Open species.txt in Notepad or other plain text editor.
    3. If you wish to add a single species entry:
      1. Scroll to the middle of the file where the single species entries occur. 
      2. Find the alphabetical location for your entry.  The species are separated by '>'.  The single species must be added alphabetically.
      3. Start your entry at the location of a '>'.
      4. Type the name of your species on the next line.  This is the same name you will use in the species.js file, which sets the species name for the HTML form.
      5. On separate successive lines, type each of the species aliases.  Remember that the aliases must be listed in the same order as in the index file seqdb\database_name.r##.sp. For the species names, do not include the '|' symbol or the number that appears after it in seqdb\database_name.r##.sp.
      6. On the next line, type >.
      7. Go to step 6.
    4. If you wish to add a multiple species entry:
      1. Scroll to the beginning of the file where the multiple species entries occur.  The multiple species entries are enclosed in [].
      2. Find a location for your entry.  (Optional:  Follow the order you wish to use in the HTML form.)
      3. Start your entry at the location of a '>'.
      4. On the next line, type [ , the name of your species and  ].  The name  is the same name you will use for the HTML form.
      5. On separate successive lines, type each of the species you wish to include.
      6. On the next line, type >.
      7. Go to step 6.
    5. If you wish to add an excluded species entry:
      1. Scroll to near the beginning of the file where the excluded species entries occur.  The excluded species entries are enclosed in ][.
      2. Find a location for your entry.  (Optional:  Follow the order you wish to use in the HTML form.)
      3. Start your entry at the location of a '>'.
      4. On the next line, type [ , the name of your species and  ].  The name  is the same name you will use for the HTML form.
      5. On separate successive lines, type each of the species you wish to exclude.
      6. On the next line, type >.
      7. Go to step 6.
    6. Save the file.
    7. Open species.js in Notepad or other plain text editor.
    8. Decide where in the HTML list you want the new species name to appear.  These names do not need to be alphabetized.
    9. Add a line for your new species.  Follow the format in the file.  The species name must be exactly the species name you typed in the species.txt file.
    10. Save the file.

    Explanation

    There are three types of entries in the msparams_mill\species.txt file:

    Within the msparams_mill\species.txt file, a single species entry must contain at least ONE line; species are separated by a line with only the ">" symbol.

    Line 1 contains the species name as it appears in the HTML input files. Line 1 is only used to relate the HTML input entry to possible aliases in a database. Every species in the HTML input pages should have an entry in this file. If one of those species is NOT present in a database, leave the entry with only one line. No error message will be generated that way.

    All other lines should contain names (aliases) by which the species may be found in a database. The aliases for a single species MUST be listed in alphabetical order (independent of line 1), or more precisely the aliases must be listed in the same order as in the index file seqdb\database_name.r##.sp.

    Example:
    CAENORHABDITIS ELEGANS
    CAEEL
    C. ELEGANS
    C.ELEGANS
    CAENORHABDITIS ELEGANS
    CAENORHABDITIS ELEGANS STRAIN=BRISTOL N2
    >

    If a program error directs you to one of these files likely problems are:

    1. The aliases for a particular species are not listed here in the correct order.
    2. Line 1 of the species doesn't match the HTML input page.
    3. The HTML input page lists a species which does not have an entry in this file.

    Multiple species entries allow you to group species together in a search. A typical example which restricts the search to the HOMO SAPIENS, BOS TAURUS and SUS SCROFA species is:

    [Mammals]
    HOMO SAPIENS
    BOS TAURUS
    SUS SCROFA
    >

    Line 1 contains the identifier for the multiple species entry as it appears in the HTML input files. The identifier is enclosed by the '[' character and the ']' character as in the example. Every multiple species entry in the HTML input pages should have an entry in the msparams_mill\species.txt file.

    The other lines should contain the names of the species that you wish to include in the search. The species that you wish to include MUST have single species entries in the msparams_mill\species.txt file. Multiple species entries must appear above the single species entries in the file.

    Excluded species entries allow you to exclude species from a search. A typical example which includes all species except HOMO SAPIENS, BOS TAURUS and SUS SCROFA is:

    ]Model Organisms[
    HOMO SAPIENS
    BOS TAURUS
    SUS SCROFA
    >

    Line 1 contains the identifier for the excluded species entry as it appears in the HTML input files. The identifier is enclosed by the ']' character and the '[' as in the example. Every excluded species entry in the HTML input pages should have an entry in the msparams_mill\species.txt file.

    The other lines should contain the names of the species that you which to exclude. The species that you wish to exclude MUST have single species entries in the msparams_mill\species.txt file. Excluded species entries must appear above the single species entries in the file.

    Click here for step-by-step instructions to add a species filter.


    To Add/Change Contaminant Mass List Files

    Before you modify any files, be sure to archive the originals so they can be restored if necessary!

    Contaminant mass list files are used in PMF Search.  To create and use a new file:

    1. Create a new contaminant mass list file under: E:\SpectrumMill\msparams_mill\contaminantMassLists\.
    2. Edit the file: E:\SpectrumMill\millhtml\SM_js\contaminants.js.

    You define the contaminant mass list in the new *.tsv file you create under msparams_mill\contaminantMassLists\, then modify contaminants.js to display the modification in the HTML form.

    The easiest way to create a new contaminant mass list file is to copy, rename, and edit an existing one.  Note that these file names cannot contain spaces.  Within the file msparams_mill\contaminantMassLists\MyFile.tsv, an entry for each modification MUST contain two columns.

    column 1) contains the contaminant mass.
    column 2) contains a description of the source of the contamination. It is not critical (from the software standpoint) that the description be accurate, but it is critical that this column have an entry.

    Below is an example of an entry:

    mass name
    1045.5642 trypsin

    Since the contaminant mass list files are in tab-separated-variable (*.tsv) format, the "columns" are indicated by tabs; that is, the fields are tab-separated.  You modify *.tsv files with a spreadsheet program or a plain text editor such as Notepad.  In doing so, you must make sure that the editor does not replace tabs with spaces, and that you do not inadvertently add or delete tabs.

    In contaminants.js, you add the name of the new contaminant mass list file.  Follow one of the following formats:

    If in the HTML form you want to display the name of the *.tsv file, then make an entry of the form:

    document.writeln("<option>MyFile.tsv</option>");

    If you want the display name to be different than the internal name (e.g., if you want the display name in the HTML form to be different than than the name of the *.tsv file), then instead add a line like the following example:

    document.writeln("<option value=\"MyFile.tsv\">My Contaminants</option>");

    In this example, the value is the internal name (MyFile.tsv), while the display name is My Contaminants.



    To Add/Change Enzymatic Digest Rules

    Before you modify any files, be sure to archive the originals so they can be restored if necessary!

    Edit the file: E:\SpectrumMill\msparams_mill\enzymes.txt.

    Detailed information on all enzymatic digests used in the programs is located on the server in the msparams_mill\enzymes.txt file. You must edit this file to add or modify the rules for an enzymatic digest.

    Within this file, an entry for an enzymatic digest MUST contain four lines:
    line 1) contains a name for the enzymatic digest;
    line 2) contains a list of cleavage amino acids;
    line 3) contains a list of exception amino acids (a '-' character indicates no exceptions);
    line 4) single letter code for cleavage specificity (C, N, c, n, g, h, b,Y, B, y);

    Below is an example of the entry for trypsin:

    Trypsin
    KR
    P
    C

    Then you must edit the enzyme name lists in the JavaScript which controls the appearance of the enzyme in the program HTML input form files:

    millhtml\SM_js\protChem.js

    You can combine the cleavage rules for two or more enzymes by having them on the same line in the enzyme name list separated by a '/' character. For example, to have an option which combines the cleavage rules for CNBr and Trypsin you would need the following line:

    <OPTION> Trypsin/CNBr

    It is possible to mix enzymes which cleave on the N-terminus side with those that cleave on the C-terminus side.



    To Add/Change Required/Disallowed Amino Acids

    Before you modify any files, be sure to archive the originals so they can be restored if necessary!

    Edit the file: E:\SpectrumMill\millhtml\SM_js\protChem.js.

    In protChem.js, you add the name of a possible required amino acid under function displayRequiredAAChoices (), and the name of a possible disallowed amino acid under function displayDisallowedAAChoices ().   Follow the format used in the file, for example:

    document.writeln("<option>s|t|y</option>");

    enables you to show only peptides that contain either phosphorylated serine, or phosphorylated threonine, or phosphorylated tyrosine.  For more details see Amino Acid Filtering.

    The values must be PERL regular expressions.



    To Add/Change Instrument Types

    Before you modify any files, be sure to archive the originals so they can be restored if necessary!

    When you select an instrument in MS/MS Search, this triggers the configuration of MS/MS Search scoring and peak detection parameters designed particularly for the type and extent of peptide fragmentation observed on that instrument. For MS-only data, selecting an instrument triggers the configuration of extraction and search parameters designed particularly for the instrument type. You can add new instrument types or edit the instrument parameters by editing the files:

    E:\SpectrumMill\msparams_mill\instrument.txt  
    E:\SpectrumMill\millhtml\SM_js\instrument.js  

    The format is setting, followed by a tab, followed by the value.

    If you add an instrument that exports peak list files, be sure to set the parameters  in instrument.txt in a way that is appropriate for the data you export from that instrument. For example, if deisotoping is accomplished by  the instrument data system, set bypassDeIsotoping = 1 in instrument.txt to avoid repeating the deisotoping in the Spectrum Mill workbench. Likewise, if the data has already been signal-to-noise filtered, set bypassSignalNoiseThresholding = 1 in instrument.txt.

    Click for examples of MS/MS instrument configurations currently described in instrument.txt.

    Click for examples of MS-only instrument configurations currently described in instrument.txt.


    To Add User-Defined Protein Categories

    Before you modify any files, be sure to archive the originals so they can be restored if necessary!

    When you mark the check box for Categories in the Review Fields within Protein/Peptide Summary, the software displays the user-defined category for each protein. To define the protein categories, edit the file:

    E:\SpectrumMill\msparams_mill\categories.#.tsv

    Category files allow users to create their own report fields to associate with a protein. The only requirements are:

    Here are some tips:


    To Add New Taxonomy Codes for IPI Databases

    Before you modify any files, be sure to archive the originals so they can be restored if necessary!

    Edit the file:

    E:\SpectrumMill\msparams_mill\ipitax_id.tsv  

    When International Protein Index adds taxonomy codes, system administrators can update \msparams_mill\ipitax_id.tsv to enable immediate Spectrum Mill support.

    Within the file msparams_mill\ipitax_id.tsv, an entry for each modification MUST contain two columns.

    column 1) contains the taxonomy ID.
    column 2) contains the species.

    Below is an example of the entry for mouse in msparams_mill\ipitax_id.tsv:

    tax_id species
    10090 mouse

    Since the ipitax_id.tsv file is in tab-separated-variable (*.tsv) format, the "columns" are indicated by tabs; that is, the fields are tab-separated.  You modify *.tsv files with a spreadsheet program or a plain text editor such as Notepad.  In doing so, you must make sure that the editor does not replace tabs with spaces, and that you do not inadvertently add or delete tabs.


    To Configure Upload of Search Results to a Database or LIMS System

    Before you modify any files, be sure to archive the originals so they can be restored if necessary!

    Expected mechanism

    Spectrum Mill provides the capability to automatically upload summary results files (PMF Summary, Protein/Peptide Summary) to a LIMS or other server. When you select Excel Export as a review field, the results are saved to a semi-colon separated variable file (.ssv) that can be uploaded to a URL. The ssv filename is specifed as a "File=" parameter to the URL that is posted to the upload server, and is represented as a UNC path to the ssv file location on the Spectrum Mill server.

    Upload Server configuration:

    The upload server must be a web server. An application, typically written using either JavaTM Server Pages (JSP) or Active Server Pages (ASP), must be available to can accept the URL for the results file, access the File= query parameter, copy the file to the server, and parse its contents into a format that is acceptable to the LIMS.

    Spectrum Mill configuration:

    The file \SpectrumMill\millscripts\libSpecMill\lsmGlobals.pm is a PERL module that contains variable settings for configuring the upload URL.

     

  • For P/P Summary results upload, configure:

    $GLOBAL_MSTAG_RESULT_UPLOAD_NAME = "LIMS";    # The name that appears on the Upload button
    $GLOBAL_MSTAG_RESULT_UPLOAD_URL = "http://LIMSServer/MyCompany.com/LIMSUpload/SMUpload.aspx?file=";    # the URL


  • For PMF Summary results upload, configure:

    $GLOBAL_MSFIT_RESULT_UPLOAD_NAME = "LIMS";    # The name that appears on the Upload button
    $GLOBAL_MSFIT_RESULT_UPLOAD_URL = "http://LIMSServer/MyCompany.com/LIMSUpload/SMUpload.aspx?file=";    # the URL
  •  

    The url is designated as the href attribute to the anchor element that is contained by the upload button.

    When a user clicks  the Upload File to LIMS button, a new browser window is opened to the URL specifying the full file, for example:

    http://LIMSServer/MyCompany.com/LIMSUpload/SMUpload.aspx?file=\\SpectrumMillServer\msdataSM\BSAcarbamylNterm\BSAcarbamylNterm\peptideExport.5.ssv


    To Configure the Ability to Disable Quality Filtering/Disable Match Filtering

    Before you modify any files, be sure to archive the originals so they can be restored if necessary!

    Edit the file:

    E:\SpectrumMill\millhtml\SM_js\SMglobals.js  

    Under CONFIGURABLE VARIABLES, find enableDisableQualityFilteringCheckbox. This variable is normally set to false. Change it to true and resave the file.

    CAUTION: Since the "Disable quality filtering" and "Disable match filtering" modes process a larger number of lower quality spectra, the likelihood of false positives increases. We recommend you use this feature only when you work with a known sample where you desire increased sequence coverage (for example, a single-protein digest).


    To Configure the Default Instrument, Cysteine Modification, or Database Location

    Before you modify any files, be sure to archive the originals so they can be restored if necessary!

    Edit the file:

    E:\SpectrumMill\millhtml\SM_js\SMglobals.js  

    See the instructions under CONFIGURABLE VARIABLES near the beginning of the file.


    To Configure Client PCs

    See Tips and Tricks.


    To Configure IEF Selector Defaults

    For Peptide Selector, you can configure these options for isoelectric focusing (IEF):

    Both are configured by editing JavaScript in the file protChem.js, which is located under \SpectrumMill\millhtml\sm_js on your server.

    Save a backup copy of protChem.js prior to editing. Once edits are complete, save a backup copy of the updated file so you can restore it if you reinstall the Spectrum Mill workbench. To edit protChem.js, you must have knowledge of JavaScript syntax.

    To customize the list of pH ranges to select:

    1. Edit protChem.js.
    2. Look for the displayIEFpHSelections()  function near the bottom of the file.
    3. Customize the function to add the appropriate "<option>" elements to the selection lists.
    4. Save the file, refresh the Peptide Selector page, and verify that the new selections are present and no JavaScript errors occur.
    5. Save a backup copy of the updated protChem.js.

    To customize the list of fractions to select:

    1. Edit protChem.js.
    2. Look for the displayIEF_fractions() function near the bottom of the file.
    3. Customize the function to add the appropriate "<option>" elements to the selection lists.
    4. Save the file, refresh the Peptide Selector page, and verify that the new selections are present and no JavaScript errors occur.
    5. Save a backup copy of the updated protChem.js.

     


    IIS Settings for Spectrum Mill Server

    See Tips and Tricks. See also Resolving Connection Timeout Problems.


    Server Administration Scripts (milladmin folder)

    The folder milladmin contains various scripts that you may use to configure a Spectrum Mill Web site installation.

    Before you run these scripts, please check with your system administrator!

    System Administrators PLEASE NOTE: We recommend that you make the milladmin folder accessible only by the Administrators group!

    Run all scripts from a command line on the server. (To display a command line, from the Windows Start menu, either select Run... and type cmd.exe, or select Programs > Accessories > Command Prompt.) Note: Run these scripts from an elevated command window or in Windows Explorer using “Run As Administrator”.

    You may customize these scripts. In some cases, you must customize them. (See instructions for individual scripts to determine which ones you must customize.) To customize, make a copy and edit your copy. A re-install of Spectrum Mill overwrites these scripts.

    The milladmin folder contains the following scripts:

    1) IIS configuration scripts for the Spectrum Mill workbench

    If CScript is the default scripting engine, you must specify wscript before the command:

    E:\SpectrumMill\milladmin> wscript getcgi.vbs

    The setcgi.vbs script requires the CGI timeout value in seconds. The Spectrum Mill default is 30000 seconds:

    > setcgi.vbs 30000

    2) Script to set critical file permissions

    The script smSetFilePermissions.pl sets file permissions for critical Spectrum Mill files. You must first copy and edit this file for your server settings. 

    This script does not set permissions for msdataSM. To set permissions for msdataSM folders, edit this script (see comments within the script), or use the smSetmsdataSMPermissions.pl script. 

    3) Script to set file access permissions on msdataSM and subfolders

    The script smSetmsdataSMPermissions.pl  grants or changes (modifies) file access permissions on msdataSM and subfolders, or on a specific subfolder under msdataSM. You may also specify a list of users.

    Usage:

    > smSetmsdataSMPermissions.pl [ /f subfolder ] [user list]

    To specify a particular subfolder, use the /f option followed by a space, then the subfolder.

    By default the user is IUSR. Specific users may be specified as space-separated lists.

    Example:

    > smSetmsdataSMPermissions.pl /f ExampleData myDomain\user1 myDomain\user2

    The above grants or changes  permission for user1 and user2 in the myDomain domain.

    If you need to remove permissions for a user, make a copy of this script, and edit the copy so that the permission is revoked (/R) instead of granted (/G). Please see the documentation for the windows CACLS.EXE program for additional details.

    4) Script to create data file placeholders to allow you to remove raw data files

    Use the PERL script smCreateDataPlaceholder.pl to create "placeholder" files for your data files. Once you have created placeholder files, you can archive and remove the raw data files to free up disk space. For each data file it finds, the script creates a placeholder with the same root file name, but with a different file suffix:

    Note that data extractor for Agilent Trap and Q-TOF data automatically creates an ".aph" placeholder file, so creation of this placeholder is not necessary.

    You must run the smCreateDataPlaceholder.pl script from the command line in the milladmin folder. By default, the script processes all of msdataSM. You can specify a particular subfolder by providing it as a parameter. For example, to process only the msdataSM\ExampleData subfolder, run:

    E:\SpectrumMill\milladmin> smCreateDataPlaceholder.pl ExampleData

    Once you have created placeholders, use the Windows Explorer's Search feature to look for raw data files (.raw) and folders (.d). You can the select them for archival to another drive, computer, or other backup device. If you choose to remove the raw data files, you can continue to search and summarize the results. However, the raw data files are required if you need to re-extract the data.

     


    Resolving Connection Timeout Problems

    The default Internet Information Server (IIS) settings applied by the Spectrum Mill installation may not be suitable when you process large data sets with long extraction and search times. To avoid having your connections time out, change IIS settings on the Spectrum Mill server, as described in this section. To apply the new settings you must be at the server, logged in as an administrator.

    1) Open the IIS Manager

    Use the Control Panel or the Computer Management Console to open the IIS Manager.

    2) Display the property sheet for the default Web site

    1. Under Internet Information Services, right-click Default Web Site and select Properties.
    2. Check that you see the properties for the default Web site (which is the Spectrum Mill Web site). 

    3) Increase the value for connection timeout

    The IIS default connection timeout is 120 seconds. For the Spectrum Mill workbench, this should be set to 900 (or higher).

    1. Click the Web Site tab.
    2. Change the Connection Timeout to 900 seconds.
    3. Click OK.
    4. Leave the Computer Management window displayed; you will need to return to it for later tasks. 

    4) Increase the value for CGI timeout

    The SpectrumMill\milladmin folder contains a getcgi.vbs script that shows the current CGI timeout, and a setcgi.vbs script that sets a new value.

    When you install the Spectrum Mill workbench, the CGI timeout is set to 30000 (about 8 hours) for the Spectrum Mill (default) Web site. The example below shows how to increase the value to 300000 seconds. Note that even larger values might be necessary in some applications. The maximum value is 2100000 seconds (about 24 days).

    To change the setting:

    1. Open a DOS command window.
      1. From the Desktop, click Start > Run.
      2. In the Open: box, type cmd.exe.
      3. Click OK.
    2. Change the directory to yourdrive:\SpectrumMill\milladmin.
      1. Change the drive to the location of the Spectrum Mill software. For example, if the current drive is C: and you installed the Spectrum Mill workbench in E:, type E:.
      2. Type chdir SpectrumMill\milladmin.
    3. Change the CGI timeout.
      1. Type setcgi.vbs 300000.
      2. Click OK when you see a message in a Windows Script Host window that indicates that the timeout was changed.
      3. Click OK when you see a message that indicates that you need to restart the Spectrum Mill Web site for the changes to occur.
    4. Restart the Spectrum Mill Web site.
      1. Return to the Computer Management window that you displayed earlier.
      2. If necessary, click to expand Internet Information Services.
      3. Right-click Default Web Site and select Stop.
      4. Right-click Default Web Site and select Start

    5) If necessary, change MinFileBytesPerSec 

    This setting is available only on Windows XP and WS2003. It is not available on WS2000.

    When connection timeouts occur, IIS logs them in the HTTPERR log files. These are located under WINDOWS\system32\LogFiles\HTTPERR. Typically, there is only one file: httperr1.log. If any of the connection timeouts for a Spectrum Mill request (typically batchTagPara.pl) indicate a Timer_MinFileBytesPerSec cause, then you need to set MinFileBytesPerSec to a lower value. The only way to do this is with a script, as described below. In general, first set the value to 0 in order to get searches to succeed, then, if time and patience permit, increase the value. The default value is 120.

    To change the setting:

    1. Open a DOS command window.
      1. From the Desktop, click Start > Run.
      2. In the Open: box, type cmd.exe.
      3. Click OK.
    2. Change the directory to yourdrive:\SpectrumMill\milladmin.
      1. Change the drive to the location of the Spectrum Mill software. For example, if the current drive is C: and you installed the Spectrum Mill workbench in E:, type E:.
      2. Type chdir SpectrumMill\milladmin.
    3. Type setMinFileBytesPerSec.vbs 0.
    4. Check that the script displays the former value and the new value.

    If you decrease the Batch Size for MS/MS Search, you may reduce the need to lower the setting for MinFileBytesPerSec, but at the expense of slightly longer overall searches.

    Additional Tips

    Make sure that you keep the browser open to the page where you submitted the search or other request. If you page back, go to another page or site,  or close the browser, the connection will be dropped.

    Please review recommended workflow and search settings for the Spectrum Mill workbench, as described in the Application Guide and the Familiarization Guide. In many cases, while the data sets may be large, you can drastically reduce the search times by following the recommended practices. Users who are accustomed to other search programs may not be familiar with the best use of Spectrum Mill.

    Security

    The above settings, while enabling long searches, do increase your web server’s vulnerability to what are called “Denial of Service Attacks.” It is important to occasionally check the HTTPERR logs for non-Spectrum Mill clients that try to run processes on your server. Look especially for the following:

    Since the Spectrum Mill directory structure is not the typical CGI-style layout, most such attacks fail because they target the typical CGI folders. The log will indicate the client IP address that initiated the request, so check that client for possible virus and worm infections. You can also configure IIS to deny all requests to a particular IP address. (See IIS Help.)

     


    To Limit the Number of Parallel Workflow Processes to Less Than the CPU Count

    Before you modify any files, be sure to archive the originals so they can be restored if necessary!

    When you execute a workflow, its tasks are added to the Spectrum Mill Request Queue, and executed in order for a particular data folder. If you select multiple data folders, the data folders are processed in parallel. The number of parallel tasks is limited by the number of (logical) processors on the server. If you want to limit the maximum number to less than the CPU count, edit the file:

    \SpectrumMill\millsrm\SMSRM.config  

    1. Stop the SRM service. For guidance, see Stop and restart the SRM service.
    2. Find the line in \SpectrumMill\millsrm\SMSRM.config that contains maxConcurrentTasks. The line of text is similar to this example:
      <provider hostname="localhost" available="true" maxConcurrentTasks="3" minRequiredTaskMemoryGb="2">
    3. Change the number after maxConcurrentTasks and resave the file.
    4. For the new settings to take effect, restart the SRM Service. For guidance, see Stop and restart the SRM service.

    Note: By default, if there are > 2 CPUs, Spectrum Mill configures the limit to numCPUs -1.  If you have less than 1Gb per CPU (including multicore), you should reduce the number of parallel workflow processes.  For example, for a dual-quad core system with only 8Gb of memory you should set the value to 3 or 4 at most.

    The new setting with multicore processing: minRequiredTaskMemoryGb="2" is the minimal amount of free memory availablefor Spectrum Mill to run more than one concurrent task. It avoids using up all memory, which can lead to poor performance when the swap file becomes heavily used. The 2Gb value is a reasonable default for 16Gb-32Gb of memory. If you find your server often runs with all available memory when it is in use, consider increasing this value or reducing the number of cores to use.


    To Start and Stop the Spectrum Mill Workflow Manager Service

    Spectrum Mill uses a Windows Service Request Manager (SRM) service to process workflows. The "Spectrum Mill Workflow Manager Service" is configured to automatically start when Windows starts.

    To stop the service (Users on Windows 7 or Windows Server 2008 must Run as administrator.):

    1. Wait until the Request Queue is empty. (Anything in the queue will be lost.)
    2. Navigate to \SpectrumMill\millsrm  
    3. Double-click stopSRM.bat

    Note: The preferred way to navigate to the folder is to open a cmd.exe window so that if the service cannot be stopped, you see the error.

    If the service continues to run, as a last resort, stop it with Windows Task Manager. In the Processes tab of Task Manager, click SRMHostSvc.exe, and then click End Process.

    To start the service:

    1. Navigate to \SpectrumMill\millsrm
    2. Double-click startSRM.bat


    To Enable the Classic Protein/Peptide Summary Modes

    Before you modify any files, be sure to archive the originals so they can be restored if necessary!

    Edit the file:

    E:\SpectrumMill\millhtml\SM_js\SMglobals.js

    Look for the following:

    /// Protein Peptide Summary mode

    /// As of B.05.00, certain modes have been removed

    /// Set the following variable to true to enable listing the older summary modes for selection

    PPSummaryClassicMode = false;

    And change the variable setting to true:

    /// Protein Peptide Summary mode

    /// As of B.05.00, certain modes have been removed

    /// Set the following variable to true to enable listing the older summary modes for selection

    PPSummaryClassicMode = true;

    Then refresh the page.


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