Mascot database search > Help > Export search results

Export search results

This utility enables Mascot search results to be exported in a variety of "machine readable" formats. When used interactively, the file format is chosen and customised using a web browser form, displayed by choosing Export Search Results in the format controls of a results report and pressing Format As. In addition, the utility can be executed by scripts, with the options specified on the command line.

Custom XML and CSV

The information contained in these two formats is identical. XML is ideal for importing into a relational database. CSV can be opened in spreadsheets such as Microsoft Excel.

For a Peptide Mass Fingerprint, the result information is structured in a very similar way to a Concise Protein Summary report. For search results that include MS/MS data, you can choose whether to structure the protein list and associated peptide matches in a similar way to a Peptide Summary report or a Protein Family report. To create an export that contains information equivalent to a particular Mascot HTML report, the settings of the format controls must match, plus:

Type of search	HTML Report	Threshold type	Protein Scoring	Same-sets	Sub-sets	Group proteins
PMF	Concise Protein Summary	N/A	N/A	checked	1	N/A
MS/MS	Peptide Summary	Identity	As format controls	checked	As format controls	not checked
MS/MS	Protein Family Report	Homology	MudPIT	checked	1	checked

Precise details for individual data items in the XML export, such as the data type and whether it is optional, can be found in the XML schema mascot_search_results_2.xsd, (documentation). For general XML Schema considerations, see the section further down this page. Documentation was auto-generated using xs3p.

The CSV file contains identical data, organised for display as a spreadsheet. The column headers are tabulated on this page. If you need to change the delimiter to something other than a comma, edit export_dat_2.pl and change the value of $delimiter, near the top of the script.

There are no column headers for quantitation information exported in CSV format. Each row contains peptide quantitation data consisting of pairs of ratio names and ratio values followed by pairs of component names and component intensities. Values are post-normalisation and post-isotope correction. Protein level information follows, in-row, after the last peptide match of each protein. Details can be found on this page.

Protein quantitation information is only available if peptide quantitation has been selected.

Usage

For interactive use, the controls are divided into blocks, with the first block corresponding to the format controls of a results report.

The Optional Search Information block controls which ancillary information is exported. Most of the options are self-explanatory.

The data items in the Header section are

Search title
Timestamp (W3C Date and Time format, e.g. 2005-03-12T08:29:11Z)
User
Email
Report URI (URL or relative path, if executed at command line)
MS data path or URL
Search type
Mascot version
Database
Fasta file
Total sequences
Total residues
Sequences after taxonomy filter
Number of entries searched in error tolerant mode (if applicable)
Number of queries
Warnings messages from the search (as required)

According to the type of search, the Header section may be followed by:

Decoy search summary statistics
Fixed modifications
Variable modifications
Search parameters
Format parameters
Quantitation normalisation factors
A list of cross-links, with specificities and monolink numbering

For speed and efficiency, leave the checkboxes marked with asterisks under Optional Protein Hit Information unchecked. (See Optional Protein Hit Information for further information on the use of these checkboxes).

pepXML

pepXML is the interchange format for database search results used in the Institute for Systems Biology Trans-Proteomic Pipeline.

The pepXML format is only applicable to MS/MS search results, and represents "raw" peptide match data. Information is exported for all matches to all queries, (MS/MS spectra). For each match, extensive information is provided for the first protein in which the peptide is found and more limited information for all the other proteins. This can make the output file very large.

Precise details for individual data items, such as the data type and whether it is optional, can be found in the XML schema. Schema documentation has been generated by xs3p. For general XML Schema considerations, see the section further down this page.

Usage

For speed and efficiency, leave all the checkboxes under Optional Protein Hit Information unchecked. (See Optional Protein Hit Information for further information on the use of these checkboxes).

Limitations

Where elements and attributes are required by the schema, but the data is not available from Mascot, zero length strings are output. For example, the base_name, raw_data_type and raw_data attributes of an msms_run_summary element.
The schema includes extensive information for the first protein in which a peptide match is found, even though this may not be the preferred or final assignment.
The amino acid residues that bracket a peptide are only available if the result file is from Mascot 2.1 or later.
The num_matched_ions attribute of the search_hit element is the number of mass values used to score the match, not the total number of mass values that could be matched to all the calculated ion series.
In a search_result element, the start_scan and end_scan attributes are always set to 0.
modification_info elements are only exported for variable modifications, not for fixed.

mzIdentML

mzIdentML is the data exchange standard for database search results developed by the PSI Proteomics Informatics Standards Group. Originally, it was to be called analysisXML.

Precise details for individual data items, such as the data type and whether it is optional, can be found in the XML schemas of mzIdentML 1.1.0 and mzIdentML 1.2.0. For general XML Schema considerations, see the section further down this page.

A semantic validator for mzIdentML documents was developed by Andreas Bertsch as part of the OpenMS project. It is currently unavailable, but check this page for alternatives.

Usage

For speed and efficiency, leave all the checkboxes under Optional Protein Hit Information unchecked. (See Optional Protein Hit Information for further information on the use of these checkboxes).

Under Query Level Information, check Matched Fragment Ions to output tables of matching experimental and calculated m/z values for each peptide match. This is obviously time consuming and causes a substantial increase in the size of the output file. Check Export data for all Queries to output details for every MS/MS spectrum, including those that got no match to an exported protein and those that got no match at all. Again, this is time consuming and causes a substantial increase in the size of the output file.

mzTab

mzTab is a simple tab-delimited format for database search results developed by the PSI Proteomics Informatics Standards Group. Precise details for individual data items, such as the data type and whether it is optional, can be found in the specification document.

Usage

For speed and efficiency, leave starred checkboxes under Protein Hit Information unchecked.

DTASelect

DTASelect is an application that was written by David L. Tabb at The Scripps Research Institute. Originally intended for analysing Sequest results, it groups peptide matches into proteins and allows a variety of filters to be applied. Although DTASelect includes built-in support for Mascot result files, the information in the result file is not fully utilised and the interface is prone to break with new Mascot releases. Choosing DTASelect in this export utility creates a DTASelect intermediate file, DTASelect.txt, containing a more complete picture of the search results. This intermediate file is then read by DTASelect to create filtered reports.

The output file is compatible with DTASelect 1.9 only. DTASelect format is only applicable to MS/MS search results.

Usage

For speed and efficiency, it is advisable to choose MudPit scoring, an ions score cut-off of 10, and leave all the checkboxes under Optional Protein Hit Information unchecked. (See Optional Protein Hit Information for further information on the use of these checkboxes). Save the exported file to a directory, make this the current directory, and execute DTASelect.

The DTASelect spectrum filters, which can be supplied on the command line or taken from DTASelect.params, should include the following changes to the defaults:

–Mascot
to set Mascot mode
-1 10.0
to set the minimum ions score for 1+ peptides to 10
-2 10.0
to set the minimum ions score for 2+ peptides to 10
-3 10.0
to set the minimum ions score for 3+ peptides to 10
-d 20
to set the minimum for (1 / expectation value) to 20
-p 1
to set the distinct peptide threshold to 1
–mw 100.0
to set the minimum protein mass to 100

In a DTASelect report of Mascot results, the following columns are different from those in a DTASelect report of Sequest results:

Filename
Mascot result filename, query number and precursor charge, separated by periods
IonsScore
Mascot ions score
Signif
1 / expectation value
SpR
Peptide match rank, between 1 (highest) and 10 (lowest)
SpScore
Identity threshold score

Limitations

The output file is compatible with DTASelect 1.9 only
Hyperlinks to Sequest utilities will not work
The number of tryptic termini for a peptide is not available
The amino acid residues that bracket a peptide are only available if the result file is from Mascot 2.1 or later. For result files from earlier versions, question marks are displayed
DTASelect reports do not display variable terminus modifications

Mascot DAT File

A convenient way to download a copy of the "raw" Mascot result file. For security reasons, this will only succeed for result files in the daily directories under the Mascot data directory.

MGF Peak List

A convenient way to extract the peak list from a search result file. May be useful when you export an mzIdentML file, because the mzIdentML schema does not support inclusion of the peak list.

xiVIEW

Search results that include intact crosslinked peptides can be exported to xiVIEW for visualisation.

xiVIEW supports:

Intact crosslinks
Monolinks
Protein ambiguity (sameset proteins)
Any protein accession as long as the correct FASTA file is uploaded too

At the time of writing, xiVIEW does not support:

Looplinks
Large data sets, (if the CSV file is more than about 2 MB, the Javascript code on xiview.org grinds to a halt)

Mascot supports both the xiVIEW CSV format and mzIdentML 1.2.

The basic steps using mzIdentML are:

Export the search as MGF in original input order
Export the search as mzIdentML. Under Protein Information, check Protein Sequence. No need to check Matched Fragment Ions.
Log in to your xiview.org account
Upload the two files

The basic steps using xiVIEW CSV format are:

Export the search as MGF in Mascot query order
Export the search as FASTA
Export the search as xiVIEW CSV
Log in to your xiview.org account
Upload the three files

Miscellaneous

Looplinks are exported as monolinks, with only one end marked in the peptide.
In the CSV format, linear matches with looplinks are omitted from the export. Only crosslinked pairs of peptides are included.
In the CSV format, Mascot exports (query – 1) in the ScanNumber column. This is necessary for alignment with the MGF file (in query order) in xiVIEW.
If any crosslinked match has monolinks, looplinks or variable mods, after uploading the CSV file and the MGF file, xiVIEW will prompt you to enter their masses. Mascot exports modifications as deltas, so these are easy to copy and paste. This step is not necessary when using mzIdentML.
xiVIEW doesn’t recognise terminal modifications. If there is a modified N-term, it’s reported as an N-terminal residue mod. Same for C-term. If a peptide has both N-term and N-terminal residue mod, the mod IDs are concatenated in the xiVIEW interface.

Optional Protein Hit Information

Only a limited amount of information about a protein hit is saved to a Mascot result file. For example, the protein sequence is not saved because this would make the result files unacceptably large. When missing information is required for a Mascot report, it has to be retrieved from the compressed database files.

Even though a single call for missing information may take only a fraction of a second, and is not noticeable when loading a Mascot report, this can become a problem if creating an export file requires thousands of calls. It is important to be aware of this, and not waste time retrieving information that is not actually required. This is a particular issue for an export format that represents "raw" result information, like pepXML. A list of all the proteins that contain all the peptides that had any matches to any of the spectra can be an extremely long list.

Description

The Fasta description line is saved for all peptide mass fingerprint protein hits. For an MS/MS search, Mascot tries to guess which protein hits will appear in the reports and saves their Fasta description lines to the result file. However, the actual hit list depends on many factors, and some hits may be missed, requiring the descriptions to be retrieved from the compressed database files.

Protein Mass

The protein mass is saved for all peptide mass fingerprint protein hits. For an MS/MS search, Mascot tries to guess which protein hits will appear in the reports and saves their masses to the result file. However, the actual hit list depends on many factors, and some hits may be missed, requiring the masses to be retrieved from the compressed database files.

On the Matrix Science public web site, the description and mass of a protein can only be exported if this information was saved to the result file. The following protein hit information options are not available on the public web site, and attempting to use them will have no effect.

Percent coverage

Percent coverage is never saved to the result file. It is calculated on the fly from the length and the set of peptides assigned to the protein.

Length in residues
Length in residues is never saved to the result file. It must be retrieved from the compressed database files.

pI

pI is never saved to the result file. The protein sequence must be retrieved from the compressed database files and the pI value calculated.

Taxonomy

Taxonomy is never saved to the result file. It must be retrieved from the compressed database files.

Taxonomy ID

Taxonomy ID is never saved to the result file. It must be retrieved from the compressed database files.

Protein sequence

The entire protein sequence is never saved to the result file. It must be retrieved from the compressed database files.

Command Line Execution

Result file conversion can be automated by using the export script as a command line utility. It must be executed on the Mascot server using the Mascot copy of the Perl interpreter and with cgi as the current directory. The command line arguments are URL-style name=value pairs, e.g. for Linux:

../perl64/bin/perl export_dat_2.pl file=../data/20120223/F004651.dat do_export=1 export_format=CSV … other arguments … pep_scan_title=1 > ../data/20120223/F004651.csv

(For Windows, replace forward slashes with back slashes.)

To obtain the command-line arguments for a given output, use the form based interface to adjust the settings then choose "Show command line arguments". The command line can then be copied and pasted as required. To direct the output to a file, add a > symbol followed by the path to the output file, as in the example above.

Note that, if Mascot security is enabled, the arguments will include a security session ID, e.g. sessionid=billy_299425468615895. You don’t need to provide a session ID for command line operations, so best to drop this argument in case it becomes invalid before you try to use it.

The script should never output the HTML for the interactive download button when called from the command line, but this can happen if it is called from a CGI script. If this is a problem, add the argument generate_file=1.

Required Arguments

do_export
must be 1 to export results
export_format
XML or CSV or pepXML or DTASelect or MascotDAT or mzIdentML or mzTab or MGF
file
relative or absolute path to result file

XML Schema

Versioning

The Mascot Search Results XML schema uses versioning to avoid applications breaking when the schema is updated. The schema definition is identified by a major version number and a minor version number.

When a change is made to the schema, and any instance document that was valid against the previous schema could become invalid, the major version number will be incremented. An example of such a change would be that a new type or element is added to the schema that is not optional. If a change is made to a schema that cannot break the validity of any existing document, such as adding a new type or element that is optional, then the minor version will be incremented.

There will be a separate schema file and name space for each major version and the file name contains the major version number. The schema also includes the major and minor version numbers as attributes of the top level element. An application that parses an instance document should compare the major and minor version attribute values against those which it was coded to support. It should not rely on an XML parser to verify the version numbers against the schema encoded restrictions, since the schema definition file used by the parser may be newer than when the application was written.

Validation

The instance documents created by this export utility have been validated against the corresponding schema definitions using XMLSpy. The following web tools can also be used:

No complex software is ever completely free of bugs. If you find an XML file created by the Export Search Results utility that fails to validate against the corresponding schema definition, please email full details to support@matrixscience.com and we will try to fix the problem as rapidly as possible.

On the other hand, if the XML file validates, but an error is reported by the application reading the file, then this is a bug in the application. In the first instance, please report this to the authors of the application.

Useful Resources

Standards and design:

Programming:

Schema support in Xerces-C++ – includes SAX2 and DOM examples for overriding xsi:schemaLocation. Xerces 2.6 adds support for grammar caching which could be used to do the same thing by preloading the known schema files.
Properties supported by Xerces2-J – it should be possible to use the external-schemaLocation property in much the same way as the C++ version to override the schema locations. Alternatively, you could use grammar caching instead.
MSXML provides an XMLSchemaCache object for preloading schemas. There are DOM examples and it should be fairly similar in SAX2 except you would use the schemas property of ISAXXMLReader.