Matrix Science header

Updating from earlier versions of Mascot Parser

Upgrading to Mascot Parser 2.6.1 from 2.6.0

The matrix_science::ms_spectral_lib_file::FILE_FORMAT enum has been replaced by the matrix_science::ms_spectral_lib::FILE_FORMAT enum.

Upgrading to Mascot Parser 2.6.1 from 2.6.0

Reading spectral library search results

Mascot 2.6 introduced integrated spectral library searches, where the peak lists are searched simultaneously against FASTA database(s) and NIST-format spectral libraries. The results file contains additional sections for spectral library metadata and matches to library entries. There are no changes to the non-library sections of the file.

Opening the files in Parser 2.5 and earlier requires no changes to your code; the file works as if it contained no spectral library data.

The default mode in Parser 2.6 and later is to mimic 2.5. That is, if you use the default flags, for example from get_ms_mascotresults_params(), then the file is opened in "Mascot-only" mode. If you want to see the library matches, specify either MSPEPSUM_SL_INTEGRATED or MSPEPSUM_SL_ONLY as the special mode flag to the ms_peptidesummary constructor.

See Spectral libraries for more information.

Modification Statistics

In Mascot 2.6, Modification Statistics are based on modifications observed in rank 1 significant matches assigned to a protein hit, whereas they used to be based on matches which could be in the unassigned list.

This change applies to methods matrix_science::ms_mascotresults::getNumDiscoveredFixedMods(), matrix_science::ms_mascotresults::getNumDiscoveredVariableMods(), matrix_science::ms_mascotresults::getNumDiscoveredLocalMods(), matrix_science::ms_mascotresults::getDiscoveredLocalModNames(), matrix_science::ms_mascotresults::getNumDiscoveredErrTolMods(), matrix_science::ms_mascotresults::getDiscoveredErrTolModNames(), matrix_science::ms_mascotresults::getDiscoveredErrTolModDeltas(), matrix_science::ms_mascotresults::getNumDiscoveredLibraryMods(), matrix_science::ms_mascotresults::getNumDiscoveredNonSpecCleavage() .

Upgrading to Mascot Parser 2.5.x from 2.4.x

Specifying xml schema file locations

In Mascot Parser, functions and classes that access Unimod or Quantitation XML configuration files require the schema files in order to validate the XML content. The required schema files are supplied with Mascot Parser in the config directory. The Mascot result files, (accessed using the ms_mascotresfile class), also contain a copy of the relevant part(s) of the XML configuration files that were used during the search. In Mascot 2.4 and earlier, some ms_mascotresfile member functions, or functions that pass a ms_mascotresfile object also require the relevant schema file. To avoid having to specify the schema file in multiple places, a directory can now be passed to the constructor to specify the location of the schema files. Additionally, a new function: setXMLschemaFilePath() may be called for finer grained access.

To ensure backward compatibility, it was necessary to add an additional parameter (with a default value) to ms_mascotresfile::getUnimod. If you are using this function, then this version of Mascot Parser is backward compatible with your existing code. However to simplify your code, if you have passed the relevant directory to the ms_mascotresfile constructor, then you may wish to remove the call to ms_umod_configfile::setSchemaFileName and then pass 'true' as useSchemaFromResfile when calling ms_mascotresfile::getUnimod.

It is strongly recommended that applications using Mascot Parser now:

ms_mascotresfile now inherits from ms_errors

For consistency and simplicity, ms_mascotresfile now inherits from ms_errors.

The enumerated definitions for errors declared in error numbers are now deprecated. The error numbers defined at ms_errs::err should be used instead for new applications. The numbers for the two lists are the same and have not been changed in any version of Parser, thus ensuring backward compatibility.

The following functions

just call the relevant ms_errs functions.

ms_connection_settings additions

In Mascot Parser 2.1 and later, it is possible to download and parse configuration files from a remote Mascot Server using http. When accessing these files remotely, for example, using ms_enzymefile it is necessary to supply an ms_connection_settings object. In versions prior to 2.5, when the Mascot Server has authentication enabled, an http username and password needed to be supplied in the url for the ms_enzymefileobject. In Parser 2.5 and later, it is more convenient to supply these values using: ms_connection_settings::setHttpUsername and ms_connection_settings::setHttpPassword

User group based modification privacy. ms_umod_configfile and ms_modfile behaviour changes

Mascot Server 2.5 now allows locally defined modifications to have restricted access based on user groups. If security is enabled then Mascot Parser 2.5 will check these restrictions and remove modifications from the ms_modfile and ms_modfile object instances. During construction, passing a valid ms_connection_settings object with a session_id into these instances will apply the restrictions for that user. If no ms_connection_settings object is used then the default session will be employed. This behaviour will work for both fat and thin client applications.

Windows Compiler support

Support for Visual Studio 6 and VS2003 has been dropped.

Support for VS2010 and VS2012 has been added.

Windows SDK 2003 SP1 required for Visual Studio 2005

Upgrading to Mascot Parser 2.4.x from 2.3.x

Multiple modifications for the same site

For all versions of Mascot, it has been possible to search using multiple variable modifications for the same residue. In this case, Mascot searches for one modification or the other on each particular site. It never searches for both modifications being applied to the same site.

In Mascot Server 2.4 and later, it is possible to search for two modifications being applied to the same site. This is most useful with chemical labels used for quantitation, so it is currently only implemented when using a Quantitation method with exclusive modifications. For example, with a SILAC method, where the label is Label:13C(6)15N(2), it is also possible to specify Acetyl (K) as a variable modification. When Mascot is searching for the 'heavy' SILAC component it will look for:

The function matrix_science::ms_peptide::getVarModsStr() returns a single string from the q1_p1= line in the results file as before. A new function matrix_science::ms_peptide::getSummedModsStr() returns a new string of the same format.

For example, consider the case where the SILAC label is specified as an exclusive modification, and Methyl (KR) and Acetyl (K) are both specified as variable modifications.

In the case where K1 has the SILAC label + Methylation and K6 has the SILAC label + Acetyl, the results file would contain:

delta1=42.010565,Acetyl (K)
NeutralLoss1=0.000000
. . .
delta3=14.015650,Methyl (KR)
NeutralLoss3=0.000000
. . .
delta6=8.014199,Label:13C(6)15N(2) (K)
NeutralLoss6=0.000000

q3_p1=2,1057.657852,0.000561,8,KQLATKAAR,17,06000060000, . . 
q3_p1_summed_mods=03000010000

matrix_science::ms_peptide::getVarModsStr() would return "06000060000" and matrix_science::ms_peptide::getSummedModsStr() would return "03000010000"

This new functionality is only available when MULTI_SITE_MODS is defined in the search input and this is not enabled by default. See matrix_science::ms_searchparams::getMULTI_SITE_MODS

When using matrix_science::ms_aahelper, use the new overloaded version of createPeptide with the summedMods and summedModsNL parameters. The varModVector passed to matrix_science::ms_aahelper::setAvailableModifications should obviously include the summed mods and the variable mods.

Upgrading to Mascot Parser 2.3.x from 2.2.x

Percolator

In Mascot 2.3 and later, ms-ms searches can also be run through Percolator, and the Percolator scores can then be shown in the Mascot reports. See Using Percolator scores for details.

Support for searching multiple fasta files

There is now support for searching multiple fasta files. A search against a single fasta file will create a results file similar to that in Mascot 2.2. However, when searching multiple fasta files, remember that the same accession may exist in different fasta databases. The following are additional/changed functions that may be useful:

New protein inferencing

New protein grouping. See Using MSRES_CLUSTER_PROTEINS. Software needs to specify the new flag and call matrix_science::ms_mascotresults::getNextFamilyProtein as described in Using MSRES_CLUSTER_PROTEINS

Caching results

It is now possible (but not required) to cache results. This is fully described in Caching Mascot Results

Support for Quantitation 2

An updated schema, version 2.1 (quantitation_2.xsd) is supplied with Mascot Parser 2.3. Version 1.0 was supplied with Mascot Parser 2.x and version 2.0 was supplied with Mascot Distiller 2.3. To support files (for example results files) with quantation_1 and quantation_2 formats, both schema must be made made available.

The following calls worked with Mascot Parser 2.1 and 2.2, but will fail with Mascot Parser 2.3 and Quantiation 2:

  $objResFile = new msparser::ms_mascotresfile("F001234.dat");
  $objQuantFile = new msparser::ms_quant_configfile();
  if ($objResFile->getQuantitation($objQuantFile)) {
    # abort on fatal error. Note that isValid() remains true if there are only warnings
    unless ($objQuantFile->isValid) {
    . . .
  }
  

The schema filenames now need to be set before the getQuantitation() call as described in matrix_science::ms_mascotresfile::getQuantitation

Upgrading to Mascot Parser 2.2.x from 2.1.x

[TODO]

Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:51