Software:TPP-MaRiMba
From SPCTools
| Revision as of 02:32, 5 March 2009 Csherwood (Talk | contribs) ← Previous diff |
Revision as of 03:05, 5 March 2009 Csherwood (Talk | contribs) (Adding filtering options table) Next diff → |
||
| Line 17: | Line 17: | ||
| '''3. Select a list of proteins or peptides to which the MRM list should be restricted [optional input]''' | '''3. Select a list of proteins or peptides to which the MRM list should be restricted [optional input]''' | ||
| - | To restrict the MRM list to a set of proteins, the input protein list must be a tab-delimited text file containing a single column of protein identifiers corresponding to the proteins of interest. These identifiers must be of the same naming system used in the protein database provided in Step 2. | + | To restrict the MRM list to a set of proteins, the input protein list must be a tab-delimited text file containing a single column of protein identifiers corresponding to the proteins of interest. These identifiers must be of the same naming system used in the protein database provided in Step 2. Providing an input list here will introduce a selection at the top of Section 5 where it must be specified that the list corresponds to proteins. |
| - | To restrict the MRM list to a set of peptides, the input peptide list must be a tab-delimited text file containing a single column of peptides in the format XXXXX/z, where XXXXX is the peptide sequence and z is the charge state. The charge state must be specified because MaRiMba works at the peptide ion level, treating peptides of different charge states as separate entries altogether, due to their unique m/z values. Modifications can be specified in the sequence by listing, to the right of the modified residue, the modified mass rounded to the nearest digit. For example, the entry LGPNYLQIPVNC[160]PYR/2 specifies the peptide LGPNYLQIPVNCPYR with charge state 2+ and carbamiodomethyl cysteine. | + | To restrict the MRM list to a set of peptides, the input peptide list must be a tab-delimited text file containing a single column of peptides in the format XXXXX/z, where XXXXX is the peptide sequence and z is the charge state. The charge state must be specified because MaRiMba works at the peptide ion level, treating peptides of different charge states as separate entries altogether, due to their unique m/z values. Modifications can be specified in the sequence by listing, to the right of the modified residue, the modified mass rounded to the nearest digit. For example, the entry LGPNYLQIPVNC[160]PYR/2 specifies the peptide LGPNYLQIPVNCPYR with charge state 2+ and carbamiodomethyl cysteine. Providing an input list here will introduce a selection at the top of Section 5 where it must be specified that the list corresponds to peptides. |
| Either a protein or peptide list can be specified, but not both. If no list is specified, all peptides from the spectral library that meet the filtering criteria will remain in the MRM list. | Either a protein or peptide list can be specified, but not both. If no list is specified, all peptides from the spectral library that meet the filtering criteria will remain in the MRM list. | ||
| Line 30: | Line 30: | ||
| This step of the MaRiMba process allows the user to fully customize the MRM list by specifying precursor peptide and product ion properties required for transitions in the MRM list. Any transition that does not meet these criteria will be filtered out and not included in the output file. These filtering options are described in the table below. | This step of the MaRiMba process allows the user to fully customize the MRM list by specifying precursor peptide and product ion properties required for transitions in the MRM list. Any transition that does not meet these criteria will be filtered out and not included in the output file. These filtering options are described in the table below. | ||
| + | |||
| + | {| class="wikitable" border="1" cellpadding="5" | ||
| + | |+ '''Filtering Options in MaRiMba''' | ||
| + | |- | ||
| + | !Option!!Recommended Setting | ||
| + | |- | ||
| + | |colspan=4|'''''Precursor Peptide Options''''' | ||
| + | |- | ||
| + | | Minimum number of transitions per peptide||3 | ||
| + | |- | ||
| + | | Maximum number of transitions per peptide||10 | ||
| + | |- | ||
| + | | Allowable charge states||+2 | ||
| + | |- | ||
| + | | m/z range||300 - 1200 | ||
| + | |- | ||
| + | | pI range||Sample-dependent | ||
| + | |- | ||
| + | | Exclude residues||M | ||
| + | |- | ||
| + | | Exclude N-terminal residues||Q | ||
| + | |- | ||
| + | | Exclude all modifications except carbamiodomethyl Cys [y/n]||Yes for samples treated with iodoacetamide | ||
| + | |- | ||
| + | | Add transitions for modified residues||Yes for isotopic labeling strategies such as SILAC | ||
| + | |- | ||
| + | | When mapping peptides to proteins, consider peptides in all contexts or in a tryptic context only||All contexts | ||
| + | |- | ||
| + | | Retain proteotypic peptides only or allow non-proteotypic peptides||Proteotypic peptides only | ||
| + | |- | ||
| + | |colspan=4|'''''Product Ion Options''''' | ||
| + | |- | ||
| + | | Allowable charge states||+1 | ||
| + | |- | ||
| + | | Allowable ion types||y-ions | ||
| + | |- | ||
| + | | Allow neutral losses [y/n]||No | ||
| + | |- | ||
| + | | Allow small secondary neutral losses [y/n]||No | ||
| + | |- | ||
| + | | Allow non-monoisotopic peaks [y/n]||No | ||
| + | |- | ||
| + | | Allow mass-shifted ions [y/n]||No | ||
| + | |- | ||
| + | | Fragment ion lengths to exclude|| 1, 2, 3 | ||
| + | |} | ||
| + | |||
| + | |||
| '''6. Click the ''Run MaRiMba'' button to generate the MRM list | '''6. Click the ''Run MaRiMba'' button to generate the MRM list | ||
Revision as of 03:05, 5 March 2009
TPP-MaRiMba: Branch of TPP containing MaRiMba, a tool for the creation of customized MRM lists from spectral libraries
MaRiMba is a software tool for the automated creation of explicitly defined transition lists required for multiple reaction monitoring (MRM) experiments. MaRiMba creates MRM transition lists from downloaded or custom-built spectral libraries, restricts output to specified proteins or peptides of interest, and filters MRM lists based on user-defined precursor peptide and product ion properties. MaRiMba can also create MRM lists containing isotopically heavy transitions for use with isotopic labeling strategies such as SILAC. MaRiMba outputs the final MRM list to a text file convenient for upload to a mass spectrometer.
Contents |
User's Guide
MaRiMba is most easily operated through the Petunia web interface of the TPP. To access MaRiMba, launch the TPP interface and browse to SpectraST Tools --> MaRiMba. The MaRiMba interface provides the user with various options for MRM list creation and customization. The steps of MRM list generation with MaRiMba are described below.
1. Select a spectral library on which to base the MRM list [required input]
The selected spectral library serves as the source of transitions for the ensuing MRM list. This spectral library can be downloaded or custom-built, but it must be in the SpectraST-compatible .splib format. If the former is desired, the user can download largely comprehensive spectral libraries from PeptideAtlas, which distributes SpectraST-compatible libraries for common NIST databases (http://www.peptideatlas.org/speclib/). If the latter is preferred, the user can create a spectral library from his/her own shotgun-MS data using SpectraST, which is available in the TPP software suite with which MaRiMba is packaged.
2. Select a protein database corresponding the organism(s) in question [required input]
This database represents the entity against which both protein identifiers and peptide-protein uniqueness are determined, as MaRiMba re-maps all library entries to the proteins in this database. By default, all unmapped peptides are removed from the spectral library. Further mapping options are included in the Filtering Options section (see Step X below).
3. Select a list of proteins or peptides to which the MRM list should be restricted [optional input]
To restrict the MRM list to a set of proteins, the input protein list must be a tab-delimited text file containing a single column of protein identifiers corresponding to the proteins of interest. These identifiers must be of the same naming system used in the protein database provided in Step 2. Providing an input list here will introduce a selection at the top of Section 5 where it must be specified that the list corresponds to proteins.
To restrict the MRM list to a set of peptides, the input peptide list must be a tab-delimited text file containing a single column of peptides in the format XXXXX/z, where XXXXX is the peptide sequence and z is the charge state. The charge state must be specified because MaRiMba works at the peptide ion level, treating peptides of different charge states as separate entries altogether, due to their unique m/z values. Modifications can be specified in the sequence by listing, to the right of the modified residue, the modified mass rounded to the nearest digit. For example, the entry LGPNYLQIPVNC[160]PYR/2 specifies the peptide LGPNYLQIPVNCPYR with charge state 2+ and carbamiodomethyl cysteine. Providing an input list here will introduce a selection at the top of Section 5 where it must be specified that the list corresponds to peptides.
Either a protein or peptide list can be specified, but not both. If no list is specified, all peptides from the spectral library that meet the filtering criteria will remain in the MRM list.
4. Specify an output file
Type the file path and file name to which the output MRM list should be written. Since this list is a tab-delimited text file, a file extension of .txt or .tsv is recommended, but not required.
5. Enter transition filtering options
This step of the MaRiMba process allows the user to fully customize the MRM list by specifying precursor peptide and product ion properties required for transitions in the MRM list. Any transition that does not meet these criteria will be filtered out and not included in the output file. These filtering options are described in the table below.
| Option | Recommended Setting | ||
|---|---|---|---|
| Precursor Peptide Options | |||
| Minimum number of transitions per peptide | 3 | ||
| Maximum number of transitions per peptide | 10 | ||
| Allowable charge states | +2 | ||
| m/z range | 300 - 1200 | ||
| pI range | Sample-dependent | ||
| Exclude residues | M | ||
| Exclude N-terminal residues | Q | ||
| Exclude all modifications except carbamiodomethyl Cys [y/n] | Yes for samples treated with iodoacetamide | ||
| Add transitions for modified residues | Yes for isotopic labeling strategies such as SILAC | ||
| When mapping peptides to proteins, consider peptides in all contexts or in a tryptic context only | All contexts | ||
| Retain proteotypic peptides only or allow non-proteotypic peptides | Proteotypic peptides only | ||
| Product Ion Options | |||
| Allowable charge states | +1 | ||
| Allowable ion types | y-ions | ||
| Allow neutral losses [y/n] | No | ||
| Allow small secondary neutral losses [y/n] | No | ||
| Allow non-monoisotopic peaks [y/n] | No | ||
| Allow mass-shifted ions [y/n] | No | ||
| Fragment ion lengths to exclude | 1, 2, 3 | ||
6. Click the Run MaRiMba button to generate the MRM list
The run-time of MaRiMba depends heavily on the sizes of the input files, but is generally on the order of a minute. When complete, the customized MRM list will be written to the user-specified location. It can be viewed through the TPP web interface via the Browse Files tool in the Utilities section. Alternatively, MaRiMba output files can be viewed through spreadsheet programs such as Excel.
Getting the Software
Current Version
The current version of TPP-MaRiMba is 4.1.0. This number reflects the main TPP version number, from which TPP-MaRiMba is branched. TPP-MaRiMba is slated for public release in early 2009, after which MaRiMba will merged with the main TPP release.
Requirments
- Windows XP, Service Pack 2 or above
- ActivePerl, version 5.8 or above
For instrument-to-mzXML conversion, a non-MaRiMba-related component of the TPP, you will also need the corresponding vendor software on the same system. See Formats:mzXML for more information.
Downloading the software
The software will be available for public download from this site after publication of the manuscript (currently under review).
Installing the software
- Download and install ActivePerl, version 5.8 or above (http://www.activestate.com/activeperl/)
- Download and run the TPP-MaRiMba installer, following the directions for default installation
Resources
- To receive email announcements regarding the TPP, sign up for the SPC Tools Announcement Group at spctools-announce.googlegroups.com
- To post a question or comment regarding TPP and/or MaRiMba, use the SPC Tools Discussion Group at spctools-discuss.googlegroups.com
- Public spectral libraries are available for download at PeptideAtlas
