Software:TPP-MaRiMba

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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.

1 User's Guide
- 1.1 MaRiMba Workflow
- 1.2 MaRiMba Output
2 Getting the Software
3 Reference
4 Resources

[edit]

User's Guide

[edit]

MaRiMba Workflow

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 5 below). The provided protein database must be in the FASTA format.

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.

**Filtering Options in MaRiMba**
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.

[edit]

MaRiMba Output

The MRM list generate by MaRiMba is a tab-delimited text file that contains only the precursor-product transitions meeting all of the user-defined criteria, with each row representing a single transition. The number of columns included in the output depends on whether or not the option to incorporate isotopic modifications is selected. If the option is not enabled, the MaRiMba-generated MRM list contains 18 columns of information for each precursor-product transition. Two additional columns are included if isotopic modifications are incorporated. Descriptions of each of these informational fields is provided below.

**MaRiMba Output Column Descriptions**
Column Number	Column Header	Description
1	PROTEIN	The protein identifier(s) of the protein(s) corresponding to the given peptide
2	NUM_PROTEINS	The number of proteins that correspond to the given peptide. This is always 1 if only proteotypic peptides are accepted.
3	MOD_PEPTIDE	The peptide sequence including modifications
4	PEPTIDE_SEQ	The stripped peptide sequence (e.g. without modifications)
5	INTENSITY	The intensity of the fragment as listed in the input spectral library
6	Q1_MZ	The m/z value of the precursor peptide
7	Q3_MZ	The m/z value of the product ion
8	SSRCALC_RT	The theoretical retention time of the peptide, as calculated by algorithm 3.0 of the Sequence Specific Retention Calculator
9	FRAGMENT_TYPE	The ion type and length of the product ion (e.g. "y7")
10	NTERM_RESIDUE	The amino acid N-terminal of the amide bond fragmented to produce the product ion
11	CTERM_RESIDUE	The amino acid C-terminal of the amide bond fragmented to produce the product ion
12	Q1_Z	The charge state of the precursor peptide
13	Q3_Z	The charge state of the product ion
14	PI	The isoelectric point of the peptide
15	SINGLE_SAMPLE_MAX_REPS	The largest number of spectrum replicates used from a single sample when producing the consensus spectrum for the peptide
16	TOTAL_NUM_REPS	The total number of spectrum replicates used to produce the consensus spectrum for the peptide (maximum of 100)
17	ALL_FRAGMENTS	The full annotation of the fragment ion in the spectral library, which includes all possible explanations of the fragment. If multiple entries are included, the first entry is the most likely explanation and is used to populate the FRAGMENT_TYPE field (column 9).
18 (20)	PEPTIDE_URL	The URL for a webpage that illustrates the location of the peptide in the sequence of each mapped protein. This is always the last column of the MRM list.
Columns specific to isotopic labeling option
18	MODIFIED	Indicates whether the transition is the heavy ("H") or light ("L") version
19	MODIFICATION_INDEX	Contains an integer value that is unique to each heavy-light transition pair

[edit]

Getting the Software

[edit]

Current Version

The current version of TPP-MaRiMba is 4.1.1, which was released for public use in July 2009. This number reflects the main TPP version number, from which TPP-MaRiMba is branched. TPP-MaRiMba is slated for merger with the main TPP during its version 4.4 release.

[edit]

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.

[edit]

Downloading the software

TPP-MaRiMba is currently available for public download at http://tools.proteomecenter.org/software/MaRiMba/TPP_Setup_v4_1_MaRiMba_rev_1.exe.

[edit]

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

[edit]

Reference

Sherwood, Carly, et al. "MaRiMba: a Software Application for Spectral Library-Based MRM Transition List Assembly." Journal of Proteome Research, 2 Oct 2009, 8 (10), pp 4396–4405. Full text.

[edit]

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
A full tutorial with example files is included in the installation package of TPP-MaRiMba

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba"

 ==User's Guide==
-MaRiMba is most easily operated through the [[http://tools.proteomecenter.org/wiki/index.php?title=Software:Petunia 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.
+===MaRiMba Workflow===
+MaRiMba is most easily operated through the [[Software:Petunia|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]'''
 '''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).
+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 5 below). The provided protein database must be in the [http://en.wikipedia.org/wiki/FASTA_format FASTA format].
 '''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.
 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
 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.
+===MaRiMba Output===
+The MRM list generate by MaRiMba is a tab-delimited text file that contains only the precursor-product transitions meeting all of the user-defined criteria, with each row representing a single transition. The number of columns included in the output depends on whether or not the option to incorporate isotopic modifications is selected. If the option is not enabled, the MaRiMba-generated MRM list contains 18 columns of information for each precursor-product transition. Two additional columns are included if isotopic modifications are incorporated. Descriptions of each of these informational fields is provided below.
+{| class="wikitable" border="1" cellpadding="5"
+|+ '''MaRiMba Output Column Descriptions'''
+|-
+!Column Number!!Column Header!!Description
+|-
+| 1||PROTEIN||The protein identifier(s) of the protein(s) corresponding to the given peptide
+|-
+| 2||NUM_PROTEINS||The number of proteins that correspond to the given peptide. This is always 1 if only proteotypic peptides are accepted.
+|-
+| 3||MOD_PEPTIDE||The peptide sequence including modifications
+|-
+| 4||PEPTIDE_SEQ||The stripped peptide sequence (e.g. without modifications)
+|-
+| 5||INTENSITY||The intensity of the fragment as listed in the input spectral library
+|-
+| 6||Q1_MZ||The m/z value of the precursor peptide
+|-
+| 7||Q3_MZ||The m/z value of the product ion
+|-
+| 8||SSRCALC_RT||The theoretical retention time of the peptide, as calculated by algorithm 3.0 of the Sequence Specific Retention Calculator
+|-
+| 9||FRAGMENT_TYPE||The ion type and length of the product ion (e.g. "y7")
+|-
+| 10||NTERM_RESIDUE||The amino acid N-terminal of the amide bond fragmented to produce the product ion
+|-
+| 11||CTERM_RESIDUE||The amino acid C-terminal of the amide bond fragmented to produce the product ion
+|-
+| 12||Q1_Z||The charge state of the precursor peptide
+|-
+| 13||Q3_Z||The charge state of the product ion
+|-
+| 14||PI||The isoelectric point of the peptide
+|-
+| 15||SINGLE_SAMPLE_MAX_REPS||The largest number of spectrum replicates used from a single sample when producing the consensus spectrum for the peptide
+|-
+| 16||TOTAL_NUM_REPS||The total number of spectrum replicates used to produce the consensus spectrum for the peptide (maximum of 100)
+|-
+| 17||ALL_FRAGMENTS||The full annotation of the fragment ion in the spectral library, which includes all possible explanations of the fragment. If multiple entries are included, the first entry is the most likely explanation and is used to populate the ''FRAGMENT_TYPE'' field (column 9).
+|-
+| 18 (20)||PEPTIDE_URL||The URL for a webpage that illustrates the location of the peptide in the sequence of each mapped protein. This is always the last column of the MRM list.
+|-
+|colspan=4|'''''Columns specific to isotopic labeling option'''''
+|-
+| 18||MODIFIED||Indicates whether the transition is the heavy ("H") or light ("L") version
+|-
+| 19||MODIFICATION_INDEX||Contains an integer value that is unique to each heavy-light transition pair
+|}
 ==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.
+The current version of TPP-MaRiMba is 4.1.1, which was released for public use in July 2009.  This number reflects the main TPP version number, from which TPP-MaRiMba is branched.  TPP-MaRiMba is slated for merger with the main TPP during its version 4.4 release.
 ===Requirments===
 ===Downloading the software===
-The software will be available for public download from this site after publication of the manuscript (currently under review).
+TPP-MaRiMba is currently available for public download at http://tools.proteomecenter.org/software/MaRiMba/TPP_Setup_v4_1_MaRiMba_rev_1.exe.
 ===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
+==Reference==
+Sherwood, Carly, ''et al.'' "MaRiMba: a Software Application for Spectral Library-Based MRM Transition List Assembly." ''Journal of Proteome Research'', 2 Oct 2009, 8 (10), pp 4396–4405. [http://dx.doi.org/10.1021/pr900010h Full text].
 ==Resources==
 * 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 [http://www.peptideatlas.org/speclib/ PeptideAtlas]
+* A full tutorial with example files is included in the installation package of TPP-MaRiMba

Software:TPP-MaRiMba

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Contents

User's Guide

MaRiMba Workflow

MaRiMba Output

Getting the Software

Current Version

Requirments

Downloading the software

Installing the software

Reference

Resources

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