comparison peptide_shaker.xml @ 11:e5bdaa2ac9c7 draft

Improved help text

10:5a74b76d48fc

<tool id="peptide_shaker" name="Peptide Shaker" version="1.18.3.0">
    <description>
        Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
    </description>
    <requirements>
        <requirement type="package" version="0.28.0">peptide_shaker</requirement>
        <requirement type="package" version="1.18.0">searchgui</requirement>
        <!--<requirement type="package" version="2.2.29">blast+</requirement>-->

        ## the following line is needed. Otherwise, Galaxy will strip away the ';'
        echo 'Finished!';
    </command>
    <inputs>
        <param format="fasta" name="input_database" type="data" label="Protein Database"
            help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/>

        <param name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" />

        <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)"
            help="Select appropriate MGF dataset(s) from history" />
        <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
            help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">

            <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
            <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
            <option value="Semi-Glu-C">Semi-Glu-C</option>
        </param>

        <param name="correct_titles" type="select" label="Correct for duplicate spectrum titles"
            help="(-correct_titles)">
            <option value="0">no correction</option>
            <option value="1" selected="True">rename spectra</option>
            <option value="2">delete spectra</option>
        </param>

        <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
            help="(-mgf_splitting)"/>
        <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
            help="(-mgf_spectrum_count)"/>

        <conditional name="species_type">
            <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
                help="(-species_type)">
                <option value="Fungi">Fungi</option>
                <option value="Plants">Plants</option>
                <option value="Metazoa">Metazoa</option>
                <option value="Vertebrates">Vertebrates</option>
                <option value="Protists">Protists</option>
                <option value="no_species_type" selected="true">No species restriction</option>
            </param>
            <when value="Protists">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="(-species)">
                    <option value="Albugo laibachii">Albugo laibachii</option>
                    <option value="Dictyostelium discoideum">Dictyostelium discoideum</option>
                    <option value="Entamoeba histolytica">Entamoeba histolytica</option>
                    <option value="Giardia lamblia">Giardia lamblia</option>
                    <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option>

                    <option value="Trypanosoma brucei">Trypanosoma brucei</option>
                </param>
            </when>
            <when value="Plants">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="(-species)">
                    <option value="Arabidopsis lyrata">Arabidopsis lyrata</option>
                    <option value="Arabidopsis thaliana">Arabidopsis thaliana</option>
                    <option value="Brachypodium distachyon">Brachypodium distachyon</option>
                    <option value="Brassica rapa genes">Brassica rapa genes</option>
                    <option value="Chlamydomonas reinhardtii">Chlamydomonas reinhardtii</option>

                    <option value="Zea mays">Zea mays</option>
                </param>
            </when>
            <when value="Metazoa">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="(-species)">
                    <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option>
                    <option value="Aedes aegypti">Aedes aegypti</option>
                    <option value="Amphimedon queenslandica">Amphimedon queenslandica</option>
                    <option value="Anopheles darlingi">Anopheles darlingi</option>
                    <option value="Anopheles gambiae">Anopheles gambiae</option>

                    <option value="Trichoplax adhaerens">Trichoplax adhaerens</option>
                </param>
            </when>
            <when value="Fungi">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="(-species)">
                    <option value="Ashbya gossypii">Ashbya gossypii</option>
                    <option value="Aspergillus clavatus">Aspergillus clavatus</option>
                    <option value="Aspergillus flavus">Aspergillus flavus</option>
                    <option value="Aspergillus fumigatus">Aspergillus fumigatus</option>
                    <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option>

                    <option value="Zymoseptoria tritici">Zymoseptoria tritici</option>
                </param>
            </when>
            <when value="Vertebrates">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="(-species)">
                    <option value="Ailuropoda melanoleuca">Ailuropoda melanoleuca</option>
                    <option value="Anolis carolinensis">Anolis carolinensis</option>
                    <option value="Bos taurus">Bos taurus</option>
                    <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
                    <option value="Callithrix jacchus">Callithrix jacchus</option>

                </param>
            </when>
        </conditional>

        <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
            help="Allow peptides to contain up to this many missed enzyme cleavage sites. 2 is the recommended value"/>
        <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
            help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
            <options from_file="searchgui_mods.loc">
                <column name="name" index="0" />
                <column name="value" index="0" />

            <when value="yes">
                <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
                <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
                <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
                <param name="protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="" type="float"
                    help="default 95%: '95.0' (-protein_fraction_mw_confidence)" />
                <conditional name="ptm_score">
                    <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
                        <option value="0" selected="True">A-score</option>
                        <option value="1">PhosphoRS</option>
                    </param>
                    <when value="0" />
                    <when value="1">
                        <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
                        <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="" type="float"
                            help="Automatic mode will be used if not set." />
                    </when>
                </conditional>
                <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
            </when>
        </conditional>

            </param>
            <when value="no" />
            <when value="yes">
                <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
                <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />
                <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." />
                <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
                    <option value="0">ppm</option>
                    <option value="1">Daltons</option>
                </param>
                <param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" />
                <param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" />
                <param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="(-max_mascot_e)" />
                <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
            </when>
        </conditional>

        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">

            <option value="4" selected="True">Protein Report</option>
            <option value="2">PSM Report</option>
            <option value="0">Certificate of Analysis</option>
            <option value="1">Hierarchical Report</option>
            <option value="cps">CPS file</option>
            <validator type="no_options" message="Please select at least one output file." />
        </param>
    </inputs>
    <outputs>
        <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
            <filter>'cps' in outputs</filter>

**What it does**

Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results.

https://code.google.com/p/peptide-shaker/
https://code.google.com/p/searchgui/

**Reports**

*PSM Report*

Protein(s)	Protein(s) to which the peptide can be attached.
Sequence	Sequence of the peptide.
Variable Modifications	The variable modifications.
D-score	D-score for variable PTM localization.
probabilistic PTM score	The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
Localization Confidence	The confidence in variable PTM localization.
Fixed Modifications	The fixed modifications.
Spectrum File	The spectrum file.
Spectrum Title	The title of the spectrum.
Spectrum Scan Number	The spectrum scan number.
RT	Retention time
m/z	Measured m/z
Measured Charge	The charge as given in the spectrum file.
Identification Charge	The charge as inferred by the search engine.
Theoretical Mass	The theoretical mass of the peptide.
Isotope Number	The isotope number targetted by the instrument.
Precursor m/z Error	The precursor m/z matching error.
Score	Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
Confidence	Confidence in percent associated to the retained PSM.
Decoy	Indicates whether the peptide is a decoy (1: yes, 0: no).
Validation	Indicates the validation level of the protein group.


*Protein Report*

Main Accession	Main accession of the protein group.
Description	Description of the protein designed by the main accession.
Gene Name	The gene names of the Ensembl gene ID associated to the main accession.
Chromosome	The chromosome of the Ensembl gene ID associated to the main accession.
PI	Protein Inference status of the protein group.
Secondary Accessions	Other accessions in the protein group (alphabetical order).
Protein Group	The complete protein group (alphabetical order).
#Peptides	Total number of peptides.
#Validated Peptides	Number of validated peptides.
#Unique	Total number of peptides unique to this protein group.
#PSMs	Number of PSMs
#Validated PSMs	Number of validated PSMs
Coverage (%)	Sequence coverage in percent of the protein designed by the main accession.
Possible Coverage (%)	Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
MW (kDa)	Molecular Weight.
Spectrum Counting NSAF 	Normalized Spectrum Abundance Factor (NSAF)
Spectrum Counting emPAI	exponentially modified Protein Abundance Index (emPAI)
Confident Modification Sites, # Confident Modification Sites	List of the sites where a variable modification was confidently localized.
Other Modification Sites, # Other Modification Sites	List of the non-confident sites where a variable modification was localized.
Score	Score of the protein group.
Confidence	Confidence in percent associated to the protein group.
Decoy	Indicates whether the protein group is a decoy (1: yes, 0: no).
Validation	Indicates the validation level of the protein group.


*Peptide Report*


Protein(s)	Protein(s) to which this peptide can be attached.
AAs Before	The amino-acids before the sequence.
Sequence	Sequence of the peptide.
AAs After	The amino-acids after the sequence.
Modified Sequence	The peptide sequence annotated with variable modifications.
Variable Modifications	The variable modifications.
Localization Confidence	The confidence in PTMs localization.
Fixed Modifications	The fixed modifications.
#Validated PSMs	Number of validated PSMs.
#PSMs	Number of PSMs.
Score	Score of the peptide.
Confidence	Confidence in percent associated to the peptide.
Decoy	Indicates whether the peptide is a decoy (1: yes, 0: no).
Validation	Indicates the validation level of the protein group.


*Hirachical Report*

Main Accession	Main accession of the protein group.
Description	Description of the protein designed by the main accession.
PI	Protein Inference status of the protein group.
Secondary Accessions	Other accessions in the protein group (alphabetical order).
Protein Group	The complete protein group (alphabetical order).
#Peptides	Total number of peptides.
#Validated Peptides	Number of validated peptides.
#Unique	Total number of peptides unique to this protein group.
#PSMs	Number of PSMs
#Validated PSMs	Number of validated PSMs
Coverage (%)	Sequence coverage in percent of the protein designed by the main accession.
Possible Coverage (%)	Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
MW (kDa)	Molecular Weight.
Spectrum Counting NSAF 	Normalized Spectrum Abundance Factor (NSAF)
Spectrum Counting emPAI	exponentially modified Protein Abundance Index (emPAI)
Confident Modification Sites, # Confident Modification Sites	List of the sites where a variable modification was confidently localized.
Other Modification Sites, # Other Modification Sites	List of the non-confident sites where a variable modification was localized.
Score	Score of the protein group.
Confidence	Confidence in percent associated to the protein group.
Decoy	Indicates whether the protein group is a decoy (1: yes, 0: no).
Validation	Indicates the validation level of the protein group.
Protein(s)	Protein(s) to which this peptide can be attached.
AAs Before	The amino-acids before the sequence.
Sequence	Sequence of the peptide.
AAs After	The amino-acids after the sequence.
Variable Modifications	The variable modifications.
Localization Confidence	The confidence in PTMs localization.
Fixed Modifications	The fixed modifications.
#Validated PSMs	Number of validated PSMs.
#PSMs	Number of PSMs.
Score	Score of the peptide.
Confidence	Confidence in percent associated to the peptide.
Decoy	Indicates whether the peptide is a decoy (1: yes, 0: no).
Validation	Indicates the validation level of the protein group.
Protein(s)	Protein(s) to which the peptide can be attached.
Sequence	Sequence of the peptide.
Modified Sequence	The peptide sequence annotated with variable modifications.
Variable Modifications	The variable modifications.
D-score	D-score for variable PTM localization.
probabilistic PTM score	The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
Localization Confidence	The confidence in variable PTM localization.
Fixed Modifications	The fixed modifications.
Spectrum File	The spectrum file.
Spectrum Title	The title of the spectrum.
Spectrum Scan Number	The spectrum scan number.
RT	Retention time
m/z	Measured m/z
Measured Charge	The charge as given in the spectrum file.
Identification Charge	The charge as inferred by the search engine.
Theoretical Mass	The theoretical mass of the peptide.
Isotope Number	The isotope number targetted by the instrument.
Precursor m/z Error	The precursor m/z matching error.
Score	Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
Confidence	Confidence in percent associated to the retained PSM.
Decoy	Indicates whether the peptide is a decoy (1: yes, 0: no).
Validation	Indicates the validation level of the protein group.




------

**Citation**

For the underlying tool, please cite `TODO`

If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker
    </help>
</tool>

11:e5bdaa2ac9c7

<tool id="peptide_shaker" name="Peptide Shaker" version="1.18.3.0">
    <description>
        Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker.
    </description>
    <requirements>
        <requirement type="package" version="0.28.0">peptide_shaker</requirement>
        <requirement type="package" version="1.18.0">searchgui</requirement>
        <!--<requirement type="package" version="2.2.29">blast+</requirement>-->

        ## the following line is needed. Otherwise, Galaxy will strip away the ';'
        echo 'Finished!';
    </command>
    <inputs>
        <param format="fasta" name="input_database" type="data" label="Protein Database"
            help="Select FASTA database from history"/>

        <param name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" help="Selecting this option will help PeptideShaker calculate FDR values" />

        <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)"
            help="Select appropriate MGF dataset(s) from history" />
        <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
            help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">

            <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
            <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
            <option value="Semi-Glu-C">Semi-Glu-C</option>
        </param>

        <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
            help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
            <option value="0">no correction</option>
            <option value="1" selected="True">rename spectra</option>
            <option value="2">delete spectra</option>
        </param>

        <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
            help="Choose a smaller value if you are running on a machine with limited memory"/>
        <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
            help="Choose a smaller value if you are running on a machine with limited memory"/>

        <conditional name="species_type">
            <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
                help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results">
                <option value="Fungi">Fungi</option>
                <option value="Plants">Plants</option>
                <option value="Metazoa">Metazoa</option>
                <option value="Vertebrates">Vertebrates</option>
                <option value="Protists">Protists</option>
                <option value="no_species_type" selected="true">No species restriction</option>
            </param>
            <when value="Protists">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="">
                    <option value="Albugo laibachii">Albugo laibachii</option>
                    <option value="Dictyostelium discoideum">Dictyostelium discoideum</option>
                    <option value="Entamoeba histolytica">Entamoeba histolytica</option>
                    <option value="Giardia lamblia">Giardia lamblia</option>
                    <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option>

                    <option value="Trypanosoma brucei">Trypanosoma brucei</option>
                </param>
            </when>
            <when value="Plants">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="">
                    <option value="Arabidopsis lyrata">Arabidopsis lyrata</option>
                    <option value="Arabidopsis thaliana">Arabidopsis thaliana</option>
                    <option value="Brachypodium distachyon">Brachypodium distachyon</option>
                    <option value="Brassica rapa genes">Brassica rapa genes</option>
                    <option value="Chlamydomonas reinhardtii">Chlamydomonas reinhardtii</option>

                    <option value="Zea mays">Zea mays</option>
                </param>
            </when>
            <when value="Metazoa">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="">
                    <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option>
                    <option value="Aedes aegypti">Aedes aegypti</option>
                    <option value="Amphimedon queenslandica">Amphimedon queenslandica</option>
                    <option value="Anopheles darlingi">Anopheles darlingi</option>
                    <option value="Anopheles gambiae">Anopheles gambiae</option>

                    <option value="Trichoplax adhaerens">Trichoplax adhaerens</option>
                </param>
            </when>
            <when value="Fungi">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="">
                    <option value="Ashbya gossypii">Ashbya gossypii</option>
                    <option value="Aspergillus clavatus">Aspergillus clavatus</option>
                    <option value="Aspergillus flavus">Aspergillus flavus</option>
                    <option value="Aspergillus fumigatus">Aspergillus fumigatus</option>
                    <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option>

                    <option value="Zymoseptoria tritici">Zymoseptoria tritici</option>
                </param>
            </when>
            <when value="Vertebrates">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="">
                    <option value="Ailuropoda melanoleuca">Ailuropoda melanoleuca</option>
                    <option value="Anolis carolinensis">Anolis carolinensis</option>
                    <option value="Bos taurus">Bos taurus</option>
                    <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
                    <option value="Callithrix jacchus">Callithrix jacchus</option>

                </param>
            </when>
        </conditional>

        <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
            help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
        <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
            help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
            <options from_file="searchgui_mods.loc">
                <column name="name" index="0" />
                <column name="value" index="0" />

            <when value="yes">
                <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
                <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
                <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
                <param name="protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="" type="float"
                    help="default 95%: '95.0'" />
                <conditional name="ptm_score">
                    <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
                        <option value="0" selected="True">A-score</option>
                        <option value="1">PhosphoRS</option>
                    </param>
                    <when value="0" />
                    <when value="1">
                        <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
                        <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="" type="float"
                            help="Automatic mode will be used if not set" />
                    </when>
                </conditional>
                <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
            </when>
        </conditional>

            </param>
            <when value="no" />
            <when value="yes">
                <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
                <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />
                <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)" />
                <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
                    <option value="0">ppm</option>
                    <option value="1">Daltons</option>
                </param>
                <param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" />
                <param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" />
                <param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" />
                <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
            </when>
        </conditional>

        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">

            <option value="4" selected="True">Protein Report</option>
            <option value="2">PSM Report</option>
            <option value="0">Certificate of Analysis</option>
            <option value="1">Hierarchical Report</option>
            <option value="cps">CPS file</option>
            <validator type="no_options" message="Please select at least one output file" />
        </param>
    </inputs>
    <outputs>
        <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
            <filter>'cps' in outputs</filter>

**What it does**

Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results.

https://code.google.com/p/peptide-shaker/

https://code.google.com/p/searchgui/

----

Reports
=======


PSM Report
----------

* Protein(s):                Protein(s) to which the peptide can be attached
* Sequence:	                Sequence of the peptide
* Variable Modifications:	The variable modifications
* D-score:	                D-score for variable PTM localization
* probabilistic PTM score:	The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
* Localization Confidence:	The confidence in variable PTM localization.
* Fixed Modifications:	    The fixed modifications.
* Spectrum File:	The spectrum file.
* Spectrum Title:	The title of the spectrum.
* Spectrum Scan Number:	The spectrum scan number.
* RT:	Retention time
* m/z:	Measured m/z
* Measured Charge:	The charge as given in the spectrum file.
* Identification Charge:	The charge as inferred by the search engine.
* Theoretical Mass:	The theoretical mass of the peptide.
* Isotope Number:	The isotope number targetted by the instrument.
* Precursor m/z Error:	The precursor m/z matching error.
* Score:	Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
* Confidence:	Confidence in percent associated to the retained PSM.
* Decoy:	Indicates whether the peptide is a decoy (1: yes, 0: no).
* Validation: Indicates the validation level of the protein group.


Protein Report
--------------

* Main Accession:	Main accession of the protein group.
* Description:	Description of the protein designed by the main accession.
* Gene Name:	The gene names of the Ensembl gene ID associated to the main accession.
* Chromosome:	The chromosome of the Ensembl gene ID associated to the main accession.
* PI:	Protein Inference status of the protein group.
* Secondary Accessions:	Other accessions in the protein group (alphabetical order).
* Protein Group:	The complete protein group (alphabetical order).
* #Peptides:	Total number of peptides.
* #Validated Peptides:	Number of validated peptides.
* #Unique:	Total number of peptides unique to this protein group.
* #PSMs:	Number of PSMs
* #Validated PSMs:	Number of validated PSMs
* Coverage (%):	Sequence coverage in percent of the protein designed by the main accession.
* Possible Coverage (%):	Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
* MW (kDa):	Molecular Weight.
* Spectrum Counting NSAF: 	Normalized Spectrum Abundance Factor (NSAF)
* Spectrum Counting emPAI:	exponentially modified Protein Abundance Index (emPAI)
* Confident Modification Sites: Number of Confident Modification Sites	List of the sites where a variable modification was confidently localized.
* Other Modification Sites: Number of other Modification Sites	List of the non*confident sites where a variable modification was localized.
* Score:	Score of the protein group.
* Confidence:	Confidence in percent associated to the protein group.
* Decoy:	Indicates whether the protein group is a decoy (1: yes, 0: no).
* Validation:	Indicates the validation level of the protein group.


Peptide Report
--------------


* Protein(s):	Protein(s) to which this peptide can be attached.
* AAs Before:	The amino-acids before the sequence.
* Sequence:	Sequence of the peptide.
* AAs After:	The amino-acids after the sequence.
* Modified Sequence:	The peptide sequence annotated with variable modifications.
* Variable Modifications:	The variable modifications.
* Localization Confidence:	The confidence in PTMs localization.
* Fixed Modifications:	The fixed modifications.
* #Validated PSMs:	Number of validated PSMs.
* #PSMs:	Number of PSMs.
* Score:	Score of the peptide.
* Confidence:	Confidence in percent associated to the peptide.
* Decoy:	Indicates whether the peptide is a decoy (1: yes, 0: no).
* Validation:	Indicates the validation level of the protein group.


Hierachical Report
------------------

* Main Accession:	Main accession of the protein group.
* Description:	Description of the protein designed by the main accession.
* PI:	Protein Inference status of the protein group.
* Secondary Accessions:	Other accessions in the protein group (alphabetical order).
* Protein Group:	The complete protein group (alphabetical order).
* #Peptides:	Total number of peptides.
* #Validated Peptides:	Number of validated peptides.
* #Unique:	Total number of peptides unique to this protein group.
* #PSMs:	Number of PSMs
* #Validated PSMs:	Number of validated PSMs
* Coverage (%):	Sequence coverage in percent of the protein designed by the main accession.
* Possible Coverage (%):	Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
* MW (kDa):	Molecular Weight.
* Spectrum Counting NSAF: 	Normalized Spectrum Abundance Factor (NSAF)
* Spectrum Counting emPAI:	exponentially modified Protein Abundance Index (emPAI)
* Confident Modification Sites: # Confident Modification Sites	List of the sites where a variable modification was confidently localized.
* Other Modification Sites: # Other Modification Sites	List of the non-confident sites where a variable modification was localized.
* Score:	Score of the protein group.
* Confidence:	Confidence in percent associated to the protein group.
* Decoy:	Indicates whether the protein group is a decoy (1: yes, 0: no).
* Validation:	Indicates the validation level of the protein group.
* Protein(s):	Protein(s) to which this peptide can be attached.
* AAs Before:	The amino-acids before the sequence.
* Sequence:	Sequence of the peptide.
* AAs After:	The amino-acids after the sequence.
* Variable Modifications:	The variable modifications.
* Localization Confidence:	The confidence in PTMs localization.
* Fixed Modifications:	The fixed modifications.
* #Validated PSMs:	Number of validated PSMs.
* #PSMs:	Number of PSMs.
* Score:	Score of the peptide.
* Confidence:	Confidence in percent associated to the peptide.
* Decoy:	Indicates whether the peptide is a decoy (1: yes, 0: no).
* Validation:	Indicates the validation level of the protein group.
* Protein(s):	Protein(s) to which the peptide can be attached.
* Sequence:	Sequence of the peptide.
* Modified Sequence:	The peptide sequence annotated with variable modifications.
* Variable Modifications:	The variable modifications.
* D-score:	D-score for variable PTM localization.
* probabilistic PTM score:	The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
* Localization Confidence:	The confidence in variable PTM localization.
* Fixed Modifications:	The fixed modifications.
* Spectrum File:	The spectrum file.
* Spectrum Title:	The title of the spectrum.
* Spectrum Scan Number:	The spectrum scan number.
* RT:	Retention time
* m/z:	Measured m/z
* Measured Charge:	The charge as given in the spectrum file.
* Identification Charge:	The charge as inferred by the search engine.
* Theoretical Mass:	The theoretical mass of the peptide.
* Isotope Number:	The isotope number targetted by the instrument.
* Precursor m/z Error:	The precursor m/z matching error.
* Score:	Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
* Confidence:	Confidence in percent associated to the retained PSM.
* Decoy:	Indicates whether the peptide is a decoy (1: yes, 0: no).
* Validation:	Indicates the validation level of the protein group.




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**Citation**

To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com  

If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker
    </help>
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