Selected Cell
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Introduction
Experiment
Contacts
CV Lookup
Protocol Steps
References
Sample
MS Instrument
MS Instrument Software
Proteins
Peptides
PTM Codes
PTMs
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This sheet contains over-arching information about the entire experiment. | Page Not Complete | ||||||||
Value (Yellow - mandatory, White - optional.) | ↓ Status | ||||||||
Project Title → | OK | ||||||||
Experiment Title → | Invalid - mandatory value | ||||||||
Experiment Accession Number → | OK | ||||||||
Short Experiment Title → | Invalid - mandatory value | ||||||||
Additional Parameters Describing the Experiment (Globally) | ↓ Status | ||||||||
CV Params | |||||||||
User Params | |||||||||
↓ CV Name | ↓ Accession | ↓ Term Name | ↓ Value (optional) | Double Click to activate buttons below | |||||
PRIDE | PRIDE:0000097 | Project | 0 | ||||||
Search for CV Term | Add Param | ||||||||
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This sheet contains details of Contacts (minimum one) that will be included in the XML file. | |||||||||
↓ Name | ↓ Institution | ↓ Contact Information (preferably email) | Double Click | ||||||
Add Contact | |||||||||
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CV Lookup entries identify and describe any ontologies or controlled vocabularies used to annotate data in the PRIDE XML file. An initial set of expected ontologies is included. You may add or remove entries here as you require, however it does not matter if you leave unused ontologies in this list. | |||||||||
↓ CV Label | ↓ Full Name | ↓ Version | ↓ Address (URI) | ↓ Status | |||||
GO | Gene Ontology | 0 | http://www.geneontology.org/ | OK | |||||
NEWT | NEWT | 0 | http://www.ebi.ac.uk/newt | OK | |||||
BTO | BRENDA Tissue Ontology | 0 | http://www.brenda.uni-koeln.de/ | OK | |||||
CL | OBO Cell Type Ontology | 0 | http://obo.sourceforge.net/cgi-bin/detail.cgi?cell | OK | |||||
DOID | Disease Ontology | 0 | http://diseaseontology.sourceforge.net/ | OK | |||||
PSI-MOD | Proteomics Standards Initiative: Protein Modifications | 0 | http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD | OK | |||||
PSI-MS | Proteomics Standards Initiative: Mass Spectrometry | 0 | http://psidev.sourceforge.net/ontology/index.html | OK | |||||
ISBN | International Standard Book Numbering | 0 | http://www.isbn-international.org/ | OK | |||||
PRIDE | PRIDE Controlled Vocabulary | 0 | http://www.ebi.ac.uk/pride/help_resources/pride_obo_CV | OK | |||||
DOI | The Digital Object Identifier System | 0 | http://www.doi.org/ | OK | |||||
PubMed | National Library of Medicine, PubMed Database | 0 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi | OK | |||||
RESID | RESID Database of Protein Modifications | 0 | http://www.ebi.ac.uk/RESID/ | OK | |||||
NEWT | The NEWT Taxonomy | 0 | http://www.ebi.ac.uk/newt | OK | Double Click | ||||
UNIMOD | UNIMOD Protein Modifications for Mass Spectrometry | 0 | http://www.unimod.org/ | OK | Add CV | ||||
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Protocol Steps - The Step number indicates the order of the steps. Each step can use 1 or more parameters to describe it. | |||||||||
↓ Status | |||||||||
Protocol Name → | Invalid - mandatory value | ||||||||
↓ Protocol Step Number | Parameters | ||||||||
CV Params | |||||||||
User Params | |||||||||
↓ CV Name | ↓ Accession | ↓ Term Name | ↓ Value (optional) | Double Click to activate buttons below | |||||
Search for CV Term | Add Param | ||||||||
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This sheet allows you to list all the literature references that you wish to associate with this Experiment | |||||||||
For each reference you must include a Reference Line as a minimum. You are also advised to add CV annotation describing the PubMed ID, DOI and / or ISBN number for the reference. Additionally, you can add CV parameters indicating the role of the article in relation to the experiment. Examples of how this should be formatted are given below. | |||||||||
Example Annotations | |||||||||
↓ CV Name | ↓ Accession | ↓ Term Name | ↓ Value (optional) | ||||||
PubMed | 16381953 | 16381953 | Set the 'Term Name' column to the same value as the 'Accession' column for PubMed, DOI or ISBN entries. | ||||||
DOI | 10.1093/nar/gkj138 | 10.1093/nar/gkj138 | |||||||
ISBN | 0-12345-678-9 | 0-12345-678-9 | |||||||
PRIDE | PRIDE:0000067 | Reference reporting this experiment | You can copy and paste any of these three rows directly into a new "Additional Parameter" row for your references. | ||||||
PRIDE | PRIDE:0000068 | Reference describing sample preparation | |||||||
PRIDE | PRIDE:0000111 | Reference describing data analysis | |||||||
Reference Line → | Add Reference (Double Click) | ||||||||
Additional Parameters Describing the Reference (e.g. ISBN, PubMed ID) | Status | ||||||||
CV Params | |||||||||
User Params | |||||||||
↓ CV Name | ↓ Accession | ↓ Term Name | ↓ Value (optional) | Double Click to activate buttons | |||||
Search for CV Term | Add Param | ||||||||
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This sheet contains information related to the sample under study | ||||||||||
Value (Yellow - mandatory, Green - optional.) | ↓ Status | |||||||||
Sample Name → | Invalid - mandatory value | |||||||||
Sample Description Comment → | OK | |||||||||
Please add optional parameters below to describe, as far as possible: | ||||||||||
* The species, using NEWT (a super-set of the NCBI Taxonomy) | http://www.ebi.ac.uk/newt | |||||||||
* The organ / tissue, using the BRENDA Tissue ontology | http://www.brenda.uni-koeln.de/ | |||||||||
* The cell type, using the OBO Cell Type ontology | http://obo.sourceforge.net/cgi-bin/detail.cgi?cell | |||||||||
* The disease state, using the OBO / DOID Disease Ontology | http://diseaseontology.sourceforge.net/ | |||||||||
* The sub-cellular location, using the GO Gene Ontology | http://www.geneontology.org/ | |||||||||
* The age / developmental stage of the organism | ||||||||||
Note: The PRIDE CV includes a term "DiseaseFree" (PRIDE:0000018) if the organism has been screened / demonstrated to be free of disease. | ||||||||||
Additional Parameters Describing the Sample | ↓ Status | |||||||||
CV Params | ||||||||||
User Params | ||||||||||
↓ CV Name | ↓ Accession | ↓ Term Name | ↓ Value (optional) | Double Click to activate buttons below | ||||||
Search for CV Term | Add Param | |||||||||
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This sheet contains information related to the instrument used for Mass Spectrometry. Note that at as a minimum you must supply at least one parameter describing the source, the analyzer components and the detector. | |||||||||
Value (Yellow - mandatory, Green - optional.) | ↓ Status | ||||||||
Instrument Name → | Invalid - mandatory value | ||||||||
MS Instrument Source File | Source File Name → | OK | |||||||
Source File Path (e.g. URL) → | OK | ||||||||
Source File Type → | OK | ||||||||
Parameters Describing the Source (At least one parameter is mandatory) | ↓ Status | ||||||||
CV Params | |||||||||
User Params | |||||||||
↓ CV Name | ↓ Accession | ↓ Term Name | ↓ Value (optional) | Double Click to activate buttons below | |||||
Search for CV Term | Add Param | ||||||||
Parameters Describing the Analyzer Components (At least one analyzer component is mandatory) | |||||||||
Note that each component may be described by one or more CV / User parameter terms. To indicate the ordering and grouping of these terms, please enter an integer in column A below. | |||||||||
↓ Analyzer Component Number | Parameters | ||||||||
CV Params | |||||||||
User Params | |||||||||
↓ CV Name | ↓ Accession | ↓ Term Name | ↓ Value (optional) | Double Click to activate buttons below | |||||
1 | Search for CV Term | Invalid - At least one analyzer component is mandatory | |||||||
Search for CV Term | Add Param | ||||||||
Parameters Describing the Detector (At least one parameter is mandatory) | ↓ Status | ||||||||
CV Params | |||||||||
User Params | |||||||||
↓ CV Name | ↓ Accession | ↓ Term Name | ↓ Value (optional) | Double Click to activate buttons below | |||||
Search for CV Term | Add Param | ||||||||
Additional Parameters Describing the MS Instrument | ↓ Status | ||||||||
CV Params | |||||||||
User Params | |||||||||
↓ CV Name | ↓ Accession | ↓ Term Name | ↓ Value (optional) | Double Click to activate buttons below | |||||
Search for CV Term | Add Param | ||||||||
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This sheet contains information related to the MS Instrument software (I.e. the software provided by the instrument vendor for immediate processing of the raw spectral data, not the search engine or other external software.) | |||||||||
Value (Yellow - mandatory, White - optional.) | ↓ Status | ||||||||
MS Instrument Software Name → | Invalid - mandatory value | ||||||||
MS Instrument Software Version → | Invalid - mandatory value | ||||||||
Completion Time → | |||||||||
Software Comments → | |||||||||
The Processing Method is a description of the default peak processing method. This describes the base method used in the generation of a particular mzData file. | |||||||||
Additional Parameters Describing the Processing Method | |||||||||
CV Params | |||||||||
User Params | |||||||||
↓ CV Name | ↓ Accession | ↓ Term Name | ↓ Value (optional) | Double Click to activate buttons below | |||||
Search for CV Term | Add Param | ||||||||
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This sheet is used to enter details of protein identifications. After entering an identification, you will be able to add details of any number of associated peptides by clicking on the button on the left of the sheet. (Column A) Note that if you enter a number into the "Peptide Count" column, rows for the number of peptides you have specified will be created in the Peptides sheet. | ||||||||||||||||||||||||||
2-D Gel Based Identifications | CV / User Parameters | |||||||||||||||||||||||||
Add Peptides to All Proteins | ↓ Protein Unique ID | ↓ Peptide Count | ↓ Type | ↓ Protein Accession | ↓ Accession Version | ↓ Splice Isoform | ↓ Search Database | ↓ Search DB Version | ↓ Spectrum Reference | ↓ Score | ↓ Threshold | ↓ Search Engine | ↓ Sequence Coverage | ↓ Gel Link | ↓ X-Coord | ↓ Y-Coord | ↓ Mol. Wt. | ↓ pI | ↓ CV Name | ↓ CV Accession | ↓ Term Name | ↓ Value | Double Click to activate buttons below | ↓ Param Status | pepsmade? | |
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To add details of a peptide, you first need to enter detail of the protein that it provides evidence for on the "Proteins" worksheet and then click on the 'Add Peptide' button on column A of sheet "Proteins". Rows will than automatically be added to this sheet as required. If you wish to add details of protein modifications to an individual peptide on this sheet, click on the "Add PTM" button in column A. This will create a record on the "PTMs" sheet that you can populate further. | ||||||||||||||
NOTE: If you wish PTMs to be automatically created from sequence annotations, you first need to define the meaning of the annotations on the worksheet "PTM Codes" | ||||||||||||||
CV / User Parameters | ||||||||||||||
↓ Peptide Unique ID | ↓ Protein Unique ID | ↓ Protein Accession | Sequence (Please do not include flanking sequences here) | ↓ Start | ↓ End | ↓ Spectrum Reference | ↓ CV Name | ↓ Accession | ↓ Term Name | ↓ Value | Double Click to activate buttons below | ↓ Status | ||
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Use this form to define the codes used in peptide sequences. This information is used to populate the PTM worksheet, based upon the annotated peptide sequence entered into the Peptides worksheet. Do not leave any gaps (empty lines in the middle of the codes) as any codes following the empty lines will be ignored. | ||||||||||
PSI-MOD: | http://www.ebi.ac.uk/ontology-lookup | |||||||||
Enter your PTM codes here. These will be used to create PTM entries from an annotated peptide sequence. | Example Entries: | |||||||||
↓ Code | ↓ Accession | ↓ PTM Database | ↓ Name | ↓ Database Version | ↓ Code | ↓ Accession | ↓ PTM Database | ↓ Name | ↓ Database Version | |
# | MOD:00419 | PSI-MOD | S-carbamoylmethylcysteine cyclization (N-terminus) | |||||||
* | MOD:00260 | PSI-MOD | O-(phospho-5'-DNA)-L-threonine | |||||||
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Enter details of protein modifications on to this form. This can be automated, by entering peptides with single-character annotations indicating the presence of PTMs on the 'Peptides' sheet. If you wish to enter details on to this sheet manually, you must first enter details of the modified peptide on the Peptides sheet and then click on the 'Add Peptide' button on the left of the Peptides sheet. This will create a correctly formatted, cross referenced row on this sheet that you can complete. | |||||||||||||||
CV / User Parameters | |||||||||||||||
↓ Peptide Unique ID | ↓ Peptide Sequence | ↓ Location (Relative to Peptide) | ↓ Accession | ↓ PTM Database | ↓ Database Version | ↓ Average Delta Value | ↓ Mono Delta Value | ↓ CV Name | ↓ Accession | ↓ Term Name | ↓ Value | Double Click to activate buttons below | ↓ Status | ||