{"text_format":"2","workbook":"xls","n_sheets":15,"sheets":["Introduction","Experiment","Contacts","CV Lookup","Protocol Steps","References","ident_hidden","Sample","MS Instrument","MS Instrument Software","Proteins","Peptides","PTM Codes","PTMs","cvParamHidden"],"not_rendered":{"charts":0,"images":4,"macros":1,"external_links":1,"defined_names":5,"comments":117,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"run_cost":"one","rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0,"cell_chars":16384,"cell_head_chars":4096},"cells_cut":0,"cells_raw":0,"read":"whole","date_system":"1900","formulas":"cached_only"}

{"sheet":"Introduction","index":0,"n_rows":97,"n_cols":4,"rows_kept":97,"cut":false,"hidden":false,"merged":[[0,0,0,3],[1,0,1,2],[5,0,5,3],[10,0,10,3],[11,0,11,3],[12,0,12,3],[14,0,14,1],[15,0,15,3],[16,0,16,1],[17,0,17,1],[18,0,18,1],[19,0,19,1],[20,0,20,1],[21,0,21,1],[22,0,22,1],[23,0,23,1],[24,0,24,1],[25,0,25,1],[26,0,26,1],[27,0,27,1],[28,0,28,1],[29,0,29,1],[30,0,30,1],[31,0,31,1],[32,0,32,1],[33,0,33,1],[34,0,34,1],[35,0,35,1],[36,0,36,1],[37,0,37,1],[38,0,38,1],[39,0,39,1],[40,0,40,1],[41,0,41,1],[42,0,42,1],[43,0,43,1],[44,0,44,1],[45,0,45,3],[46,0,46,3],[47,0,47,3],[48,0,48,3],[55,0,55,3],[56,0,56,3],[57,0,57,3],[58,0,58,3],[59,0,59,3],[60,0,60,3],[61,0,61,3],[62,0,62,3],[63,0,63,3],[64,0,64,3],[65,0,65,3],[66,0,66,3],[67,0,67,3],[68,0,68,3],[69,0,69,3],[70,0,70,3],[71,0,71,3],[72,0,72,3],[73,0,73,3],[74,0,74,3],[75,0,75,3],[76,0,76,3],[77,0,77,3],[78,0,78,3],[79,0,79,3],[80,0,80,3],[81,0,81,3],[82,0,82,3],[83,0,83,3],[84,0,84,3],[85,0,85,3],[86,0,86,3],[87,0,87,3],[88,0,88,3],[89,0,89,3],[90,0,90,3],[91,0,91,3],[92,0,92,3],[93,0,93,3],[94,0,94,3],[95,0,95,3],[96,0,96,1],[97,0,97,3],[98,0,98,3],[99,0,99,3],[100,0,100,3],[101,0,101,3],[102,0,102,3],[103,0,103,3],[104,0,104,3],[105,0,105,3],[106,0,106,3],[107,0,107,3],[108,0,108,3],[109,0,109,3],[110,0,110,3],[111,0,111,3],[112,0,112,3],[113,0,113,3],[114,0,114,3],[115,0,115,3],[116,0,116,3],[117,0,117,3],[118,0,118,3],[119,0,119,3],[120,0,120,3],[121,0,121,3]],"flags":["formulas_cached_only"]}
["PRIDE 2.1 Proteomics Data XML Export Workbook"]
["This Excel workbook has been designed to allow the compilation of a complete PRIDE 2.1 XML file.  As far as possible, automation is used to assist you in compiling the data.  Features of the spreadsheet are described in the Help section below.  It is strongly recommended that you read through this page before starting to work with this Excel workbook."]
[null,null,null,"Double Click Buttons"]
["Optional: Embed mzData XML file located here:",null,null,"Browse for mzData File"]
[]
["IMPORTANT: Embedding an external mzData file will result in any mzData related content that you have entered on to this spreadsheet being ignored.  Sheets that will be ignored include 'Contacts', 'CV Lookup', 'Sample', 'MS Instrument' and 'MS Instrument Software'.  See point 4 below for further details."]
[null,null,null,"Double Click Buttons"]
[null,null,null,"Generate PRIDE XML"]
[]
["Help Documentation"]
["1  Only Use Microsoft Excel 2000 or later versions on a Microsoft Windows platform.  This workbook makes extensive use of 'Visual Basic for Applications' (VBA), the programming language embedded in Excel.  Consequently, you will not be able to use this spreadsheet productively in an 'Office clone' that is capable of opening Excel workbooks, but not capable of running VBA code."]
["2  Save and Backup Regularly:  This is a complex Excel workbook that includes many pages and will take time to complete.  It is therefore essential that you both save the workbook regularly and also create interim backup copies of the spreadsheet at regular intervals to ensure you do not lose the data that you have entered."]
["3  Automated Controlled Vocabulary Lookup:  You can look up controlled vocabulary / ontology terms directly from this spreadsheet via the Ontology Lookup Service (OLS) at the EBI:"]
["http://www.ebi.ac.uk/ontology-lookup","for more information…"]
["To select a CV term, double-click on any of the buttons that look like this:",null,null,"Search for CV Term"]
["The resulting dialogue box, described below, can be used to search for CV terms or to retrieve the correct term name, given a known accession number."]
{"$rows_empty":29}
["4  Inclusion of External mzData File:  As described above, you may wish to embed an externally generated mzData XML file in your output.  This option will allow you to include mass spectra, however it is unlilkely to include sample annotation as required for a PRIDE submission.  It is recommended that you edit your mzData file to include this information as described here."]
["The use of an external mzData file is required if you wish to include spectra in your submission.  Normally the mzData file will be generated by the mass spectrometer instrument software that you are using.  Please note that this is unlikely to include the kind of sample description information normally expected for a PRIDE submission, e.g. NCBI Taxonomy / NEWT ID, BRENDA term for anatomical location, Cell Type Ontology term for cell type etc.  It is possible to edit the XML file following generation to add this information - See help point 4 below."]
["If you are not submitting spectra, it is recommended that you make use of this spreadsheet to construct the mzData element within the PRIDE XML file."]
["Sample information that is highly desirable in a PRIDE submission includes, where appropriate: the NCBI Taxonomy / NEWT taxonomy ID; BRENDA term for anatomical location, Cell Type Ontology term for cell type and GO terms to describe the sub-cellular location of the sample.  You may also use the DOID Disease Ontology to define disease states of the organism.  This information should be annotated in the mzData/description/admin/sampleDescription element as exemplified below:"]
{"$rows_empty":7}
["This can be achieved using a text editor such as Textpad."]
["5  Data entry using the workbook: General Points. This workbook is split into several separate sheets, each of which is relatively simple to complete, collectively allowing you to enter the complex information required to generate a complete PRIDE XML submission.  On all sheets, the convention is followed that mandatory data elements have a yellow background and optional data elements have a green background. "]
["Where possible, the data you have entered will be validated at the point of entry, however in some cases this is not possible, in which case the completeness of the data entry will be validated when you attempt to generate the PRIDE XML file (by double clicking on the 'Generate PRIDE XML' button near the top of this page.)"]
["Some general points to bear in mind:"]
["Wherever it is possible or desirable to add additional rows to annotate your data more completely, you will find a button provided on the spreadsheet itself to allow you to do this.  Do not attempt to add more rows manually / using cutting and pasting etc. as these rows may not be correctly parsed by the code that generates the PRIDE XML."]
["Avoid leaving blank rows in data tables.  Any data entered below a row that has been left blank will be ignored and not included in the generated XML file."]
[]
["Useful information specific to each sheet is given below."]
["Experiment Sheet"]
["This sheet allows the entry of over-arching experiment data including the mandatory experiment title and short label and an optional experiment accession number.  Note that when submitting an experiment to PRIDE for the first time, the experiment accession number should not be set.  You will only need to provide this number if you are re-submitting an experiment, in which case the number should be the same as the assigned experiment number from your previous submission.  Please also note that the same user will need to log in to PRIDE to re-submit the experiment."]
["As commonly found throughout the PRIDE XML schema, it is possible to annotate the experiment with additional parameters, being either 'CV Parameters' that make use of external controlled vocabularies and ontologies to annotate the data, or 'User Parameters' that allow the entry of free text.  Wherever possible, you are encouraged to make use of controlled vocabulary terms to annotate your data.  It is possible to make use of the Ontology Lookup Service to search for appropriate controlled vocabulary terms as described in point 3 above."]
["If you wish to enter more than one CV or user parameter to annotate the experiment as a whole, you should double click on the button labelled 'Add Param' that can be found in column F on the Experiment sheet.  This will add an additional row.  You are advised to avoid adding rows manually.  A similar mechanism is provided on most of the sheets in the workbook to allow the addition of CV and User parameters."]
["Contacts"]
["This simple sheet allows you to enter the details of any number of contact people or organisations for the data submission.  Generally speaking, you are advised to provide an email address in the 'Contact Information' column, however this is not mandatory and you may wish to enter a postal address or other contact details."]
["CV Lookup"]
["This sheet allows the entry of details of the controlled vocabularies and ontologies referenced from the PRIDE XML file that you are generating.  You are provided with a likely starting set of controlled vocabularies, however you are free to add any controlled vocabularies that you require.  If you inadvertantly include references to CVs that are not used in your submission, there are no adverse consequences.  You can however remove references on this sheet if you wish.  You can either over-type a CV reference, or just completely delete the row by selecting it and then using the menu item 'Edit'...'Delete'."]
["Protocol Steps"]
["The protocol followed to prepare the sample for analysis, including steps such as digestion, separation by gel or column etc. can be described in this section.  The protocol should be given a meaningful, descriptive title ('Protocol Name').  Each step (ordered) of the protocol can then be described using any number of CV parameters or user parameters.  To allow you to associate each CV or user parameter with a specific step, you should enter a step number in column A.  Note that you can have any number of rows annotated with the same step number, allowing you to describe a single step using more than one controlled vocabulary and / or free text term.  Useful controlled vocabularies for annotating this kind of sample processing includes the PSI-MI ontology and the PRIDE controlled vocabulary."]
["References"]
["This sheet allows you to enter the details of any number of published references that are associated with the experiment.  Space is initially provided for one reference, however to add additional references, you should double-click the 'Add Reference' button on the right hand side of the sheet."]
["For each reference described, you must enter a reference line.  You are also recommended to add CV parameters including details of the PubMed ID, ISBN and / or DOI numbers for the article.  Again, it is possible to annotate each reference with any number of CV or user parameters."]
["It is also possible to annotate each reference using any of the following terms from the PRIDE Controlled vocabulary, as appropriate:"]
["PRIDE:0000067   \"Reference reporting this experiment\".  This CV parameter indicates that this reference is directly supported by the data included in this submission."]
["PRIDE:0000068   \"Reference describing sample preparation\"."]
["PRIDE:0000111   \"Reference describing data analysis\"."]
["Sample"]
["This sheet allows you to enter details of the sample under investigation, including the mandatory \"Sample Name\" and optional \"Description Comment\".  In addition to these data, you are highly recommended to include CV parameters to describe the species, tissue, sub-cellular location, disease state and developmental stage of the organism / sample as appropriate.  Suggested controlled vocabularies and ontologies for these purposes are listed on the sheet itself."]
["MS Instrument"]
["This sheet allows you to enter details of the sample under investigation, including the mandatory \"Sample Name\" and optional \"Description Comment\".  In addition to these data, you are highly recommended to include CV parameters to describe the species, tissue, sub-cellular location, disease state and developmental stage of the organism / sample as appropriate.  Suggested controlled vocabularies and ontologies for these purposes are listed on the sheet itself."]
["MS Instrument Software"]
["This sheet allows you to enter details of the mass spectrometer instrument software as supplied by the instrument vendor.  As a minumum you must supply the name and the version number of the software."]
["Proteins"]
["Here you should enter details of all of your protein identifications.  If you already have this data in a separate spread sheet, it may be convenient to re-arrange this sheet with the appropriate column order and then paste the values into the Proteins sheet.  Note that you can add any number of additional controlled vocabulary or user defined parameters to each protein identification on this sheet by clicking on the Add Param button in column Y. Other important columns on this sheet are described below."]
["Add Peptides to All Proteins.  This column contains two kinds of button that allow you to automatically create row entries on the 'Peptides' sheet that are cross-referenced to the protein entry.  To use this you first need to enter the number of peptides for each protein in the Peptide Count column.  Note that to cross reference from the protein sheet to the peptide sheet relies on the presence of a unique identifier (ascending integer) in the Protein Unique ID column on the Proteins sheet.  This value is provided in the blank Proteome Harvest spreadsheet.  There is no need to edit or modify this value.  This value is only used within the spreadsheet and does not appear in any form on the final XML file."]
["Type.  This column provides a choice of two types of protein identification: \"2D-GE Based\" or \"Gel-Free\" identifications.  If you select \"2D-GE Based\" in this column then five additional data columns will be made available to you, in which you can enter a hyperlink to the gel image, x and y coodinates of the identified spot and the predicted MW and pI of the protein.  These columns are hidden for the row in question if you select the type \"Gel-Free\"."]
["Peptides, PTM Codes and PTMs"]
["These three sheets are described together as they interact with each other.  A degree of automation of data entry is provided that is especially useful where you have peptide sequences that are annotated with protein modifications using single character codes.  If this is the case, the first sheet that you should complete is the PTM Codes sheet.  On this sheet you can define each single character code in terms of the most appropriate PSI-MOD ontology term.  "]
["After you have defined each single character code for protein modifications, you can paste your annotated peptide sequences into the sequence column on the Peptides sheet.  These single character codes will then be used to automatically populate the PTMs sheet.  The single character codes will also be stripped out of the peptide sequence, as required for PRIDE entry.  Note that you can paste peptides on to multiple rows in one action and they will all be processed automatically in this manner."]
["Optional, but important columns on the Peptides sheet include the start, end and Spectrum Reference columns.  Note that the end column is automatically populated as soon as you enter a value in the start column but can be over-written if required.  The spectrum reference column should be completed if you are using an external mzData file that contains spectra.  This allows the generated PRIDE XML file to cross reference identified peptides to the appropriate mass spectrum.  If you are not including spectra you should leave this column empty.  "]
["Funded by the BBSRC, under the \"Proteome Harvest\" grant"]
["Developed by Philip Jones, EMBL - European Bioinformatics Institute.   Made available under the Apache License Version 2.0, January 2004 (See http://www.apache.org/licenses/LICENSE-2.0.html)"]

{"sheet":"Experiment","index":1,"n_rows":13,"n_cols":7,"rows_kept":13,"cut":false,"hidden":false,"merged":[[4,1,4,2],[5,1,5,2],[0,0,0,1],[7,0,7,3],[1,1,1,2],[2,1,2,2],[3,1,3,2],[7,6,10,6],[8,0,8,3],[9,0,9,1],[9,2,9,3],[10,4,10,5]],"flags":["formulas_cached_only"]}
["This sheet contains over-arching information about the entire experiment.  ",null,null,"Page Not Complete"]
[null,"Value (Yellow - mandatory, White - optional.)",null,"↓ Status"]
["Project Title →",null,null,"OK"]
["Experiment Title →",null,null,"Invalid - mandatory value"]
["Experiment Accession Number →",null,null,"OK"]
["Short Experiment Title →",null,null,"Invalid - mandatory value"]
[]
["Additional Parameters Describing the Experiment (Globally)",{"$nulls":5},"↓ Status"]
["CV Params"]
[null,null,"User Params"]
["↓ CV Name","↓ Accession","↓ Term Name","↓ Value (optional)","Double Click to activate buttons below"]
["PRIDE","PRIDE:0000097","Project",0]
[{"$nulls":4},"Search for CV Term","Add Param",""]

{"sheet":"Contacts","index":2,"n_rows":3,"n_cols":4,"rows_kept":3,"cut":false,"hidden":false,"merged":[[0,0,0,2]],"flags":["formulas_cached_only"]}
["This sheet contains details of Contacts (minimum one) that will be included in the XML file."]
["↓ Name","↓ Institution","↓ Contact Information (preferably email)","Double Click"]
[null,null,null,"Add Contact"]

{"sheet":"CV Lookup","index":3,"n_rows":17,"n_cols":6,"rows_kept":17,"cut":false,"hidden":false,"merged":[[0,0,0,3]],"flags":["formulas_cached_only"]}
["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"]

{"sheet":"Protocol Steps","index":4,"n_rows":8,"n_cols":8,"rows_kept":8,"cut":false,"hidden":false,"merged":[[0,0,0,4],[1,0,1,4],[3,7,6,7],[3,0,6,0],[3,1,3,4],[4,1,4,4],[5,3,5,4],[6,5,6,6],[5,1,5,2],[2,1,2,4]],"flags":["formulas_cached_only"]}
["Protocol Steps - The Step number indicates the order of the steps.  Each step can use 1 or more parameters to describe it."]
[{"$nulls":7},"↓ Status"]
["Protocol Name →",{"$nulls":6},"Invalid - mandatory value"]
["↓ Protocol Step Number","Parameters"]
[null,"CV Params"]
[null,null,null,"User Params"]
[null,"↓ CV Name","↓ Accession","↓ Term Name","↓ Value (optional)","Double Click to activate buttons below"]
[{"$nulls":5},"Search for CV Term","Add Param",""]

{"sheet":"References","index":5,"n_rows":17,"n_cols":8,"rows_kept":17,"cut":false,"hidden":false,"merged":[[15,4,15,5],[7,4,9,7],[4,4,6,7],[0,0,0,6],[11,1,11,6],[1,0,1,4],[11,7,16,7],[12,4,14,5],[12,0,12,3],[12,6,15,6],[13,0,13,3],[14,0,14,1],[14,2,14,3]],"flags":["formulas_cached_only"]}
["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,null,"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",null,"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 →",{"$nulls":6},"Add Reference (Double Click)"]
["Additional Parameters Describing the Reference (e.g. ISBN, PubMed ID)",{"$nulls":5},"Status"]
["CV Params"]
[null,null,"User Params"]
["↓ CV Name","↓ Accession","↓ Term Name","↓ Value (optional)","Double Click to activate buttons"]
[{"$nulls":4},"Search for CV Term","Add Param",""]

{"sheet":"ident_hidden","index":6,"n_rows":22,"n_cols":16,"rows_kept":22,"cut":false,"hidden":true,"merged":[[0,0,0,6],[1,0,1,2],[2,0,2,2],[3,1,3,2],[3,4,3,5],[4,1,4,2],[4,4,4,5],[5,0,5,5],[6,4,6,5],[9,0,9,6],[9,7,14,7],[10,0,10,1],[10,4,10,5],[10,6,12,6],[11,0,11,1],[11,4,11,5],[12,0,12,5],[13,4,13,5]],"flags":["formulas_cached_only"]}
["Modification (Pre or Post translational)"]
["↓ Location (Relative to Peptide)",null,null,"↓ Accession","↓ PTM Database","↓ Database Version"]
[]
["Mass Delta Type →","Average",null,"Value →",null,null,"Double Click button below"]
["Mass Delta Type →","Monoisotopic",null,"Value →",null,null,"Add Mass Delta"]
["Modification Additional Parameters"]
["↓ CV Name","↓ Accession","↓ Term Name","↓ Value (optional)","Double Click to activate buttons ↓",null,"↓ Status"]
[{"$nulls":4},"Search for CV Term","Add Param",""]
[]
["Peptide",{"$nulls":6},"Add Peptide (will appear above this one)"]
["↓ Sequence",null,"↓ Start","↓ End","↓ Spectrum Reference"]
[]
["Peptide Additional Parameters"]
["↓ CV Name","↓ Accession","↓ Term Name","↓ Value (optional)","Double Click to activate buttons ↓",null,"↓ Status"]
[{"$nulls":4},"Search for CV Term","Add Param",""]
[]
["Add PTM"]
[]
[]
["Add PTM","[Automatic]","[Automatic]","[Automatic]",{"$nulls":8},"Search for CV Term","Add Param",""]
[]
["[Auto]","[Auto]",{"$nulls":6},"Add Mass Delta",{"$nulls":4},"Search for CV Term","Add Param",""]

{"sheet":"Sample","index":7,"n_rows":20,"n_cols":7,"rows_kept":20,"cut":false,"hidden":false,"merged":[[7,5,7,10],[13,0,13,6],[14,0,14,6],[11,0,11,2],[11,3,11,4],[12,0,12,2],[12,3,12,4],[7,0,7,2],[8,0,8,2],[10,0,10,2],[7,3,7,4],[8,3,8,4],[10,3,10,4],[0,0,0,1],[1,1,1,2],[6,0,6,4],[4,1,4,2],[3,1,3,2],[9,0,9,2],[15,6,18,6],[16,0,16,3],[17,0,17,1],[17,2,17,3],[18,4,18,5],[15,0,15,3]],"flags":["formulas_cached_only"]}
["This sheet contains information related to the sample under study"]
[null,"Value (Yellow - mandatory, Green - optional.)",null,"↓ Status"]
[]
["Sample Name →",null,null,"Invalid - mandatory value"]
["Sample Description Comment →",null,null,"OK"]
[]
["Please add optional parameters below to describe, as far as possible:"]
["* The species, using NEWT (a super-set of the NCBI Taxonomy)",null,null,"http://www.ebi.ac.uk/newt"]
["* The organ / tissue, using the BRENDA Tissue ontology",null,null,"http://www.brenda.uni-koeln.de/"]
["* The cell type, using the OBO Cell Type ontology",null,null,"http://obo.sourceforge.net/cgi-bin/detail.cgi?cell"]
["* The disease state, using the OBO / DOID Disease Ontology",null,null,"http://diseaseontology.sourceforge.net/"]
["* The sub-cellular location, using the GO Gene Ontology",null,null,"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",{"$nulls":5},"↓ Status"]
["CV Params"]
[null,null,"User Params"]
["↓ CV Name","↓ Accession","↓ Term Name","↓ Value (optional)","Double Click to activate buttons below"]
[{"$nulls":4},"Search for CV Term","Add Param",""]

{"sheet":"MS Instrument","index":8,"n_rows":37,"n_cols":8,"rows_kept":37,"cut":false,"hidden":false,"merged":[[32,0,32,3],[32,6,35,6],[33,0,33,3],[34,0,34,1],[34,2,34,3],[35,4,35,5],[25,0,25,3],[25,6,28,6],[26,0,26,3],[27,0,27,1],[27,2,27,3],[28,4,28,5],[16,0,16,6],[17,7,20,7],[18,1,18,4],[19,1,19,2],[19,3,19,4],[20,5,20,6],[17,0,20,0],[17,1,17,4],[15,0,15,6],[8,0,8,3],[8,6,11,6],[9,0,9,3],[10,0,10,1],[10,2,10,3],[11,4,11,5],[0,0,0,3],[3,2,3,3],[4,2,4,3],[5,2,5,3],[3,0,5,0],[1,2,1,3],[2,2,2,3]],"flags":["formulas_cached_only"]}
["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."]
[null,null,"Value (Yellow - mandatory, Green - optional.)",null,"↓ Status"]
[null,"Instrument Name →",null,null,"Invalid - mandatory value"]
["MS Instrument Source File","Source File Name →",null,null,"OK"]
[null,"Source File Path (e.g. URL) →",null,null,"OK"]
[null,"Source File Type →",null,null,"OK"]
[]
[]
["Parameters Describing the Source (At least one parameter is mandatory)",{"$nulls":5},"↓ Status"]
["CV Params"]
[null,null,"User Params"]
["↓ CV Name","↓ Accession","↓ Term Name","↓ Value (optional)","Double Click to activate buttons below"]
[{"$nulls":4},"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"]
[null,"CV Params"]
[null,null,null,"User Params"]
[null,"↓ CV Name","↓ Accession","↓ Term Name","↓ Value (optional)","Double Click to activate buttons below"]
[1,{"$nulls":4},"Search for CV Term",null,"Invalid - At least one analyzer component is mandatory"]
[{"$nulls":5},"Search for CV Term","Add Param",""]
[]
[]
["Parameters Describing the Detector (At least one parameter is mandatory)",{"$nulls":5},"↓ Status"]
["CV Params"]
[null,null,"User Params"]
["↓ CV Name","↓ Accession","↓ Term Name","↓ Value (optional)","Double Click to activate buttons below"]
[{"$nulls":4},"Search for CV Term","Add Param",""]
[]
[]
["Additional Parameters Describing the MS Instrument",{"$nulls":5},"↓ Status"]
["CV Params"]
[null,null,"User Params"]
["↓ CV Name","↓ Accession","↓ Term Name","↓ Value (optional)","Double Click to activate buttons below"]
[{"$nulls":4},"Search for CV Term","Add Param",""]

{"sheet":"MS Instrument Software","index":9,"n_rows":15,"n_cols":6,"rows_kept":15,"cut":false,"hidden":false,"merged":[[13,4,13,5],[10,0,10,3],[11,0,11,3],[12,0,12,1],[12,2,12,3],[0,0,0,4],[9,0,9,3],[2,1,2,2],[3,1,3,2],[4,1,4,2],[6,1,6,2],[5,1,5,2]],"flags":["formulas_cached_only"]}
["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.)"]
[]
[null,"Value (Yellow - mandatory, White - optional.)",null,"↓ Status"]
["MS Instrument Software Name →",null,null,"Invalid - mandatory value"]
["MS Instrument Software Version →",null,null,"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"]
[null,null,"User Params"]
["↓ CV Name","↓ Accession","↓ Term Name","↓ Value (optional)","Double Click to activate buttons below"]
[{"$nulls":4},"Search for CV Term","Add Param"]

{"sheet":"Proteins","index":10,"n_rows":10001,"n_cols":27,"rows_kept":10001,"cut":false,"hidden":false,"merged":[[2,23,2,24],[0,0,0,16],[1,19,1,22],[1,14,1,18],[1,2,1,13]],"flags":["formulas_cached_only"]}
["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."]
[{"$nulls":14},"2-D Gel Based Identifications",{"$nulls":4},"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",null,"↓ Param Status","pepsmade?"]
["Add Peptides",1,{"$nulls":21},"Search for CV Term","Add Param",""]
["Add Peptides",2,{"$nulls":21},"Search for CV Term","Add Param",""]
["Add Peptides",3,{"$nulls":21},"Search for CV Term","Add Param",""]
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{"sheet":"Peptides","index":11,"n_rows":4,"n_cols":15,"rows_kept":4,"cut":false,"hidden":false,"merged":[[2,8,2,11],[3,12,3,13],[1,0,1,4],[0,0,0,4]],"flags":["formulas_cached_only"]}
["To add details of a peptide, you first need to enter detail of the protein that it provides evidence for on the \"Proteins\" worksheet and then click on the 'Add Peptide' button on column A of sheet \"Proteins\".  Rows will than automatically be added to this sheet as required.  If you wish to add details of protein modifications to an individual peptide on this sheet, click on the \"Add PTM\" button in column A.  This will create a record on the \"PTMs\" sheet that you can populate further."]
["NOTE: If you wish PTMs to be automatically created from sequence annotations, you first need to define the meaning of the annotations on the worksheet \"PTM Codes\""]
[{"$nulls":8},"CV / User Parameters"]
[null,"↓ 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",null,"↓ Status"]

{"sheet":"PTM Codes","index":12,"n_rows":7,"n_cols":11,"rows_kept":7,"cut":false,"hidden":false,"merged":[[0,0,0,4],[3,6,3,10],[8,7,8,10],[9,7,9,10],[3,0,3,4],[1,1,1,4]],"flags":["formulas_cached_only"]}
["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.",{"$nulls":5},"Example Entries:"]
["↓ Code","↓ Accession","↓ PTM Database","↓ Name","↓ Database Version",null,"↓ Code","↓ Accession","↓ PTM Database","↓ Name","↓ Database Version"]
[{"$nulls":6},"#","MOD:00419","PSI-MOD","S-carbamoylmethylcysteine cyclization (N-terminus)"]
[{"$nulls":6},"*","MOD:00260","PSI-MOD","O-(phospho-5'-DNA)-L-threonine"]

{"sheet":"PTMs","index":13,"n_rows":3,"n_cols":16,"rows_kept":3,"cut":false,"hidden":false,"merged":[[1,9,1,12],[2,13,2,14],[0,0,0,6]],"flags":["formulas_cached_only"]}
["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."]
[{"$nulls":9},"CV / User Parameters"]
["↓ Peptide Unique ID","↓ Peptide Sequence","↓ Location (Relative to Peptide)","↓ Accession","↓ PTM Database","↓ Database Version","↓ Average Delta Value","↓ Mono Delta Value",null,"↓ CV Name","↓ Accession","↓ Term Name","↓ Value","Double Click to activate buttons below",null,"↓ Status"]

{"sheet":"cvParamHidden","index":14,"n_rows":49,"n_cols":11,"rows_kept":49,"cut":false,"hidden":true,"merged":[],"flags":["formulas_cached_only"]}
["Accession","Concept Name","Ontology","Available Ontologies",{"$nulls":5},"IdentificationTypes","MassDeltaTypes"]
[null,null,null,"Short Name","Full Name",{"$nulls":4},"2D-GE Based","Average"]
[null,null,null,"BS","Biosapiens Annotations",{"$nulls":4},"Gel Free","Monoisotopic"]
[null,null,null,"BTO","BRENDA tissue / enzyme source"]
[null,null,null,"CHEBI","Chemical Entities of Biological Interest"]
[null,null,null,"CL","Cell Type"]
[null,null,null,"DDANAT","Dictyostelium discoideum Anatomy"]
[null,null,null,"DOID","Human Disease"]
[null,null,null,"ECO","Evidence Codes"]
[null,null,null,"EHDA","Human Developmental Anatomy, timed version"]
[null,null,null,"EHDAA","Human Developmental Anatomy, abstract version"]
[null,null,null,"EMAP","Mouse Gross Anatomy and Development"]
[null,null,null,"EO","Plant Environmental Conditions"]
[null,null,null,"EV","eVOC (Expressed Sequence Annotation for Humans)"]
[null,null,null,"FAO","Fungal Gross Anatomy"]
[null,null,null,"FBbi","Biological Imaging Methods"]
[null,null,null,"FBbt","Drosophila Gross Anatomy"]
[null,null,null,"FBcv","Flybase Controlled Vocabulary"]
[null,null,null,"FBdv","Drosophila Development"]
[null,null,null,"FIX","Physico-Chemical Methods and Properties"]
[null,null,null,"GO","Gene Ontology"]
[null,null,null,"GRO","Cereal Plant Development"]
[null,null,null,"IEV","Event (INOH)"]
[null,null,null,"IMR","Molecule Role (INOH)"]
[null,null,null,"MA","Mouse Adult Gross Anatomy"]
[null,null,null,"MFO","Medaka Fish Anatomy and Development"]
[null,null,null,"MI","Molecular Interaction (PSI MI 2.5)"]
[null,null,null,"MOD","Protein Modifications (PSI-MOD)"]
[null,null,null,"MP","Mammalian Phenotype"]
[null,null,null,"MPATH","Mouse Pathology"]
[null,null,null,"NEWT","NEWT UniProt Taxonomy Database"]
[null,null,null,"OBO_REL","OBO Relationship Types"]
[null,null,null,"PATO","Phenotypic qualities (properties)"]
[null,null,null,"PM","Phenotypic manifestation (genetic context)"]
[null,null,null,"PO","Plant Ontology (Structure, Growth and Developmental Stage)"]
[null,null,null,"PRIDE","PRIDE Controlled Vocabulary"]
[null,null,null,"PSI","Mass Spectroscopy CV (PSI-MS)"]
[null,null,null,"PW","Pathway Ontology"]
[null,null,null,"REX","Physico-Chemical Process"]
[null,null,null,"RO","Multiple Alignment"]
[null,null,null,"SEP","Separation Methods"]
[null,null,null,"SO","Sequence Types and Features"]
[null,null,null,"TAIR","Arabidopsis Development"]
[null,null,null,"TGMA","Mosquito Gross Anatomy"]
[null,null,null,"TO","Cereal Plant Trait"]
[null,null,null,"UO","Unit Ontology"]
[null,null,null,"WBls","C. elegans Development"]
[null,null,null,"ZDB","Zebrafish Anatomy and Development"]
[null,null,null,"ZEA","Maize Gross Anatomy"]