with the abundance of dna sequence information currently available , researchers are now looking to comprehensively identify and characterize the proteomic products of the genetic blueprint .
the most widespread and high - throughput methodology being used to address this goal is mass spectrometry ( ms ) . using ms to perform large - scale experiments generates substantial amounts of peptide and protein mass spectra .
the informatics issues involved in dealing with these volumes of data can be overwhelming even within an individual laboratory .
this matter , together with a lack of open standard formats , has contributed towards the general shortage of publicly available ms - based proteomic data . however , there is increasing recognition within the community , granting bodies and publishing agencies ( 1 ) that published proteomic data can , and should , be fully accessible .
open access policies such as these allow the community to review and comprehensively re - examine the data upon which experimental conclusions are based . from the researcher 's ; perspective , the long - term archiving of proteomic data at a centralized repository not only increases the data usability and visibility but also decreases the risk of data loss .
in addition , the availability of large collections of ms data can benefit the field in a wider sense , for example , by enabling informaticians to develop better algorithms or construct spectral libraries .
several databases already exist to store and disseminate proteomic data including pride ( 2 ) , peptideatlas ( 3 ) , tranche ( 4 ) , the gpm ( 5 ) , and human proteinpedia ( 6 ) .
peptidome ( 7 ) aims to complement these resources ; the major goals of the peptidome project are to : 
 build and maintain a robust database in which to efficiently store tandem ms data at a level of detail appropriate for both ms professionals and the wider biological community , develop simple deposit procedures that minimize the burden of submission while supporting well - annotated data deposits from the research community , exchange data with established ms repositories , offer user - friendly tools that enable users to query , locate , analyze and review the data of interest . 
 
build and maintain a robust database in which to efficiently store tandem ms data at a level of detail appropriate for both ms professionals and the wider biological community , develop simple deposit procedures that minimize the burden of submission while supporting well - annotated data deposits from the research community , exchange data with established ms repositories , offer user - friendly tools that enable users to query , locate , analyze and review the data of interest .
the information captured in the online database is designed to represent the final results based upon the submitter 's ; interpretation of the raw ms / ms spectra .
this is intended to provide a quick overview for mass spectrometrists and accessibility for other non - specialists .
the original submitted files are the true record , and will always be available for download .
proteins and  peptides. proteins contain links to their member peptides , and peptides know which proteins they are members of .
spectra through peptide identifications ( pepidents ) , thus allowing more than one interpretation of a spectrum , and providing storage for post - translational modifications and identification scores . a schematic overview of peptidome .
proteins and  peptides. proteins contain links to their member peptides , and peptides know which proteins they are members of .
spectra through peptide identifications ( pepidents ) , thus allowing more than one interpretation of a spectrum , and providing storage for post - translational modifications and identification scores .
a study is a collection of related samples and provides a focal point for , and description of , the whole experiment .
a sample contains all the data related to the biological material , which may be derived from one or more ms instrument runs .
each sample record contains a list of identified proteins and a list of identified peptides .
each protein points to a sublist of peptides by which it was identified , and each peptide is linked to the protein(s ) that it is a member of .
these pepidents denote any post - translational modifications as well as any identification scores for the match between a given spectrum and a peptide .
note that this allows a spectrum to have more than one peptide associated with it .
a sample also contains descriptive information about the biological material , protocols used to generate the data , instrumentation and informatics parameters .
both studies and samples are accessioned objects ; each record is assigned a unique and stable peptidome accession number that may be cited in a manuscript describing the data .
the accession consists of a number and a letter prefix indicating whether the record is a peptidome study ( psexxx ) or peptidome sample ( psmxxxx ) .
our goal is to make data submission procedures as straightforward as possible , while encouraging a high level of experimental annotation . to minimize the burden of data submission
there are four components that are required for a complete submission : 
 a metadata file that describes the overall experiment , each associated biological sample , the instruments and protocols used to generate the data and the relationship of the corresponding data files .
this information is provided by completing a metadata spreadsheet ; templates and example spreadsheets are provided within the peptidome submission guidelines from a link on the petidome homepage.raw data files contain the original ms and ms / ms information from the instrument .
peptidome currently accepts any of the standard xml formats ( mzdata , mzxml or mzml ) that contain both the ms and ms / ms data from a single fraction .
in addition , text formats ( .mgf , .pkl , .sqt , .dta ) are also accepted , but not preferred .
proprietary binary data directly from the manufacturers ( e.g. .raw or .wiff ) are not accepted.output files from any peptide identification program . these files contain matches of the ms / ms scans to the peptides .
currently , peptidome supports dat files from mascot , asn.1 or xml formatted files from omssa , and any search engine output files that have been converted to pepxml format ( e.g. x!tandem or sequest ) .
if manual identification was used to interpret the spectra , or the search engine output formats are not supported by peptidome , the submitted results table must include references to spectrum files and additional information that is usually extracted from the search engine output files , e.g. charge state and identification scores.results tables that describe the submitter 's ; view of the final , processed results according to whatever criteria they use to determine acceptability .
results tables list the proteins discovered in each sample in the study . for each protein ,
the peptides should be listed , and for each peptide , the matching spectrum files should be listed .
if the matching spectrum file list is omitted , then every spectrum matched to that peptide / protein in the peptide identification output files is assumed to be correct .
similarly , if the results table contains only proteins , then all associated peptides and spectra will be gleaned from the peptide identification output files . 

peptidome supports post - translational modification annotations in the unimod i d ( 8) format .
fixed modifications for given residues are listed separately and are assumed to apply to all residues of that type .
in the modified peptide strings , each residue is followed by a unimod i d in parenthesis if it is modified and fixed modifications need not be listed . a metadata file that describes the overall experiment , each associated biological sample , the instruments and protocols used to generate the data and the relationship of the corresponding data files .
this information is provided by completing a metadata spreadsheet ; templates and example spreadsheets are provided within the peptidome submission guidelines from a link on the petidome homepage .
raw data files contain the original ms and ms / ms information from the instrument .
peptidome currently accepts any of the standard xml formats ( mzdata , mzxml or mzml ) that contain both the ms and ms / ms data from a single fraction .
in addition , text formats ( .mgf , .pkl , .sqt , .dta ) are also accepted , but not preferred .
proprietary binary data directly from the manufacturers ( e.g. .raw or .wiff ) are not accepted .
currently , peptidome supports dat files from mascot , asn.1 or xml formatted files from omssa , and any search engine output files that have been converted to pepxml format ( e.g. x!tandem or sequest ) .
if manual identification was used to interpret the spectra , or the search engine output formats are not supported by peptidome , the submitted results table must include references to spectrum files and additional information that is usually extracted from the search engine output files , e.g. charge state and identification scores .
results tables that describe the submitter 's ; view of the final , processed results according to whatever criteria they use to determine acceptability .
results tables list the proteins discovered in each sample in the study . for each protein ,
the peptides should be listed , and for each peptide , the matching spectrum files should be listed .
if the matching spectrum file list is omitted , then every spectrum matched to that peptide / protein in the peptide identification output files is assumed to be correct .
similarly , if the results table contains only proteins , then all associated peptides and spectra will be gleaned from the peptide identification output files .
there are many different methods for ms quantification , with new ones being invented all the time .
therefore , for peptide and protein quantification , each quantification value with a single number per protein , peptide and/or spectrum per sample is denoted , where the units ( if applicable ) and methodology used to quantify the sample are required in the metadata annotation .
when all submission files are assembled , they can be transferred to peptidome via ftp .
a curator will collect the files and manually curate and validate them before depositing in the database .
some journals require accession numbers for ms proteomic data before acceptance of a paper for publication .
thus , ideally , data should be deposited in peptidome before a manuscript describing the data is sent to a journal for review .
a reviewer url can be generated and disclosed to journal editors ; this url grants anonymous , confidential access to private data during the manuscript review period .
all submissions undergo both syntactic validation and manual review by a curator before being uploaded to the peptidome database , thus enforcing good quality data deposits .
when any issues , such as mangled formats or missing components , are identified , a curator will work with the submitter until the problems are resolved .
early exemplar submissions in peptidome were gathered from selected data in peptideatlas ( 3 ) , with the metadata manually enriched from publications associated with those experiments .
submissions are processed using custom software to upload the metadata and results into the database .
the spectra files are not loaded into the database , instead they are converted to a custom format , based upon hdf5 ( available from http://www.hdfgroup.org/hdf5/ ) , that is both more compact and allows faster retrieval of individual spectra than the original xml format .
proteins are linked with the corresponding entries in ncbi entrez in a best effort fashion .
this flexibility allows submitters to reference novel proteins that are not yet in the mainstream databases , and to use custom protein databases .
peptidome protein links are updated in an ongoing process , in order that they remain up - to - date .
the data in peptidome may be browsed by studies or samples , and the individual samples may be examined from the identified proteins and peptides down to the individual spectra as shown in figure 2 . 

figure 2.a series of screenshots showing navigation from a top level list of studies ( 1 ) , to its list of samples ( 2 ) , to the protein list for a sample ( 3 ) , to the list of peptide identifications for that protein ( 4 ) and finally to three individual spectra for different peptide identifications ( 5 ) . a series of screenshots showing navigation from a top level list of studies ( 1 ) , to its list of samples ( 2 ) , to the protein list for a sample ( 3 ) , to the list of peptide identifications for that protein ( 4 ) and finally to three individual spectra for different peptide identifications ( 5 ) .
metadata for all public studies and samples , and the associated proteins for each sample , are loaded into ncbi 's ; powerful entrez search and linking system ( 9 ) .
this facilitates cross - linkage with other ncbi resources like entrez protein , pubmed and taxonomy .
the entrez interface also allows users to search peptidome using simple free text or complex fielded queries .
additionally , all original data , including spectra files , output results and supplementary data are available for bulk download via anonymous ftp at ftp://ftp.ncbi.nih.gov / pub / peptidome/.
peptidome was recently established at ncbi with the goal to enhance proteomic research by providing a high - quality mass spectra repository .
we are now accepting submissions and invite researchers to deposit their tandem ms data sets with us so that we can disseminate them to the wider community .
currently , the peptidome team is working to expand and improve existing indexing , linking , searching , exploring and retrieving functionalities .
additional advanced data mining and visualization tools for the convenience of proteomic researchers are under design and development .
funding for open access charge : intramural research program of the national institutes of health , national library of medicine .
 peptidome is a public repository that archives and freely distributes tandem mass spectrometry peptide and protein identification data generated by the scientific community . 
 data from all stages of a mass spectrometry experiment are captured , including original mass spectra files , experimental metadata and conclusion - level results . 
 the submission process is facilitated through acceptance of data in commonly used open formats , and all submissions undergo syntactic validation and curation in an effort to uphold data integrity and quality . 
 peptidome is not restricted to specific organisms , instruments or experiment types ; data from any tandem mass spectrometry experiment from any species are accepted . 
 in addition to data storage , web - based interfaces are available to help users query , browse and explore individual peptides , proteins or entire samples and studies . 
 results are integrated and linked with other ncbi resources to ensure dissemination of the information beyond the mass spectroscopy proteomics community . 
 peptidome is freely accessible at http://www.ncbi.nlm.nih.gov/peptidome . 
INTRODUCTION
ORGANIZATION OF THE DATABASE
SUBMISSION PROCEDURES
BUILDING THE DATABASE
RETRIEVING PEPTIDOME DATA
CONCLUSIONS AND FUTURE DEVELOPMENT
FUNDING