Mass spectrometry data

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First found May 22, 2018

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Mass spectrometry data
Mass spectrometry data should be provided in the mzML format following the HUPO Protein
Standards Initiative guidelines; for peptide mass fingerprinting the total percentage of sequence
coverage and number of peptides matching it should be given
Mass spectrometric analysis and quantification of proteins and peptides: the authors should
provide detailed information on how raw data was converted into a format for database searching
(e.g. peak list from raw MS or MS/MS data), the search engine used, the database(s), scoring
function(s), false discovery rate (how calculated) and statistical methods employed
For posttranslational protein modifications results of fragmentation analysis and spectra should be
provided. If no evidence for assigning a modification to a single amino acid is provided it should be
reported as ambiguous.
a) Proteomics
To ensure reproducibility, please provide experimental details for (gel-based) proteomics data such as
how the duplicates were performed and how the data was processed with what standard.
Protein interaction
Recommended databases
PeptideAtlas, ProteomeXchange
MEx consortium
b) Functional genomics data/deep sequencing data (such as microarray, RNA-seq
or ChIP-seq data)
Functional genomics data (e.g. microarray, RNA-seq or ChIP-seq data) should follow the
standards proposed by the Functional Genomics Data Society, and Gene nomenclature should be
standardised with human gene names and symbols from a gene nomenclature database.
For unpublished genomic data the guidelines of the Fort Lauderdale and Toronto agreements
should be followed and the authors should contact the owner of the genomic data before starting their
Genomic data generated from HeLa cells: We highly recommend authors to comply with the NIH
HeLa Genome Data Use Agreement.
Recommended databases
Expression, epigenetics, phenol- or genotypes,
genomic variants (GWAS studies), human
sequence data
Database of Genotypes and Phenotypes
Protein-protein, protein-DNA/RNA and molecular The IntAct molecular interaction database
miRNA sequences and annotation
Human genomic data, genetic polymorphisms
dbSNP, the Database of Genomic Variants
Archive (DGVa), Database of Genomic
Structural Variation (dbVAR)
c) Sequence variants
Nucleic acids sequences and variation
Nucleic acid sequences
Metagenome, sequence alignment,
sequence information
Recommended databases
DNA Data Bank of Japan (DDBJ)
European Molecular Biology Laboratory (EMBL/EBI)
Nucleotide Sequence Database
GenBank (National Center for Biotechnology Information)
NCBI Sequence Read Archive (SRA), ENA’s Sequence Read
Archive, NCBI Trace Archive
European Variation Archive (EVA)
Database of Genomic Variants Archive (DGVa)
EBI Metagenomics
Protein sequences
Protein sequences
Recommended databases
Universal Protein Resource (UniProt)

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