乐天堂游戏网站

How to submit complete crosslinking dataset

Crosslinking data submitted to PRIDE will receive complete submission status when the project meets the following criteria (in addition to the existing criteria at /pride/markdownpage/submitdatapage):

1. Identifications MUST be provided as valid mzIdentML 1.2.0 files. That is, all mzIdentML files must validate against the mzIdentML 1.2.0 schema, located at . Tools which validate XML files against an xsd schema include: .

2. The mzIdentML files SHOULD be semantically valid. That is, the use of CV terms should conform to the requirements of the mzIdentML 1.2.0 specification document. An official semantic validator for mzIdentML 1.2.0 has been developed: . Files which have semantic validation errors but which can, none the less, be read by the repository鈥檚 processing software () will receive 鈥榗omplete submission鈥� status but with a warning.

3. The peaklist data MUST be submitted as .mgf, .mzML or .ms2. These are the peaklist files exactly as searched.

4. The mzIdentML files MUST correctly reference the submitted peaklists. It must be possible to identify and read the spectrum for each identification based on the information in the mzIdentML file, see Section 5.1.2 of the mzIdentML 1.2.0 specification document.

5. The accession attribute of target elements SHOULD be a , if it is a natural protein that has an accession number. That is, the value of the accession attribute for elements should match the regular expression: [OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z]0-9{1,2}

6. Every <DBSequence> element that describes a target protein MUST include the protein sequence in a <Seq> subelement. This is the protein sequence in the protein database used to perform the analysis.

Validate Dataset

Please follow the following three simple steps to validate your dataset prior submitting your dataset to PRIDE which will help to get completed the submission without a delay.

STEP 1: As the first step, place your all the mzIdentML files and peak files into a one folder. Peakfiles needs to be corrected reference by mzIdentML files to read them.

STEP 2: Secondly, make sure you have python > 3.10 and pip installed in your machine. Pip installation guide can be found .
Then please install a python library in order to validate your dataset.

1. Check if all the mzIdentML files match with the
2. Check the references to the peaklist files are correct
3. Check all the accession references of protein, peptide and spectra are correctly referenced
4. Check for any duplicate IDs in protein, peptide and spectra

1. Information in mzIdentML files on scores and the passing of thresholds at higher levels of consolidation (unique peptide; crosslink level; PPI) are not processed by , only the PSM level scores/threshold passes.

2. Doesn鈥檛 read linked FASTA files, hence item (6) above.

3. Doesn鈥檛 support the 鈥渃ombined spectra file type鈥� from mzIdentML 1.2.0

Tools tested in PRIDE crosslinking resource

While multiple tools can be used to analyze crosslinking data, only the following tools have been tested and produce valid files that can be loaded into the PRIDE crosslinking resource:

• : xiSEARCH is a library of routines for peptide-based mass spectrometry, prominently featuring a search engine for identifying crosslinked peptides. xiFDR is a tool for calculating false discovery rates for crosslinked peptides. Example dataset: PXD019437
• : Scout is a computational methodology that facilitates interactomic analysis by identifying mass spectra of peptides linked with cleavable cross-linking reagents. Utilizing machine learning techniques, Scout ensures a controlled false discovery rate (FDR) at multiple levels, including cross-linked spectrum matches, residue pairs, and protein-protein interactions (PPIs). Example dataset: PXD042173
• : Mascot is a powerful search engine and proteomics analysis sofware that uses mass spectrometry data to identify proteins from primary sequence databases. Example dataset: PXD054720
• : Kojak is a free, open-source application for identification of cross-linked peptides from mass spectra. Example dataset: PXD056910

Note: If you have used a different tool to analyze your crosslinking data, and you are not able to perform a complete submission following the previous guidelines, please contact the PRIDE team at [email protected].