CSV result

A typical reports folder contains following CSV files:

All files with prefix database_name_search_date, for example the uniprot-ecoli-20171023_2017.12.22 means the data is searched against the uniprot-ecoli-20171023 database, and the search date is 2017.12.22.

There are mainly four types of result files:

• uniprot-ecoli-20171023_2017.12.22.csv with the shortest file name, it contains all unfiltered PSMs, each line with one PSM, it maybe cross-linked, loop-linked, mono-linked, or regular PSM.
• uniprot-ecoli-20171023_2017.12.22.filtered_X_Y.csv contains filtered results for different peptide types (X) at different level (Y). X can be cross-linked, loop-linked, mono-linked, or regular; Y can be spectra, peptides, or sites.
• uniprot-ecoli-20171023_2017.12.22.precursor_error_distribution.csv and uniprot-ecoli-20171023_2017.12.22.filtered_precursor_error_distribution.csv contain precursor errors from unfiltered and filtered PSMs respectively. They are visualized on the web page result, so they can be skipped when reading this page.
• uniprot-ecoli-20171023_2017.12.22.summary.txt contains summary information about the search, such as the number of identified PSMs, the search time, etc.

uniprot-ecoli-20171023_2017.12.22.filtered_cross-linked_spectra.csv contains all cross-linked PSMs filtered by TDA-FDR and without decoy results, one PSM per line. uniprot-ecoli-20171023_2017.12.22.filtered_cross-linked_peptides.csv and uniprot-ecoli-20171023_2017.12.22.filtered_cross-linked_sites.csv are directly inferred from the uniprot-ecoli-20171023_2017.12.22.filtered_cross-linked_spectra.csv.

There are 21 columns in uniprot-ecoli-20171023_2017.12.22.filtered_cross-linked_spectra.csv:

1. Order: the order of PSMs, start from 1.
2. Title: the title of this spectrum. If RAW file is used, the scheme of title is RAWName.Scan.Scan.Charge.pParseID.dta . For example RD_pH_8point3_step2.7566.7566.3.0.dta means the MS2 scan 7566 from RAW RD_pH_8point3_step2, the charge is 3 and the pParseID is 0. pParseID is the order of precursor ID extracted from MS1 by pParse, the lower the higher credibility, 0 is the best. For more details about pParse, please see pParse.
3. Charge: the charge of this spectrum.
4. Precursor_Mass: the experimental [MH+] of precursor.
5. Peptide: the peptide sequence of identification. AKLESLVEDLVNR(2)-HMNIKVTR(5) means peptide AKLESLVEDLVNR cross-link with HMNIKVTR in site 2 and 5 respectively. For mono-linked and loop-linked peptides, there are one or two cross-linked sites on one peptide.
6. Peptide_Type: the peptide type of identification, it can be Cross-Linked, Loop-Linked, Mono-Linked, or Regular/Common.
7. Linker: the cross-linker name identified. For regular results, it is null.
8. Peptide_Mass: the theoretical [MH+] of peptide.
9. Modifications: the identified modifications on this peptide. For example, Carbamidomethyl[C](6) means Carbamidomethyl happens on 6th site, which is a Cysteine. If more than one modification, they are splitted by semicolon. null means no modifications.
10. Evalue: the E-value of this peptide.
11. Score: the SVM score of this peptide.
12. Precursor_Mass_Error(Da): precursor mass error in Da.
13. Precursor_Mass_Error(ppm): precursor mass error in ppm.
14. Proteins: inferred proteins from this peptide. For example, sp|P0A6Y8|DNAK_ECOLI (304)-sp|P0A6Y8|DNAK_ECOLI (299)/ means sp|P0A6Y8|DNAK_ECOLI cross-link with sp|P0A6Y8|DNAK_ECOLI in site 304 and 299 respectively. If more than one protein pair is inferred, they are splitted by slash.
15. Protein_Type: the protein type of this identification. Whether it is a Intra-protein or Inter-protein cross-link. For mono-linked, loop-linked, and regular results, it is None.
16. FileID: Which RAW file was this PSM identified from? Start from 1. The ID of one RAW file is decided by the order when added. The map of RAW file and FileID is shown in the parameter file.