CSV Formats
The tables below describe the formats for CSV input of peptide identifications.
Minimal CSV: link positions only, no peptide info, no peak lists
| column | required? | notes | default | example |
|---|---|---|---|---|
| AbsPos1 | Yes | Position of cross-linked residue in protein 1 (1-based) | - | 2 |
| AbsPos2 | Yes | Position of cross-linked residue in protein 2 (1-based) | - | 14; 24 |
| Protein1 | Yes | Identifier for protein 1. Ambiguous results are represented by listing the alternative proteins separated by semi-colons | - | HSA |
| Protein2 | Yes | Identifier for protein 2. Ambiguous results are represented by listing the alternative proteins separated by semi-colons | - | P02768;P13645 |
| Decoy1 | No | Set to true if the peptide 1 is matched to a decoy sequence | FALSE | TRUE |
| Decoy2 | No | Set to true if the peptide 2 is matched to a decoy sequence | FALSE | TRUE |
| Score | No | Confidence score for the identification (number) | 0 | 10.5641 |
CSV without peak lists
| column | required? | notes | default | example |
|---|---|---|---|---|
| PepSeq1 | Yes | Peptide sequence for peptide 1 in one letter amino acid code (uppercase) with modifications following the amino acid and consisting of the following characters: a-z:0-9.()\- | - | LKECcmCcmEKPLLEK |
| PepSeq2 | Yes | Peptide sequence for peptide 2 in one letter amino acid code (uppercase) with modifications following the amino acid and consisting of the following characters: a-z:0-9.()\- | - | HPYFYAPELLFFAKR |
| PepPos1 | Yes | Position of peptide 1 in protein 1 (1-based). Ambiguous results are represented by listing the alternative positions separated by semi-colons | - | 10 |
| PepPos2 | Yes | Position of peptide 2 in protein 2 (1-based). Ambiguous results are represented by listing the alternative positions separated by semi-colons | - | 20; 40 |
| LinkPos1 | Yes | Position of cross-linked residue for peptide 1 (1-based) | - | 2 |
| LinkPos2 | Yes | Position of cross-linked residue for peptide 2 (1-based) | - | 14 |
| Protein1 | Yes | Identifier for protein 1. Ambiguous results are represented by listing the alternative proteins separated by semi-colons | - | HSA |
| Protein2 | Yes | Identifier for protein 2. Ambiguous results are represented by listing the alternative proteins separated by semi-colons | - | P02768;P13645 |
| Rank | No* | Rank of the identification quality as scored by the search engine (1 is the top rank) | 1 | 1 |
| Charge | No | Precursor charge state | - | 3 |
| CrossLinkerModMass | No | Modification mass of the used cross-linker | 0 | 138.06808 |
| ScanId | No | - | ||
| PeakListFileName | No | |||
| FragmentTolerance | No | MS2 tolerance for annotating fragment peaks (in ppm or Da) | 10 ppm | 0.2 Da |
| IonTypes | No | Fragment ion types to be considered separated by semicolon | peptide;b;y | peptide;a;b;c;x;y;z |
| ExpMz | No | The mass-to-charge value measured in the experiment in Daltons / charge. | - | 985.4341 |
| CalcMz | No | The theoretical mass-to-charge value calculated for the peptide in Daltons / charge. | - | 985.6531 |
| Decoy 1 | No | Set to true if the peptide 1 is matched to a decoy sequence | FALSE | TRUE |
| Decoy 2 | No | Set to true if the peptide 2 is matched to a decoy sequence | FALSE | TRUE |
| Score | No | Confidence score for the identification (number) | 0 | 10.5641 |
| PassThreshold | No | True if the identification has passed a given threshold or been validated as correct | TRUE | FALSE |
*required if there are multiple alternative explanations for the same spectrum.
CSV with peaks lists
| column | required? | notes | default | example |
|---|---|---|---|---|
| PepSeq1 | Yes | Peptide sequence for peptide 1 in one letter amino acid code (uppercase) with modifications following the amino acid and consisting of the following characters: a-z:0-9.()\- | - | LKECcmCcmEKPLLEK |
| PepSeq2 | Yes | Peptide sequence for peptide 2 in one letter amino acid code (uppercase) with modifications following the amino acid and consisting of the following characters: a-z:0-9.()\- | - | HPYFYAPELLFFAKR |
| PepPos1 | Yes | Position of peptide 1 in protein 1 (1-based). Ambiguous results are represented by listing the alternative positions separated by semi-colons | - | 10 |
| PepPos2 | Yes | Position of peptide 2 in protein 2 (1-based). Ambiguous results are represented by listing the alternative positions separated by semi-colons | - | 20; 40 |
| LinkPos1 | Yes | Position of cross-linked residue for peptide 1 (1-based) | - | 2 |
| LinkPos2 | Yes | Position of cross-linked residue for peptide 2 (1-based) | - | 14 |
| Protein1 | Yes | Identifier for protein 1. Ambiguous results are represented by listing the alternative proteins separated by semi-colons | - | HSA |
| Protein2 | Yes | Identifier for protein 2. Ambiguous results are represented by listing the alternative proteins separated by semi-colons | - | P02768;P13645 |
| Charge | Yes | Precursor charge state | - | 3 |
| CrossLinkerModMass | Yes | Modification mass of the used cross-linker | 0 | 138.06808 |
| ScanId | Yes | mzML: 1-based scan number; MGF: 0-based index in file | - | 2256 |
| PeakListFileName | Yes | File name of the associated peak list file that contains the scan | - | example_file.mzML |
| Rank | No* | Rank of the identification quality as scored by the search engine (1 is the top rank) | 1 | 1 |
| FragmentTolerance | No | MS2 tolerance for annotating fragment peaks (in ppm or Da) | 10 ppm | 0.2 Da |
| IonTypes | No | Fragment ion types to be considered separated by semicolon | peptide;b;y | peptide;a;b;c;x;y;z |
| ExpMz | No | The mass-to-charge value measured in the experiment in Daltons / charge. | - | 985.4341 |
| CalcMz | No | The theoretical mass-to-charge value calculated for the peptide in Daltons / charge. | - | 985.6531 |
| Decoy 1 | No | Set to true if the peptide 1 is matched to a decoy sequence | FALSE | TRUE |
| Decoy 2 | No | Set to true if the peptide 2 is matched to a decoy sequence | FALSE | TRUE |
| Score | No | Confidence score for the identification (number) | 0 | 10.5641 |
| PassThreshold | No | True if the identification has passed a given threshold or been validated as correct | TRUE | FALSE |
*required if there are multiple alternative explanations for the same spectrum.
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