xiSPEC Feature support
- Saving a dataset
- Zooming
- Measure distances
- Move labels
- Change crosslinker position
- Change modification position
- Compare annotations using butterfly plot
- Highlight fragments
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Saving a dataset
- After data processing you can view your data as a temporary dataset
- To save your dataset simply click on the save icon
- Fill out the form and click save ⇨ You will be redirected to your saved dataset!
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Zooming
- Click and drag the cursor below the x-axis to zoom into a specific area of the spectrum.
- Alternatively you can zoom in/out using the mouse wheel. ⇨ xiSPEC updates the annotated spectrum!
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Measure distances
- Activate measuring mode by checking the 'Measure' option.
- Your cursor will change to a crosshair.
- Click and drag in the spectrum to measure distances between peaks. ⇨ xiSPEC displays potential amino acid residue hits in the tooltip!
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Move labels
- Activate moveable labels by checking the 'Move labels' option.
- Click and drag labels to move them around. ⇨ xiSPEC draws dashed lines to the corresponding peaks!
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Change crosslinker position
- Click on the crosslink line.
- Move the mouse over the desired crosslinked amino acids.
- Click on the amino acid to confirm the position(s). ⇨ xiSPEC updates the annotated spectrum!
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Change modification position
- Click on the modification.
- Move the mouse over the desired modified amino acids.
- Click on the amino acid to confirm the position. ⇨ xiSPEC updates the annotated spectrum!
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Compare annotations using butterfly plot
- Change the annotation of the spectrum (e.g. changing annotated ions).
- Click on butterfly or check the adjacent checkbox. ⇨ xiSPEC will show you both annotations for direct comparison of annotations!
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Highlight fragments
- Hover over fragments in any view to highlight the corresponding fragment all views.
- Click on a fragment to make the highlight permanent.
- Ctrl+Click to add additional fragments to permanent selection.
- Click on the spectrum background to reset highlighting.
Peptide identification csv column headings
| column | required? | notes | default | example |
|---|---|---|---|---|
| PepSeq 1 | 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 |
| PepSeq 2 | No** | 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 |
| LinkPos 1 | No** | Position of cross-linked residue for peptide 1 (1-based) | - | 2 |
| LinkPos 2 | No** | Position of cross-linked residue for peptide 2 (1-based) | - | 14 |
| Protein 1 | Yes | Identifier for protein 1. Ambiguous results are represented by listing the alternative proteins separated by semi-colons | - | HSA |
| Protein 2 | No** | Identifier for protein 2. Ambiguous results are represented by listing the alternative proteins separated by semi-colons | - | P02768;P13645 |
| 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 |
| Rank | No* | Rank of the identification quality as scored by the search engine (1 is the top rank) | 1 | 1 |
| 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 |
| Charge | Yes | Precursor charge state | - | 3 |
| CrossLinkerModMass | No** | Modification mass of the used cross-linker | 0 | 138.06808 |
| 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 |
| 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 |
| 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 |
| meta_xxx | No | Up to 3 user defined columns are allowed (using prefix meta_) | - | |
| meta_yyy | No | Up to 3 user defined columns are allowed (using prefix meta_) | - | |
| meta_zzz | No | Up to 3 user defined columns are allowed (using prefix meta_) | - |
*required if there are multiple alternative explanations for the same spectrum. **required for crosslinked peptides.
Input data format for manual data input & re-annotation requests
Peptide Sequence
Peaklist
| What? | How? | Example(s) |
|---|---|---|
| amino acid residues | uppercase one letter code | ARNDCEQGHILKMFPSTWYV |
| modifications | anything not uppercase (following the residue) |
Mox | Kbs3nh2 | K(+16) |
| peptide delimiter | ; | K#LM;DAHK#SEVR |
| crosslinked residue | # |
The peak list format accepted by xiSPEC is simple and easily extracted from most MS formats. Each line contains a pair of numbers: the first is a m/z value and the second is the corresponding intensity. The two numbers should be separated by either spaces or tabs.
Example:
104.31995 1077.574
110.07077 1154.813
116.98479 1330.395
120.08031 6500.032