xiSPEC Feature support
- Saving a dataset
- Measure distances
- Move labels
- Change cross-linker position
- Change modification position
- Highlight fragments
- 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!
- 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!
- 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!
- 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!
- Click on the cross-link line.
- Move the mouse over the desired cross-linked amino acids.
- Click on the amino acid to confirm the position(s). ⇨ xiSPEC updates the annotated spectrum!
- 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!
- 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
|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 cross-linked peptides.
Input data format for manual data input & re-annotation requests
|amino acid residues||uppercase one letter code||ARNDCEQGHILKMFPSTWYV|
|modifications||anything not uppercase
(following the residue)
|Mox | Kbs3nh2 | K(+16)|
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.