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| Revision as of 18:15, 27 August 2008 Dcampbel (Talk | contribs) ← Previous diff |
Current revision Dcampbel (Talk | contribs) |
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| - | This page is for discussing open questions on the content or format of the list. | + | This page is for discussing open questions on the content or format of the list. (Back to main [[Glyco-peptide]] project page) |
| Discussion topics (please feel free to add): | Discussion topics (please feel free to add): | ||
| Line 5: | Line 5: | ||
| From Bernd W | From Bernd W | ||
| 1. Only 64% of all N-glycosites are predicted to be actually glycosylated. Should we focus on the peptides we actually have measured first? | 1. Only 64% of all N-glycosites are predicted to be actually glycosylated. Should we focus on the peptides we actually have measured first? | ||
| + | |||
| 2. How many N-glycosites per protein should we order (all or max 2,3,4 per protein)? | 2. How many N-glycosites per protein should we order (all or max 2,3,4 per protein)? | ||
| + | |||
| 3. Should we order for a subset of N-glycosite containing proteins additional non-glycopeptides as controls? | 3. Should we order for a subset of N-glycosite containing proteins additional non-glycopeptides as controls? | ||
| - | 4. In case of of tricky peptides such as | ||
| + | 4. In case of of tricky peptides such as | ||
| HNNSSLNTR | HNNSSLNTR | ||
| TIVLIPFLEQNNSSPNTR | TIVLIPFLEQNNSSPNTR | ||
| QAYHPNNSSPVCYEVLGNDTAK | QAYHPNNSSPVCYEVLGNDTAK | ||
| TPEINNSSGLSLSYGPVSPIIR | TPEINNSSGLSLSYGPVSPIIR | ||
| - | |||
| Which deamidated peptide should we order if the MS data is not clear or if the peptide was predicted? | Which deamidated peptide should we order if the MS data is not clear or if the peptide was predicted? | ||
| Line 24: | Line 25: | ||
| 7. A third observation to discuss: We do see a lot of miss-cleaved, double-tryptic N-glycosites in a reproducible fashion. In a lot of these cases we never saw | 7. A third observation to discuss: We do see a lot of miss-cleaved, double-tryptic N-glycosites in a reproducible fashion. In a lot of these cases we never saw | ||
| the shorter "correctly" cleaved double-tryptic peptide. Should we include some peptides to look into this in more detail? | the shorter "correctly" cleaved double-tryptic peptide. Should we include some peptides to look into this in more detail? | ||
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| + | From Dave C | ||
| + | |||
| + | 1) What about peptide sequences for which more than one peptide ion has been observed, i.e seen in multiple charge states, multiple modification states? Should | ||
| + | we report just one value, the most prevalent? | ||
| + | |||
| + | 2) What if we have additional accession numbers, can we include those as columns at the end? Or is this superfluous? | ||
| + | |||
| + | 3) It was suggested that we provide sample information for all the observed peptides, should we have a final column with a comma-separated list of samples? | ||
| + | |||
| + | 4) Should we use a consistent PeptideProphet cutoff for our lists? Peptide Atlas builds use 0.9 by default, which is the criteria that I plan to apply | ||
| + | to UniPep data. | ||
| + | |||
| + | 5) Can we use SILAC data? | ||
Current revision
This page is for discussing open questions on the content or format of the list. (Back to main Glyco-peptide project page)
Discussion topics (please feel free to add):
From Bernd W
1. Only 64% of all N-glycosites are predicted to be actually glycosylated. Should we focus on the peptides we actually have measured first?
2. How many N-glycosites per protein should we order (all or max 2,3,4 per protein)?
3. Should we order for a subset of N-glycosite containing proteins additional non-glycopeptides as controls?
4. In case of of tricky peptides such as HNNSSLNTR TIVLIPFLEQNNSSPNTR QAYHPNNSSPVCYEVLGNDTAK TPEINNSSGLSLSYGPVSPIIR Which deamidated peptide should we order if the MS data is not clear or if the peptide was predicted?
5. An observation to discuss: A lot of our cell surface N-glycosites contain Cysteine residues. Is this also the case for serum N-glycosites?
6. A second observation to discuss: We do see a lot of semi-tryptic N-glycosites in a reproducible fashion. How should we go about these peptides in the future? They could be valuable for quantification of proteins in cases were we can't observe additional N-glycosites, but they can screw up the quantification too. We don't know at this point.
7. A third observation to discuss: We do see a lot of miss-cleaved, double-tryptic N-glycosites in a reproducible fashion. In a lot of these cases we never saw the shorter "correctly" cleaved double-tryptic peptide. Should we include some peptides to look into this in more detail?
From Dave C
1) What about peptide sequences for which more than one peptide ion has been observed, i.e seen in multiple charge states, multiple modification states? Should we report just one value, the most prevalent?
2) What if we have additional accession numbers, can we include those as columns at the end? Or is this superfluous?
3) It was suggested that we provide sample information for all the observed peptides, should we have a final column with a comma-separated list of samples?
4) Should we use a consistent PeptideProphet cutoff for our lists? Peptide Atlas builds use 0.9 by default, which is the criteria that I plan to apply to UniPep data.
5) Can we use SILAC data?
