[Liam McDonnell]

Hi Markus

My postdoc Benjamin Balluff has just indicated there is an error in the database, which mirrors an error in the cited paper.

In the database it is current listed as

3371 DEFA1
3442 DEFA2

However according to Uniprot (http://www.uniprot.org/uniprot/P59665) DEFA1 is the heavier peptide.

[Liam McDonnell]

New entry for the database
m/z 2778 (linear MALDI ToF) in human chondrosarcoma (bone tumor)
identified as a nontryptic, C- terminal fragment of the protein vimentin, LIKTVETRDGQVINETSQHHDDLE using ETD on an Orbitrap Velos.
DOI of paper: DOI: 10.1021/pr301190g
Uniprot ID: P08670
On-tissue validation method: synthesis of isotopically labeled variant and comparison of on-tissue MS/MS

The same paper also reports another 350 top down ID’s but these have not been confirmed in the MALDI data.

[Liam McDonnell]

Another point, it would be helpful if the list differentiated between peptides/proteins that had been assigned only on the basis of mass accuracy and those which have been validated, either by on-tissue MS/MS or IHC. The link to the original article would then also provide the validation method.

[Liam McDonnell]

The MSi list is looking very good indeed, and will be of enormous help to the field. Well done! The lists are likely to get quite long, especially for on-tissue digestion (and in the future lipids) so I would recommend splitting the lists into the different biomolecular classes and ionization method. Even if there is no immediate scope for filling lists for lipids etc the presence of protein and tryptic peptide lists should spur similar efforts for imaging MS of other molecular classes, and using other ionization methods.

If we consider MALDI imaging MS of proteins I would separate the lists into one for imaging of tryptic peptides and one for (non-tryptic) peptides and proteins. The reason for this is that there are different considerations for the two identifications. For example, as seen in the current list tryptic peptides can be non-specific, and so will have multiple hits. For tryptic peptides it would be useful to indicate which tryptic peptide was detected along with its modifications and missed cleavages (which increase the peptide search space and the risk of false positives).

On the other hand MALDI imaging MS of (non-tryptic) peptides and proteins can detect the products of proteolytic processing. Several reported biomarker proteins (e.g. Cazares et al. in Cancer Res) are non-tryptic fragments of larger proteins. Many of the peptides and small proteins detected by protein imaging experiments of resected tissues could be protein fragments because of post-mortem degradation during the resection procedure and subsequent tissue handling steps. The database should include which fragments were detected.

In short having different lists for the different molecular classes will enable the tables to include the most relevant information (for that class) within the available space.

Please let me know what you think.

With best regards
Liam

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