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Schüler, J.-A.; Neumann, S.; Müller-Hannemann, M.; Brandt, W. ChemFrag: Chemically meaningful annotation of fragment ion mass spectra J Mass Spectrom 53, 1104-1115, (2018) DOI: 10.1002/jms.4278

Identification and structural determination of small molecules by mass spectrometry is an important step in chemistry and biochemistry. However, the chemically realistic annotation of a fragment ion spectrum can be a difficult challenge. We developed ChemFrag, for the detection of fragmentation pathways and the annotation of fragment ions with chemically reasonable structures. ChemFrag combines a quantum chemical with a rule‐based approach. For different doping substances as test instances, ChemFrag correctly annotates fragment ions. In most cases, the predicted fragments are chemically more realistic than those from purely combinatorial approaches, or approaches based on machine learning. The annotation generated by ChemFrag often coincides with spectra that have been manually annotated by experts. This is a major advance in peak annotation and allows a more precise automatic interpretation of mass spectra.

Gerlich, M.; Neumann, S. MetFusion: integration of compound identification strategies<!--[if gte mso 9]><![endif]--><!--[if gte mso 9]><xml> Normal 0 21 false false false DE X-NONE X-NONE</xml><![endif]--><!--[if gte mso 9]><![endif]--><!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Normale Tabelle"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Arial","sans-serif"; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi; mso-fareast-language:EN-US;}</style> <![endif]--> J Mass Spectrom 48(3), 291-298, (2013) DOI: 10.1002/jms.3123

Mass spectrometry (MS) is an important analytical technique for the detection and identification of small compounds. The main bottleneck in the interpretation of metabolite profiling or screening experiments is the identification of unknown compounds from tandem mass spectra.Spectral libraries for tandem MS, such as MassBank or NIST, contain reference spectra for many compounds, but their limited chemical coverage reduces the chance for a correct and reliable identification of unknown spectra outside the database domain.On the other hand, compound databases like PubChem or ChemSpider have a much larger coverage of the chemical space, but they cannot be queried with spectral information directly. Recently, computational mass spectrometry methods and in silico fragmentation prediction allow users to search such databases of chemical structures.We present a new strategy called MetFusion to combine identification results from several resources, in particular, from the in silico fragmenter MetFrag with the spectral library MassBank to improve compound identification. We evaluate the performance on a set of 1062 spectra and achieve an improved ranking of the correct compound from rank 28 using MetFrag alone, to rank 7 with MetFusion, even if the correct compound and similar compounds are absent from the spectral library. On the basis of the evaluation, we extrapolate the performance of MetFusion to the KEGG compound database.

Brunner, F.; Rosahl, S.; Lee, J.; Rudd, J.J.; Geiler, C.; Kauppinen, S.; Rasmussen, G.; Scheel, D.; Nürnberger, T. Pep-13, a plant defense-inducing pathogen-associated pattern from <em>Phytophthora transglutaminases</em> EMBO J 21, 6681-6688, (2002)

Innate immunity, an ancient form of defense against microbial infection, is well described for animals and is also suggested to be important for plants. Discrimination from self is achieved through receptors that recognize pathogen-associated molecular patterns (PAMPs) not found in the host. PAMPs are evolutionarily conserved structures which are functionally important and, thus, not subject to frequent mutation. Here we report that the previously described peptide elicitor of defense responses in parsley, Pep-13, constitutes a surface-exposed fragment within a novel calcium-dependent cell wall transglutaminase (TGase) from Phytophthora sojae. TGase transcripts and TGase activity are detectable in all Phytophthora species analyzed, among which are some of the most destructive plant pathogens. Mutational analysis within Pep-13 identified the same amino acids indispensable for both TGase and defense-eliciting activity. Pep-13, conserved among Phytophthora TGases, activates defense in parsley and potato, suggesting its function as a genus-specific recognition determinant for the activation of plant defense in host and non-host plants. In summary, plants may recognize PAMPs with characteristics resembling those known to trigger innate immune responses in animals.
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