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MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation.

Degroeve S, Maddelein D, Martens L - Nucleic Acids Res. (2015)

Bottom Line: The server integrates the Unimod public domain post-translational modification database for modified peptides.The prediction model is an improvement of the previously published MS(2)PIP model for Orbitrap-LTQ CID spectra.Predicted MS(2) spectra can be downloaded as a spectrum file and can be visualized in the browser for comparisons with observations.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium sven.degroeve@vib-ugent.be.

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Related in: MedlinePlus

Grid of boxplots each representing the Pearson correlation (R) between predicted and observed MS2 peak intensities in the synthetic peptides dataset for the fragment ions listed in the text. Each box represents 50% of the data (Q1, Q2 and Q3), the lowest datum is at 1.5 × Q1 and the highest datum is at 1.5 × Q3. The top row contains the correlation distributions for the CID spectra, the bottom row for the HCD spectra. For each fragmentation type the results are partitioned based on the presence of a specific PTM in the identified peptide: Oxidation of methionine (mox) or Carbamidomethylcysteine (cmm). The first boxplots on each row show the results for the peptides that did not contain a PTM (no ptm).
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Figure 2: Grid of boxplots each representing the Pearson correlation (R) between predicted and observed MS2 peak intensities in the synthetic peptides dataset for the fragment ions listed in the text. Each box represents 50% of the data (Q1, Q2 and Q3), the lowest datum is at 1.5 × Q1 and the highest datum is at 1.5 × Q3. The top row contains the correlation distributions for the CID spectra, the bottom row for the HCD spectra. For each fragmentation type the results are partitioned based on the presence of a specific PTM in the identified peptide: Oxidation of methionine (mox) or Carbamidomethylcysteine (cmm). The first boxplots on each row show the results for the peptides that did not contain a PTM (no ptm).

Mentions: In Figure 2 we partitioned the CID and HCD intensity correlation results based on the PTMs present in the identified peptides (carbamidomethylcysteine, oxidation of methionine or no PTM). For CID we observe no difference in median R values, the models perform well for both types of modifications. For HCD we also observe good performance for both types of PTMs, but in this case the R distribution of the unmodified peptides shows better performance. This could be due to the less frequent modification of amino acids observed in the HCD training set (Table 1).


MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation.

Degroeve S, Maddelein D, Martens L - Nucleic Acids Res. (2015)

Grid of boxplots each representing the Pearson correlation (R) between predicted and observed MS2 peak intensities in the synthetic peptides dataset for the fragment ions listed in the text. Each box represents 50% of the data (Q1, Q2 and Q3), the lowest datum is at 1.5 × Q1 and the highest datum is at 1.5 × Q3. The top row contains the correlation distributions for the CID spectra, the bottom row for the HCD spectra. For each fragmentation type the results are partitioned based on the presence of a specific PTM in the identified peptide: Oxidation of methionine (mox) or Carbamidomethylcysteine (cmm). The first boxplots on each row show the results for the peptides that did not contain a PTM (no ptm).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489309&req=5

Figure 2: Grid of boxplots each representing the Pearson correlation (R) between predicted and observed MS2 peak intensities in the synthetic peptides dataset for the fragment ions listed in the text. Each box represents 50% of the data (Q1, Q2 and Q3), the lowest datum is at 1.5 × Q1 and the highest datum is at 1.5 × Q3. The top row contains the correlation distributions for the CID spectra, the bottom row for the HCD spectra. For each fragmentation type the results are partitioned based on the presence of a specific PTM in the identified peptide: Oxidation of methionine (mox) or Carbamidomethylcysteine (cmm). The first boxplots on each row show the results for the peptides that did not contain a PTM (no ptm).
Mentions: In Figure 2 we partitioned the CID and HCD intensity correlation results based on the PTMs present in the identified peptides (carbamidomethylcysteine, oxidation of methionine or no PTM). For CID we observe no difference in median R values, the models perform well for both types of modifications. For HCD we also observe good performance for both types of PTMs, but in this case the R distribution of the unmodified peptides shows better performance. This could be due to the less frequent modification of amino acids observed in the HCD training set (Table 1).

Bottom Line: The server integrates the Unimod public domain post-translational modification database for modified peptides.The prediction model is an improvement of the previously published MS(2)PIP model for Orbitrap-LTQ CID spectra.Predicted MS(2) spectra can be downloaded as a spectrum file and can be visualized in the browser for comparisons with observations.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium sven.degroeve@vib-ugent.be.

Show MeSH
Related in: MedlinePlus