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FilenameFormatSizeDescription
pmic7361-sup-0001-FigureS1.tif690KFigure S1. E. coli data set. 47 search runs have been performed by allowing methionine oxidation and one additional modification as variable modification. The additional modification was suggested by the modification discovery tool
pmic7361-sup-0002-FigureS2.tif613KFigure S2. Human data set. 18 search runs have been performed by allowing methionine oxidation and one additional modification as variable modification. The additional modification was suggested by the modification discovery tool
pmic7361-sup-0003-FigureS3.tif584KFigure S3. On the human data set, five independent database searches with methionine oxidation and each time one of the top modifications from the modification discovery, as well as a search run using all six modifications at once and the Stouffer combination of all six runs. For all analysis a q-value cut-off of 0.01 was used.
pmic7361-sup-0004-FigureS4.tif500KFigure S4. Two characteristic spectra from the E. coli data set with modified sequences that were annotated as the best hit. (A) The multiple oxidized peptide shows characteristic mass shifts for methionine and tyrosine oxidation (delta mass=15.994915). Following Stouffer's meta-analysis this PSM was given a stouffer combination score of 0.4434. This was calculated from an initial E-value of 0.66319 and after target-decoy-based q-value filter the PSM received a q-value of 0.00646. (B) This PSM corresponds to a acetylated peptide sequence with a characteristic shift for acetylation (delta mass=42.010565 Da). The PSM was given a highly significant stouffer combination score of 1.0213e-05, calculated from an OMSSA E-value of 1.1848e-10. The final filtering indicated a q-value of 0.00104.
pmic7361-sup-0005-FigureS5.tif500KFigure S5. Two characteristic spectra from the human data set with modified sequences that were annotated as the best hit. (A) The multiple modified peptide show characteristic mass shifts for methionine oxidation and deamidation of asparagine (delta mass = 0.984016). The PSM was given a stouffer combination score of 1.57899e-09. This was calculated from an initial E-value of 0.288e-297 and after target-decoy-based q-value filter the PSM received a q-value of 4.755e-08. To avoid cluttering of the figure, we do only annotate the b ion series in the spectrum. (B) This PSM corresponds to a peptide sequence with a neutral loss (Gln -> pyro-Glu) at the peptide N-terminus (delta mass = -17.026549). The PSM was given a highly significant stouffer combination score of 4.3e-08, calculated from an OMSSA E-value of 4.8485e-16. The final filtering indicated a q-value of 8.6434e-05.
pmic7361-sup-0006-FigureS6.tif204KFigure 6. The MS/MS spectra from the E. coli data set were analyzed using the PTMeta algorithm and the top ten hits were kept for each spectrum. All peptide sequences were then mapped back to their proteins of origin (which was either a target or a decoy protein). All searches were performed against a target-decoy database, as outlined in the manuscript. To evaluate the fairness of the final statistical procedures, we mapped all (we allowed 10 candidates per spectrum) peptide candidates back to their proteins. This experiment shows that the top hits (from the PTMeta analysis) are frequently annotated by sequences from target proteins, whereas all other hits show the assumed and known patterns. The hits 2-10 are equally well annotated by target and decoy sequences.
pmic7361-sup-0007-FigureS7.tif176KFigure 7. This figures illustrates the comparison of PTMeta and MODa. Here we illustrate how ‘Oxidation’ is assigned to different amino acids by both tools. The x-axis shows all possible amino acids and the y-axis shows the frequency of occurrence.
pmic7361-sup-0008-TableS1.doc98KTable S1. human_Beck_et_al_MODD.xlsx shows all modification discoveries for the human data set. These discoveries include the modification mass, as extracted from Unimod, the most likely residues, the MODD-score, as well as the most likely mapping to the true modification.
pmic7361-sup-0009-TableS2.xlsx19KTable S2. Ecolil_MODD.xlsx shows all modification discoveries for the E. coli data set. These discoveries include the modification mass, as extracted from Unimod, the most likely residues, the MODD-score, as well as the most likely mapping to the true modification.
pmic7361-sup-0010-TableS3.xlsx20KTable S3. E. coli data set. Modifications suggested by the discovery tool for pairwise search runs
pmic7361-sup-0011-TableS4.xls43KTable S4. Human data set. Modifications suggested by the discovery tool for pairwise search runs

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