Tabb, DLMurugan, BDOkendo, JNair, OBlackburn, JMButhelezi, Sindisiwe GStoychev, Stoyan H2020-07-272020-07-272020-02Tabb et al. 2020. Open search unveils modification patterns in formalin-fixed, paraffin-embedded thermo HCD and SCIEX TripleTOF shotgun proteomes. International Journal of Mass Spectrometry, vol 448: 1-101387-38061873-2798https://doi.org/10.1016/j.ijms.2019.116266https://www.sciencedirect.com/science/article/pii/S1387380618304354http://hdl.handle.net/10204/11509Copyright: 2019, Elsevier. Due to copyright restrictions, the attached PDF file contains the abstract of the full-text item. For access to the full-text item, please consult the publisher's website. https://doi.org/10.1016/j.ijms.2019.116266The application of database search algorithms with very wide precursor mass tolerances for the “Open Search” paradigm has brought new efforts at post-translational modification discovery in shotgun proteomes. This approach has motivated the acceleration of database search tools by incorporating fragment indexing features. In this report, we compare open searches and sequence tag searches of high-resolution tandem mass spectra to seek a common “palette” of modifications when analyzing multiple formalin-fixed, paraffin-embedded (FFPE) tissues from Thermo Q-Exactive and SCIEX TripleTOF instruments. While open search in MSFragger produced some gains in identified spectra, careful FDR control limited the best result to 24% more spectra than narrow search (worst result: a loss of 9%). Open pFind produced high apparent sensitivity for PSMs, but entrapment sequences hinted that the actual error rate may be higher than reported by the software. Combining sequence tagging, open search, and chemical knowledge, we converged on this set of PTMs for our four FFPE sets: mono- and di-methylation (nTerm and Lys), single and double oxidation (Met and Pro), and variable carbamidomethylation (nTerm and Cys).enFormalin-fixed paraffin-embeddedOpen searchSequence taggingTripleTOFArticleTabb, D., Murugan, B., Okendo, J., Nair, O., Blackburn, J., Buthelezi, S. G., & Stoychev, S. H. (2020). Open search unveils modification patterns in formalin-fixed, paraffin-embedded thermo HCD and SCIEX TripleTOF shotgun proteomes. http://hdl.handle.net/10204/11509Tabb, DL, BD Murugan, J Okendo, O Nair, JM Blackburn, Sindisiwe G Buthelezi, and Stoyan H Stoychev "Open search unveils modification patterns in formalin-fixed, paraffin-embedded thermo HCD and SCIEX TripleTOF shotgun proteomes." (2020) http://hdl.handle.net/10204/11509Tabb D, Murugan B, Okendo J, Nair O, Blackburn J, Buthelezi SG, et al. Open search unveils modification patterns in formalin-fixed, paraffin-embedded thermo HCD and SCIEX TripleTOF shotgun proteomes. 2020; http://hdl.handle.net/10204/11509.TY - Article AU - Tabb, DL AU - Murugan, BD AU - Okendo, J AU - Nair, O AU - Blackburn, JM AU - Buthelezi, Sindisiwe G AU - Stoychev, Stoyan H AB - The application of database search algorithms with very wide precursor mass tolerances for the “Open Search” paradigm has brought new efforts at post-translational modification discovery in shotgun proteomes. This approach has motivated the acceleration of database search tools by incorporating fragment indexing features. In this report, we compare open searches and sequence tag searches of high-resolution tandem mass spectra to seek a common “palette” of modifications when analyzing multiple formalin-fixed, paraffin-embedded (FFPE) tissues from Thermo Q-Exactive and SCIEX TripleTOF instruments. While open search in MSFragger produced some gains in identified spectra, careful FDR control limited the best result to 24% more spectra than narrow search (worst result: a loss of 9%). Open pFind produced high apparent sensitivity for PSMs, but entrapment sequences hinted that the actual error rate may be higher than reported by the software. Combining sequence tagging, open search, and chemical knowledge, we converged on this set of PTMs for our four FFPE sets: mono- and di-methylation (nTerm and Lys), single and double oxidation (Met and Pro), and variable carbamidomethylation (nTerm and Cys). DA - 2020-02 DB - ResearchSpace DP - CSIR KW - Formalin-fixed paraffin-embedded KW - Open search KW - Sequence tagging KW - TripleTOF LK - https://researchspace.csir.co.za PY - 2020 SM - 1387-3806 SM - 1873-2798 T1 - Open search unveils modification patterns in formalin-fixed, paraffin-embedded thermo HCD and SCIEX TripleTOF shotgun proteomes TI - Open search unveils modification patterns in formalin-fixed, paraffin-embedded thermo HCD and SCIEX TripleTOF shotgun proteomes UR - http://hdl.handle.net/10204/11509 ER -