Empowering Peptidomics: Utilizing Computational Tools and Approaches

References

• Vitorino R . Digging deep into peptidomics applied to body fluids. Proteomics18(2), 1700401C (2018).
   Web of Science ®Google Scholar
• Basith S , ManavalanB. Machine intelligence in peptide therapeutics: a next-generation tool for rapid disease screening. Med. Res. Rev.40(4), 1276–1314 (2020).
   PubMed Web of Science ®Google Scholar
• Johnson RS , SearleBC, NunnBLet al. Assessing protein sequence database suitability using de novo sequencing. Mol. Cell. Proteom.19(1), 198–208 (2020).
   PubMed Web of Science ®Google Scholar
• Keenan EK , ZachmanDK, HirscheyMD. Discovering the landscape of protein modifications. Mol. Cell81(9), 1868–1878 (2021).
   PubMed Web of Science ®Google Scholar
• Doll S , BurlingameAL. Mass spectrometry-based detection and assignment of protein posttranslational modifications. ACS Chem. Biol.10(1), 63–71 (2015).
   PubMed Web of Science ®Google Scholar
• Kreitmaier P , KatsoulaG, ZegginiE. Insights from multi-omics integration in complex disease primary tissues. Trends Genet.39(1), 46–58 (2023).
   PubMed Web of Science ®Google Scholar
• Ma B . Novor: real-time peptide de novo sequencing software. J. Am. Soc. Mass Spectrom.26(11), 1885–1894 (2015).
   PubMed Web of Science ®Google Scholar
• Deschamps E , CalabreseV. Advances in ultra-high-resolution mass spectrometry for pharmaceutical analysis. 28(5), 2061 (2023).
   Google Scholar
• Cunningham R , MaD, LiL. Mass spectrometry-based proteomics and peptidomics for systems biology and biomarker discovery. Front. Biol.7(4), 313–335 (2012).
   Google Scholar
• de Sousa-Pereira P , CovaM, AbrantesJet al. Cross-species comparison of mammalian saliva using an LC-MALDI based proteomic approach. Proteomics15(9), 1598–1607 (2015).
   PubMed Web of Science ®Google Scholar
• Vitorino R , KrenkovaJ, ForetF, DominguesP, AmadoF. Protein identification using nano-HPLC–MS: ESI-MS and MALDI-MS interfaces. Methods Mol. Biol. (Clifton)790, 31–46 (2011).
   PubMedGoogle Scholar
• Eliuk S , MakarovA. Evolution of orbitrap mass spectrometry instrumentation. Ann. Rev. Anal. Chem.8(1), 61–80 (2015).
   PubMedGoogle Scholar
• Williams TI , KowalchykC, CollinsLB, ReadingBJ. Discovery proteomics and absolute protein quantification can be performed simultaneously on an orbitrap-based mass spectrometer. ACS Omega8(13), 12573–12583 (2023).
   PubMed Web of Science ®Google Scholar
• De Vijlder T , ValkenborgD, LemièreF, RomijnEP, LaukensK, CuyckensF. A tutorial in small molecule identification via electrospray ionization-mass spectrometry: the practical art of structural elucidation. Mass Spectrom. Rev.37(5), 607–629 (2018).
   PubMed Web of Science ®Google Scholar
• Eng JK , FischerB, GrossmannJ, MaccossMJ. A fast SEQUEST cross correlation algorithm. J. Proteome Res.7(10), 4598–4602 (2008).
   PubMed Web of Science ®Google Scholar
• Koenig T , MenzeBH, KirchnerMet al. Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics. J. Proteome Res.7(9), 3708–3717 (2008).
   PubMed Web of Science ®Google Scholar
• Craig R , BeavisRC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics (Oxford)20(9), 1466–1467 (2004).
   PubMed Web of Science ®Google Scholar
• Cox J , MannM. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol.26(12), 1367–1372 (2008).
   PubMed Web of Science ®Google Scholar
• Eng JK , JahanTA, HoopmannMR. Comet: an open-source MS/MS sequence database search tool. Proteomics13(1), 22–24 (2013).
   PubMed Web of Science ®Google Scholar
• Kim S , PevznerPA. MS-GF+ makes progress towards a universal database search tool for proteomics. Nat. Commun.5, 5277–5287 (2014).
   PubMed Web of Science ®Google Scholar
• Geer LY , MarkeySP, KowalakJAet al. Open mass spectrometry search algorithm. J. Proteome Res.3(5), 958–964 (2004).
   PubMed Web of Science ®Google Scholar
• Muqaku B , OecklP. Peptidomic approaches and observations in neurodegenerative diseases. Int. J.Mol.Sci.23(13), 7332 (2022).
   PubMed Web of Science ®Google Scholar
• Pandey S , MalviyaG. Role of peptides in diagnostics. Int. J. Mol. Sci.22(16), 8828 (2021).
   PubMed Web of Science ®Google Scholar
• Egertson JD , KuehnA, MerrihewGEet al. Multiplexed MS/MS for improved data-independent acquisition. Nat. Methods10(8), 744–746 (2013).
   PubMed Web of Science ®Google Scholar
• Chapman JD , GoodlettDR, MasselonCD. Multiplexed and data-independent tandem mass spectrometry for global proteome profiling. Mass Spectrom. Rev.33(6), 452–470 (2014).
   PubMed Web of Science ®Google Scholar
• Egertson JD , MacLeanB, JohnsonR, XuanY, MacCossMJ. Multiplexed peptide analysis using data-independent acquisition and Skyline. Nat. Protoc.10(6), 887–903 (2015).
   PubMed Web of Science ®Google Scholar
• Walzer M , García-SeisdedosD, PrakashAet al. Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas. Sci. Data9(1), 335 (2022).
   PubMed Web of Science ®Google Scholar
• Lima T , RodriguesJE, ManadasB, HenriqueR, FardilhaM, VitorinoR. A peptide-centric approach to analyse quantitative proteomics data–an application to prostate cancer biomarker discovery. J. Proteomics272, 104774 (2023).
   PubMed Web of Science ®Google Scholar
• Lima T , BarrosAS, TrindadeFet al. Application of proteogenomics to urine analysis towards the identification of novel biomarkers of prostate cancer: an exploratory study. Cancers14(8), 2001 (2022).
   PubMed Web of Science ®Google Scholar
• Ning Z , ZhangX, MayneJ, FigeysD. Peptide-centric approaches provide an alternative perspective to re-examine quantitative proteomic data. Anal. Chem.88(4), 1973–1978 (2016).
   PubMed Web of Science ®Google Scholar
• Donovan MKR , HuangY, BlumeJEet al. Peptide-centric analyses of human plasma enable increased resolution of biological insights into non-small cell lung cancer relative to protein-centric analysis. BioRxiv doi: 10.1021/acs.analchem.5b04148 (2022).
   Google Scholar