Abstract
Recently a mass-tolerant search approach was proposed which suggested novel types of abundant modification with delta masses that left many scratching their heads. These surprising new findings which were hard to explain were later referred to as dark matter of mass spectrometry-based proteomics. Rewards were promised for those who could solve these intriguing new findings. We propose here simple solutions to the novel delta masses identified by mass-tolerant database search.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Chick JM, Kolippakkam D, Nusinow DP, Zhai B, Rad R, Huttlin EL, Gygi SP (2015) A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides. Nat Biotechnol 33(7):743–749. https://doi.org/10.1038/nbt.3267
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA (2005) Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol 23(12):1562–1567. https://doi.org/10.1038/nbt1168
Craig R, Beavis RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20(9):1466–1467. https://doi.org/10.1093/bioinformatics/bth092
Matthiesen R, Trelle MB, Hojrup P, Bunkenborg J, Jensen ON (2005) VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins. J Proteome Res 4(6):2338–2347. https://doi.org/10.1021/pr050264q
Carvalho AS, Ribeiro H, Voabil P, Penque D, Jensen ON, Molina H, Matthiesen R (2014) Global mass spectrometry and transcriptomics array based drug profiling provides novel insight into glucosamine induced endoplasmic reticulum stress. Mol Cell Proteomics 13(12):3294–3307. https://doi.org/10.1074/mcp.M113.034363
Spivak M, Weston J, Bottou L, Kall L, Noble WS (2009) Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets. J Proteome Res 8(7):3737–3745. https://doi.org/10.1021/pr801109k
He L, Diedrich J, Chu YY, Yates JR (2015) Extracting accurate precursor information for tandem mass spectra by rawconverter. Anal Chem 87:11361–11367
Ternent T, Csordas A, Qi D, Gomez-Baena G, Beynon RJ, Jones AR, Hermjakob H, Vizcaino JA (2014) How to submit MS proteomics data to ProteomeXchange via the PRIDE database. Proteomics 14(20):2233–2241. https://doi.org/10.1002/pmic.201400120
Acknowledgments
R.M. is supported by Fundação para a Ciência e a Tecnologia (FCT investigator program 2012). iNOVA4Health—UID/Multi/04462/2013, a program financially supported by Fundação para a Ciência e Tecnologia/Ministério da Educação e Ciência, through national funds and cofunded by FEDER under the PT2020 Partnership Agreement is acknowledged. This work is also funded by FEDER funds through the COMPETE 2020 Programme and National Funds through FCT - Portuguese Foundation for Science and Technology under the projects number PTDC/BTM-TEC/30087/2017 and PTDC/BTM-TEC/30088/2017
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Matthiesen, R. (2020). Solution to Dark Matter Identified by Mass-Tolerant Database Search. In: Matthiesen, R. (eds) Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology, vol 2051. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9744-2_9
Download citation
DOI: https://doi.org/10.1007/978-1-4939-9744-2_9
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-4939-9743-5
Online ISBN: 978-1-4939-9744-2
eBook Packages: Springer Protocols