Sequence tag

16 methods · 1994–2021

Sequence tag: Short, high-confidence stretches of sequence read straight off the spectrum and used as a filter or a query rather than as the final answer. A tag plus its flanking masses can identify a peptide on its own.

Short, high-confidence stretches of sequence read straight off the spectrum and used as a filter or a query rather than as the final answer. A tag plus its flanking masses can identify a peptide on its own.

The earliest of its 16 methods is Peptide sequence tags (1994); 15 more have followed.

Methods 16
Papers describing them 19
Authors 73
Active 1994-12-15 to 2021-12-29
Kinds adjacent (14), algorithm, post-processor
Acquisition DDA (16)

Methods (16)

Oldest first, by the paper that describes each one.

  • Peptide sequence tags (1994): Error-tolerant peptide identification using short de novo sequence tags and flanking masses.
  • MultiTag (2003): Searches several error-tolerant peptide sequence tags at once, so a protein can be identified across species by sequence similarity even when no tag is individually correct. Tolerating errors in the tags is what lets de novo output drive a homology search.
  • GutenTag (2003): High-throughput sequence tagging using an empirically derived fragmentation model.
  • Gapped sequence tag automata matching (2005): An automaton-based algorithm that matches gapped de novo sequence tags, where mass gaps stand for unresolved residues, against a protein database.
  • InsPecT (2005): Uses peptide sequence tags derived from the spectrum as a database filter, discarding the vast majority of candidate peptides before scoring, which makes blind searches for post-translational modifications tractable.
  • Sequence-tag filtration for database search (2005): Generates short de novo sequence tags to filter the database BLAST-style, dramatically speeding searches for modified peptides.
  • MODi (2006): Error-tolerant search for multiple unrestricted PTMs that chains de novo sequence tags into tag chains to localise modified regions, also offered as a web server.
  • DirecTag (2008): Open-source statistical scoring algorithm for accurate sequence tags from peptide MS/MS spectra.
  • Unique sequence tags for PTM discovery (2008): Reads short, uniquely assignable sequence tags de novo and uses them to find post-translational modifications, trading the full-length sequence for the reliability that made early de novo output hard to trust in routine proteomics.
  • Graph-search sequence tag generation (2011): Generates peptide sequence tags from MS/MS spectra by graph search, aiming for fast and accurate tags for identification.
  • ScanRanker (2011): Ranks MS/MS spectra by sequence-tag quality to find high-quality unidentified spectra for de novo or cross-link analysis.
  • b2-ion N-terminal sequence tagging (2014): Shows that b2 ions in HCD spectra can be assigned with over 97% certainty when a2 and the complementary y ion are present, and uses the resulting two-residue N-terminal tags to filter PSMs and deconvolute co-fragmented spectra.
  • JUMP (2014): Hybrid tag-based database search that derives amino acid tags as short as one residue and combines tag and pattern-matching scores to rank PSMs.
  • Tagger (2017): Uses Novor de novo sequence tags for approximate matching against protein databases to accelerate database search.
  • TagGraph (2019): Matches de novo sequence tags against a proteome with an unrestricted string-based search and a probabilistic model, identifying thousands of modification types across large datasets.
  • Bottom-up tag convolution (2021): Tells a correct spectrum interpretation from its plausible alternatives by convolving the set of length-k sequence tags a candidate implies, attacking the step de novo sequencing is weakest at: not producing a sequence but choosing between the ones it produced.

Papers describing them (19)

Authors (73)

Aaron W. Miller, Adam J. Liska, Alexander Golod, Amy-Joan L. Ham, Andrej Shevchenko, Anita Saraf, Anna Shevchenko, Ari Frank, Arun Devabhaktuni, Bin Ma, Birgit Schilling, Carlos G. Gonzalez, Chunmei Liu, Corbin W. Whitwell, Daniel B. Martin, David L. Tabb, Ebrahim Zandi, Eunok Paek, Fedor Kryuchkov, Frank Kjeldsen, Gordon A. Anderson, H. Kim, Haiyan Tan, Hans-Rudolf Aerni, Heejin Park, Hong Wang, Hongjun Shu, Hui Li, J. W. Sim, Jaeho Jeong, Jangho Seo, John R. Yates, Joshua E. Elias, Junmin Peng, Kaizhong Zhang, Kavya Swaminathan, Keith Rawson, Kim K. Hixson, Kira Vyatkina, Kong-Joo Lee, Kristin L. Cheek, Lauren Scott, Legand Burge, Lichao Zhang, Ling-Chi Wang, Marc Mumby, Matthew C. Chambers, Matthias Mann, Matthias Wilm, Mugizi Rwebangira, Niclas Olsson, Nikola Tolić, Pavel A. Pevzner, Qi Tang, Richard D. Smith, Richard M. Caprioli, S. Kim, Samuel M. Pearlman, Samuel O. Purvine, Sarah Lin, Seungjin Na, Shamil Sunyaev, Stephen Tanner, Thiago Verano-Braga, Vineet Bafna, William Southerland, Xusheng Wang, Y. Seo, Yonghua Han, Yufeng Shen, Yuxin Li, Ze-Qiang Ma, Zhiping Wu

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