pFind–Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data

Grover's database search algorithm, although discovered in the context of quantum computation, can be implemented using any system that allows superposition of states. A physical realization of this algorithm is described using coupled simple harmonic oscillators, which can be exactly solved in both classical and quantum domains. Classical wave algorithms are far more stable against decoherence compared to their quantum counterparts. In addition to providing convenient demonstration models, they may have a role in practical situations, such as catalysis.

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A hierarchical MS2 /MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra

PROTEOMICS ◽

10.1002/pmic.200800282 ◽

2009 ◽

Vol 9 (7) ◽

pp. 1763-1770 ◽

Cited By ~ 11

Author(s):

Hua Xu ◽

Liwen Wang ◽

Larry Sallans ◽

Michael A. Freitas

Keyword(s):

Mass Spectra ◽

Search Algorithm ◽

Automated Analysis ◽

Database Search ◽

Tandem Mass ◽

Tandem Mass Spectra

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QUANTUM ORACLES IN TERMS OF UNIVERSAL GATE SET

International Journal of Quantum Information ◽

10.1142/s0219749911008106 ◽

2011 ◽

Vol 09 (06) ◽

pp. 1363-1381 ◽

Cited By ~ 2

Author(s):

YUJI TANAKA ◽

TSUBASA ICHIKAWA ◽

MASAHITO TADA-UMEZAKI ◽

YUKIHIRO OTA ◽

MIKIO NAKAHARA

Keyword(s):

Arbitrary Number ◽

Search Algorithm ◽

Circuit Complexity ◽

Database Search ◽

Quantum Circuits ◽

Systematic Construction ◽

Universal Gate

We present a systematic construction of quantum circuits implementing Grover's database search algorithm for arbitrary number of targets. We introduce a new operator which flips the sign of the targets and evaluate its circuit complexity. We find the condition under which the circuit complexity of the database search algorithm based on this operator is less than that of the conventional one.

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A streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics

Nature Communications ◽

10.1038/s41467-020-19052-w ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 2

Author(s):

Pan Fang ◽

Yanlong Ji ◽

Ivan Silbern ◽

Carmen Doebele ◽

Momchil Ninov ◽

...

Keyword(s):

Mass Spectrometry ◽

High Resolution ◽

Sample Preparation ◽

Large Scale ◽

Handling Time ◽

Database Search ◽

High Confidence ◽

Site Specific ◽

Sample Handling ◽

Data Processing Tool

Abstract Regulation of protein N-glycosylation is essential in human cells. However, large-scale, accurate, and site-specific quantification of glycosylation is still technically challenging. We here introduce SugarQuant, an integrated mass spectrometry-based pipeline comprising protein aggregation capture (PAC)-based sample preparation, multi-notch MS3 acquisition (Glyco-SPS-MS3) and a data-processing tool (GlycoBinder) that enables confident identification and quantification of intact glycopeptides in complex biological samples. PAC significantly reduces sample-handling time without compromising sensitivity. Glyco-SPS-MS3 combines high-resolution MS2 and MS3 scans, resulting in enhanced reporter signals of isobaric mass tags, improved detection of N-glycopeptide fragments, and lowered interference in multiplexed quantification. GlycoBinder enables streamlined processing of Glyco-SPS-MS3 data, followed by a two-step database search, which increases the identification rates of glycopeptides by 22% compared with conventional strategies. We apply SugarQuant to identify and quantify more than 5,000 unique glycoforms in Burkitt’s lymphoma cells, and determine site-specific glycosylation changes that occurred upon inhibition of fucosylation at high confidence.

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A New Probabilistic Database Search Algorithm for ETD Spectra

Journal of Proteome Research ◽

10.1021/pr900153b ◽

2009 ◽

Vol 8 (6) ◽

pp. 3198-3205 ◽

Cited By ~ 26

Author(s):

Rovshan G. Sadygov ◽

David M. Good ◽

Danielle L. Swaney ◽

Joshua J. Coon

Keyword(s):

Search Algorithm ◽

Database Search ◽

Probabilistic Database

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Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2 data

10.1101/290858 ◽

2018 ◽

Author(s):

Andy Lin ◽

J. Jeffry Howbert ◽

William Stafford Noble

Keyword(s):

Mass Spectrometry ◽

High Resolution ◽

Statistical Power ◽

State Of The Art ◽

Score Function ◽

Shotgun Proteomics ◽

Database Search ◽

Mass Spectrometry Data ◽

P Value ◽

Score Functions

AbstractTo achieve accurate assignment of peptide sequences to observed fragmentation spectra, a shotgun proteomics database search tool must make good use of the very high resolution information produced by state-of-the-art mass spectrometers. However, making use of this information while also ensuring that the search engine’s scores are well calibrated—i.e., that the score assigned to one spectrum can be meaningfully compared to the score assigned to a different spectrum—has proven to be challenging. Here, we describe a database search score function, the “residue evidence” (res-ev) score, that achieves both of these goals simultaneously. We also demonstrate how to combine calibrated res-ev scores with calibrated XCorr scores to produce a “combined p-value” score function. We provide a benchmark consisting of four mass spectrometry data sets, which we use to compare the combined p-value to the score functions used by several existing search engines. Our results suggest that the combined p-value achieves state-of-the-art performance, generally outperforming MS Amanda and Morpheus and performing comparably to MS-GF+. The res-ev and combined p-value score functions are freely available as part of the Tide search engine in the Crux mass spectrometry toolkit (http://crux.ms).

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