OLAV: Towards high‐throughput tandem mass spectrometry data identification

Colinge, Jacques; Masselot, Alexandre; Giron, M.; Dessingy, Thierry; Magnin, Jérôme

doi:10.1002/pmic.200300485

Cited by 297 publications

(261 citation statements)

References 32 publications

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“…Currently available search engines such as Mascot [24], Phenyx [39], OMSSA [40], or Modiro [41] all have properties to evaluate ETD spectra, and the latest version of Mascot allows for searching of combined ETD and CID datasets. It will also be interesting to determine whether ETD can be applied to alternative approaches for the detection of ubiquitination, such as using a Glu-C digest and detection of a 12 mer peptide fragment [42,43].…”

Section: Discussionmentioning

confidence: 99%

Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination

Sobott

Watt

Smith

et al. 2009

J. Am. Soc. Mass Spectrom.

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Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to be challenging. More recently, mass spectrometry has been applied to identify ubiquitinated proteins and also their sites of modification. Typically, liquid chromatography tandem mass spectrometry (LC-MS/MS) based approaches, including collision-induced fragmentation (CID), have been successfully used in the past. However, a potential difficulty arises from the unstable nature of this modification, and also that the isopeptide bond linkage between C-terminal glycine and the N( ) lysyl side chain is susceptible to fragmentation under these conditions. Here we investigate the utility of electron-transfer dissociation (ETD)-based fragmentation to detect ubiquitination sites in proteins. Our results indicate that ETD can provide alternative fragmentation patterns that allow detection of gly-gly-modified lysyl side chains, in particular zϩ1 fragment ions derived from triply charged precursor ions. We subsequently applied ETD fragmentation-based analysis and detected novel ubiquitination sites on DNA polymerase B1 that were not easily observed using CID. We conclude that ETD can provide significant alternative fragmentation information that complements CID-derived data to improve the coverage when mapping ubiquitination sites in proteins. (J Am Soc Mass

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Section: Discussionmentioning

confidence: 99%

Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination

Sobott

Watt

Smith

et al. 2009

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

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“…A number of algorithms and scoring models have been developed to assess the likelihood of a match. They can show different selectivity and sensitivity at the edge of good spectral quality, and some programs have enough flexibility to permit the use of different types of MS/ MS data or modification patterns 6,7,[40][41][42][43][44][45][46][47][48][49][50][51][52][53] . Four basic approaches have been developed to model matches to sequences: descriptive, interpretative, stochastic and probability-based modeling (Box 2).…”

Section: Review Of Database Search Algorithmsmentioning

confidence: 99%

“…The program OLAV uses an approach similar to the one used in SCOPE, except that some simplifications are made to avoid overexpansion of terms 51 . OLAV uses the maximum likelihood ratio as the identification score.…”

Section: Box 3 Strategy For Large Scale Data Analysismentioning

confidence: 99%

“…Statistical and probability models for database searching This group of methods uses models based on empirically generated fragment ion probabilities 45,48,51 . In these methods no a priori determined probabilities are used.…”

Section: Box 3 Strategy For Large Scale Data Analysismentioning

confidence: 99%

“…Thus, in the simplest models the frequencies of matches of b-and y-ions are determined and used to calculate a probability of sequence identification determined by the product of probabilities of its fragment matches. Several variations of this approach have been implemented in database searching algorithms 43,45,48,51 . Mascot 41 uses a model analogous to the one previously developed for identifying proteins from their peptide mass fingerprint 3 .…”

Section: Box 3 Strategy For Large Scale Data Analysismentioning

confidence: 99%

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Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book

2004

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Database searching is an essential element of large-scale proteomics. Because these methods are widely used, it is important to understand the rationale of the algorithms. Most algorithms are based on concepts first developed in SEQUEST and PeptideSearch. Four basic approaches are used to determine a match between a spectrum and sequence: descriptive, interpretative, stochastic and probability-based matching. We review the basic concepts used by most search algorithms, the computational modeling of peptide identification and current challenges and limitations of this approach for protein identification.An unintended consequence of whole-genome sequencing has been the birth of large-scale proteomics. What drives proteomics is the ability to use mass spectrometry data of peptides as an 'address' or 'zip code' to locate proteins in sequence databases. Two mass spectrometry methods are used to identify proteins by database search methods. The first method uses a molecular weight fingerprint measured from a protein digested with a site-specific protease [1][2][3][4][5] . A second method uses tandem mass spectra derived from individual peptides of a digested protein 6,7 (Fig. 1). Because each tandem mass spectrum represents an independent and verifiable piece of data, this approach to database searching has the ability to identify proteins in mixtures, enabling a rapid and comprehensive approach for the analysis of protein complexes and other complicated mixtures of proteins 6,[8][9][10][11][12] . New biology has been discovered based on fast and accurate protein identification [13][14][15][16][17][18] . As tandem mass spectral protein identification has proliferated, it has become increasingly important to understand the rationale of individual database search algorithms, their relative strengths and weaknesses, and the mathematics used to match sequence to spectrum.In this review we discuss the prevailing fragmentation models, spectral preprocessing, methods to match tandem mass spectra to sequences and several approaches to matching tandem mass spectra of peptides whose exact sequences may not be present in the database. Space limitations restrict a detailed description of all algorithms in this rapidly expanding field. Also, some algorithms are proprietary, and thus, details on how they work are unknown. This review should supplement and update earlier reviews on database search algorithms [19][20][21][22][23][24] . Peptide fragmentation and data preprocessingIn tandem mass spectrometry (MS/MS), gas phase peptide ions undergo collision-induced dissociation (CID) with molecules of an inert gas such as helium or argon 25 . Other methods of dissociation have been developed, such as electron capture dissociation (ECD), surface induced dissociation (SID) and electron transfer dissociation (ETD), but gas-phase CID is the most widely used in commercial tandem mass spectrometers. The dissociation pathways are strongly dependent on the collision energy, but the vast majority of instruments use low-energy CID (<100 eV) 26 ....

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Tandem mass spectrometry database searching

Eng

Martin

Aebersold

2005

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

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Associated with the emergence of mass spectrometry–based proteomics analysis, a host of novel algorithms for tandem mass spectrometry database searching have been published. These tools apply a breadth of computational and statistical approaches to solving the problem of identifying peptides based on interpreting tandem mass spectra with the constraint of sequences present in publicly available protein, transcript, and genomic sequence database repositories. With increasing data volumes due to continuous advances in instrumentation, the need for tools that perform automated peptide identifications and validation of those identifications will be magnified. An overview of database search and postsearch validation tools is summarized.

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OLAV: Towards high‐throughput tandem mass spectrometry data identification

Cited by 297 publications

References 32 publications

Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination

Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination

Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book

Tandem mass spectrometry database searching

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