SwissPIT: An workflow‐based platform for analyzing tandem‐MS spectra using the Grid

Quandt, Andreas; Masselot, Alexandre; Hernandez, Patricia; Hernandez, Céline; Maffioletti, Sergio; Appel, Ron D.; Lisacek, Frédérique

doi:10.1002/pmic.200800207

Cited by 15 publications

(12 citation statements)

References 24 publications

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“…without isolating a peptide ion species of a specific m/z value as in the conventional data dependent acquisition methods). The database search time remains an important consideration and can be improved via database indexing [42-44] or other algorithmic improvements [45-47], as well as using grid [48] or cloud [49] computing.…”

Section: Peptide Sequence Assignment To Ms/ms Spectramentioning

confidence: 99%

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

Nesvizhskii

2010

Journal of Proteomics

475

503

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This manuscript provides a comprehensive review of the peptide and protein identification process using tandem mass spectrometry (MS/MS) data generated in shotgun proteomic experiments. The commonly used methods for assigning peptide sequences to MS/MS spectra are critically discussed and compared, from basic strategies to advanced multi-stage approaches. A particular attention is paid to the problem of false-positive identifications. Existing statistical approaches for assessing the significance of peptide to spectrum matches are surveyed, ranging from single-spectrum approaches such as expectation values to global error rate estimation procedures such as false discovery rates and posterior probabilities. The importance of using auxiliary discriminant information (mass accuracy, peptide separation coordinates, digestion properties, and etc.) is discussed, and advanced computational approaches for joint modeling of multiple sources of information are presented. This review also includes a detailed analysis of the issues affecting the interpretation of data at the protein level, including the amplification of error rates when going from peptide to protein level, and the ambiguities in inferring the identifies of sample proteins in the presence of shared peptides. Commonly used methods for computing protein-level confidence scores are discussed in detail. The review concludes with a discussion of several outstanding computational issues.

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Section: Peptide Sequence Assignment To Ms/ms Spectramentioning

confidence: 99%

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

Nesvizhskii

2010

Journal of Proteomics

475

503

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“…The benefi t of the database reduction step is that it decreases the search time and it can be performed externally. For instance, Swiss Protein Identifi cation Toolbox, SwissPIT (Quandt et al 2009 ), combines multiple identifi cation tools to create a concise protein database which is then transferred to a PTM search engine such as Popitam or InsPecT.…”

Section: Inference Of Ptms From Ms Datamentioning

confidence: 99%

Post-translational Modifications in the Human Proteome

Lichti

Wildburger

Emmett

et al. 2014

Translational Bioinformatics

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The Chromosome-Centric Human Proteome Project (C-HPP) is a global project aimed to identify at least one protein isoform encoded by the approximately 20, 300 human genes. In addition, protein post-translational modifi cations will be characterized, with the initial goal of detecting phosphorylation, acetylation, and glycosylation sites in each protein. In this chapter, we provide an overview of known post-translational modifi cations, their known biological functions, and present strategies to detect them on both a single protein and proteomic scales. In future proteomic studies, global characterization of post-translation modifi cations, splice variants, and variants caused by single nucleotide polymorphisms (SNPs) will be necessary to fully understand the role of proteins in human biology and disease.

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“…Several of the OMS tools do not include a database‐filtering step, but it is then recommended that this is done externally. The Swiss Protein Identification Toolbox, SwissPIT 64, provides an automated solution where several identification tools can be combined in multiple‐round workflows. The results are merged to create a reduced but comprehensive protein database, which is passed on to a second identification step where it is explored for modifications with the OMS tools Popitam 53 and InsPecT 56.…”

Section: Unrestricted Identification Of Modified Peptidesmentioning

confidence: 99%

“…This makes lens samples excellent candidates for exploring and evaluating the ability of OMS tools to detect protein modifications. Several of the recently developed OMS tools have been tested on such data sets including InsPecT 56, PTMExplorer 71, SIMS 57 and SwissPIT 64. Willmarth et al 99 identified a total of 155 modification sites in crystallins analysing a human lens data set produced on two different instruments; LCG Classic ion trap and a Q‐TOF hybrid mass spectrometer, using the InsPecT software suite.…”

Section: Oms Studiesmentioning

confidence: 99%

Unrestricted identification of modified proteins using MS/MS

Ahrné¹,

Müller²,

Lisacek³

2010

Proteomics

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Proteins undergo PTM, which modulates their structure and regulates their function. Estimates of the PTM occurrence vary but it is safe to assume that there is an important gap between what is currently known and what remains to be discovered. The highest throughput and most comprehensive efforts to catalogue protein mixtures have so far been using MS-based shotgun proteomics. The standard approach to analyse MS/MS data is to use Peptide Fragment Fingerprinting tools such as Sequest, MASCOT or Phenyx. These tools commonly identify 5-30% of the spectra in an MS/MS data set while only a limited list of predefined protein modifications can be screened. An important part of the unidentified spectra is likely to be spectra of peptides carrying modifications not considered in the search. Bioinformatics for PTM discovery is an active area of research. In this review we focus on software solutions developed for unrestricted identification of modifications in MS/MS data, here referred to as open modification search tools. We give an overview of the conceptually different algorithmic solutions to evaluate the large number of candidate peptides per spectrum when accounting for modifications of unrestricted size and demonstrate the value of results of large-scale open modification search studies. Efficient and easy-to-use tools for protein modification discovery should prove valuable in the quest for mapping the dynamics of proteomes.

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SwissPIT: An workflow‐based platform for analyzing tandem‐MS spectra using the Grid

Cited by 15 publications

References 24 publications

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

Post-translational Modifications in the Human Proteome

Unrestricted identification of modified proteins using MS/MS

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