PXD002726

PXD002726 is an original dataset announced via ProteomeXchange.

Title	Optimized data analysis avoiding trypsin artefacts
Description	Most bottom-up proteomics experiments share two features: The use of trypsin to digest proteins for mass spectrometry and the statistic driven matching of the measured peptide fragment spectra against protein database derived in silico generated spectra. While this extremely powerful approach in combination with latest generation mass spectrometers facilitates very deep proteome coverage, the assumptions made have to be met to generate meaningful results. One of these assumptions is that the measured spectra indeed have a match in the search space, since the search engine will always report the best match. However, one of the most abundant proteins in the sample, the protease, is often not represented in the employed database. It is therefore widely accepted in the community to include the protease and other common contaminants in the database to avoid false positive matches. Although this approach accounts for unmodified trypsin peptides, the most widely employed trypsin preparations are chemically modified to prevent autolysis and premature activity loss of the protease. In this study we observed numerous spectra of modified trypsin derived peptides in samples from our laboratory as well as in datasets downloaded from public repositories. In many cases the spectra were assigned to other proteins, often with good statistical significance. We therefore designed a new database search strategy employing an artificial amino acid which accounts for these peptides with a minimal increase in search space and the concomitant loss of statistical significance. Moreover, this approach can be easily implemented into existing workflows for many widely used search engines.
HostingRepository	PRIDE
AnnounceDate	2016-04-15
AnnouncementXML	Submission_2016-04-15_06:25:22.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD002726
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Katarina Fritz
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	Acetyl; Oxidation; Carbamidomethyl
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-08-14 05:48:44	ID requested
⏵ 1	2016-04-15 06:25:23	announced

Schittmayer M, Fritz K, Liesinger L, Griss J, Birner-Gruenberger R, Cleaning out the Litterbox of Proteomic Scientists' Favorite Pet: Optimized Data Analysis Avoiding Trypsin Artifacts. J Proteome Res, 15(4):1222-9(2016) [pubmed]

curator keyword: Technical

submitter keyword: autolysis protected trypsin, data base search

Ruth Birner-Gruenberger
contact affiliation	Omics Center Graz Research Unit "Functional Proteomics and Metabolic Pathways" Institute of Pathology Medical University Graz, Austria
contact email	ruth.birner-gruenberger@medunigraz.at
lab head
Katarina Fritz
contact affiliation	Medical University of Graz
contact email	katarina.fritz@medunigraz.at
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002726
     1. Label: PRIDE project
     2. Name: Optimized data analysis avoiding trypsin artefacts