FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4224261010> ?p ?o ?g. }

• W4224261010 endingPage "100238" @default.
• W4224261010 startingPage "100238" @default.
• W4224261010 abstract "Isobaric stable isotope labeling techniques such as tandem mass tags (TMTs) have become popular in proteomics because they enable the relative quantification of proteins with high precision from up to 18 samples in a single experiment. While missing values in peptide quantification are rare in a single TMT experiment, they rapidly increase when combining multiple TMT experiments. As the field moves toward analyzing ever higher numbers of samples, tools that reduce missing values also become more important for analyzing TMT datasets. To this end, we developed SIMSI-Transfer (Similarity-based Isobaric Mass Spectra 2 [MS2] Identification Transfer), a software tool that extends our previously developed software MaRaCluster (© Matthew The) by clustering similar tandem MS2 from multiple TMT experiments. SIMSI-Transfer is based on the assumption that similarity-clustered MS2 spectra represent the same peptide. Therefore, peptide identifications made by database searching in one TMT batch can be transferred to another TMT batch in which the same peptide was fragmented but not identified. To assess the validity of this approach, we tested SIMSI-Transfer on masked search engine identification results and recovered >80% of the masked identifications while controlling errors in the transfer procedure to below 1% false discovery rate. Applying SIMSI-Transfer to six published full proteome and phosphoproteome datasets from the Clinical Proteomic Tumor Analysis Consortium led to an increase of 26 to 45% of identified MS2 spectra with TMT quantifications. This significantly decreased the number of missing values across batches and, in turn, increased the number of peptides and proteins identified in all TMT batches by 43 to 56% and 13 to 16%, respectively." @default.
• W4224261010 created "2022-04-26" @default.
• W4224261010 creator A5014230342 @default.
• W4224261010 creator A5022425218 @default.
• W4224261010 creator A5031508585 @default.
• W4224261010 creator A5058082024 @default.
• W4224261010 creator A5060782206 @default.
• W4224261010 date "2022-08-01" @default.
• W4224261010 modified "2023-10-01" @default.
• W4224261010 title "SIMSI-Transfer: Software-Assisted Reduction of Missing Values in Phosphoproteomic and Proteomic Isobaric Labeling Data Using Tandem Mass Spectrum Clustering" @default.
• W4224261010 cites W1480858518 @default.
• W4224261010 cites W1970083690 @default.
• W4224261010 cites W2011710911 @default.
• W4224261010 cites W2013955377 @default.
• W4224261010 cites W2073371472 @default.
• W4224261010 cites W2079675844 @default.
• W4224261010 cites W2094041121 @default.
• W4224261010 cites W2121386739 @default.
• W4224261010 cites W2149070651 @default.
• W4224261010 cites W2170505850 @default.
• W4224261010 cites W2170776626 @default.
• W4224261010 cites W2212342797 @default.
• W4224261010 cites W2264190236 @default.
• W4224261010 cites W2544360569 @default.
• W4224261010 cites W2801679611 @default.
• W4224261010 cites W2802938642 @default.
• W4224261010 cites W2857722519 @default.
• W4224261010 cites W2901496258 @default.
• W4224261010 cites W2922140724 @default.
• W4224261010 cites W2947763854 @default.
• W4224261010 cites W2956732318 @default.
• W4224261010 cites W2963597305 @default.
• W4224261010 cites W2977090104 @default.
• W4224261010 cites W2983417391 @default.
• W4224261010 cites W2991491873 @default.
• W4224261010 cites W3006211741 @default.
• W4224261010 cites W3037094874 @default.
• W4224261010 cites W3041397352 @default.
• W4224261010 cites W3084177209 @default.
• W4224261010 cites W3087749616 @default.
• W4224261010 cites W3104755560 @default.
• W4224261010 doi "https://doi.org/10.1016/j.mcpro.2022.100238" @default.
• W4224261010 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/35462064" @default.
• W4224261010 hasPublicationYear "2022" @default.
• W4224261010 type Work @default.
• W4224261010 citedByCount "6" @default.
• W4224261010 countsByYear W42242610102022 @default.
• W4224261010 countsByYear W42242610102023 @default.
• W4224261010 crossrefType "journal-article" @default.
• W4224261010 hasAuthorship W4224261010A5014230342 @default.
• W4224261010 hasAuthorship W4224261010A5022425218 @default.
• W4224261010 hasAuthorship W4224261010A5031508585 @default.
• W4224261010 hasAuthorship W4224261010A5058082024 @default.
• W4224261010 hasAuthorship W4224261010A5060782206 @default.
• W4224261010 hasBestOaLocation W42242610101 @default.
• W4224261010 hasConcept C104317684 @default.
• W4224261010 hasConcept C104397665 @default.
• W4224261010 hasConcept C121332964 @default.
• W4224261010 hasConcept C124101348 @default.
• W4224261010 hasConcept C146211579 @default.
• W4224261010 hasConcept C154945302 @default.
• W4224261010 hasConcept C159985019 @default.
• W4224261010 hasConcept C162356407 @default.
• W4224261010 hasConcept C184185385 @default.
• W4224261010 hasConcept C185592680 @default.
• W4224261010 hasConcept C192562407 @default.
• W4224261010 hasConcept C202157981 @default.
• W4224261010 hasConcept C2777814067 @default.
• W4224261010 hasConcept C2779281246 @default.
• W4224261010 hasConcept C31827203 @default.
• W4224261010 hasConcept C41008148 @default.
• W4224261010 hasConcept C43617362 @default.
• W4224261010 hasConcept C46111723 @default.
• W4224261010 hasConcept C55493867 @default.
• W4224261010 hasConcept C70721500 @default.
• W4224261010 hasConcept C73555534 @default.
• W4224261010 hasConcept C80311884 @default.
• W4224261010 hasConcept C86153913 @default.
• W4224261010 hasConcept C86803240 @default.
• W4224261010 hasConcept C97355855 @default.
• W4224261010 hasConceptScore W4224261010C104317684 @default.
• W4224261010 hasConceptScore W4224261010C104397665 @default.
• W4224261010 hasConceptScore W4224261010C121332964 @default.
• W4224261010 hasConceptScore W4224261010C124101348 @default.
• W4224261010 hasConceptScore W4224261010C146211579 @default.
• W4224261010 hasConceptScore W4224261010C154945302 @default.
• W4224261010 hasConceptScore W4224261010C159985019 @default.
• W4224261010 hasConceptScore W4224261010C162356407 @default.
• W4224261010 hasConceptScore W4224261010C184185385 @default.
• W4224261010 hasConceptScore W4224261010C185592680 @default.
• W4224261010 hasConceptScore W4224261010C192562407 @default.
• W4224261010 hasConceptScore W4224261010C202157981 @default.
• W4224261010 hasConceptScore W4224261010C2777814067 @default.
• W4224261010 hasConceptScore W4224261010C2779281246 @default.
• W4224261010 hasConceptScore W4224261010C31827203 @default.
• W4224261010 hasConceptScore W4224261010C41008148 @default.
• W4224261010 hasConceptScore W4224261010C43617362 @default.
• W4224261010 hasConceptScore W4224261010C46111723 @default.

• next