To confirm the existence of missing proteins, we need to identify at least two unique peptides with length of 9-40 amino acids of a missing protein in bottom-up mass-spectrometry-based proteomic experiments. However, an identified unique peptide of the missing protein, even identified with high level of confidence, could possibly coincide with a peptide of a commonly observed protein due to isobaric substitutions, mass modifications, alternative splice isoforms, or single amino acid variants (SAAVs). Besides unique peptides of missing proteins, identified variant peptides (SAAV-containing peptides) could also alternatively map to peptides of other proteins due to the aforementioned issues. Therefore, we conducted a thorough comparative analysis on data sets in PeptideAtlas Tiered Human Integrated Search Proteome (THISP, 2017-03 release), including neXtProt (2017-01 release), to systematically investigate the possibility of unique peptides in missing proteins (PE2-4), unique peptides in dubious proteins, and variant peptides affected by isobaric substitutions, causing doubtful identification results. In this study, we considered 11 isobaric substitutions. From our analysis, we found <5% of the unique peptides of missing proteins and >6% of variant peptides became shared with peptides of PE1 proteins after isobaric substitutions.
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http://dx.doi.org/10.1021/acs.jproteome.7b00342 | DOI Listing |
J Proteome Res
November 2024
Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States.
Mass spectrometry-based sample multiplexing with isobaric tags permits the development of high-throughput and precise quantitative biological assays with proteome-wide coverage and minimal missing values. Here, we nearly doubled the multiplexing capability of the TMTpro reagent set to a 35-plex through the incorporation of one deuterium isotope into the reporter group. Substituting deuterium frequently results in suboptimal peak coelution, which can compromise the accuracy of reporter ion-based quantification.
View Article and Find Full Text PDFChemosphere
February 2024
Centro de Investigación y Asistencia en Tecnología y Diseño Del Estado de Jalisco A.C., Sede Noreste, Vía de La Innovación 404, Autopista Monterrey-Aeropuerto Km 10, Parque PIIT, Apodaca, Nuevo León, C.P. 66628, Mexico. Electronic address:
Pharmaceutical active compounds (PhACs) are organic pollutants detected in wastewater and aquatic environments worldwide in concentrations ranging from ng L to μg L. Wastewater effluents containing PhACs residues is discharged in municipal sewage and, subsequently collected in municipal wastewater treatment plants (WWTPs) where are not entirely removed. Thus, PhACs and its transformation products (TPs) are discharged into water bodies.
View Article and Find Full Text PDFClin Chem Lab Med
February 2024
Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA.
Proteomics
October 2023
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
Relative and absolute intensity-based protein quantification across cell lines, tissue atlases and tumour datasets is increasingly available in public datasets. These atlases enable researchers to explore fundamental biological questions, such as protein existence, expression location, quantity and correlation with RNA expression. Most studies provide MS1 feature-based label-free quantitative (LFQ) datasets; however, growing numbers of isobaric tandem mass tags (TMT) datasets remain unexplored.
View Article and Find Full Text PDFJ Phys Chem A
May 2023
Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States.
We had reported the isotopic envelopes in differential IMS (FAIMS) separations depending on the ion structure. However, this new approach to distinguish isomers was constrained by the unit-mass resolution commingling all nominally isobaric isotopologues. Here, we directly couple high-definition FAIMS to ultrahigh-resolution (Orbitrap) MS and employ the resulting platform to explore the FAIMS spectra for isotopic fine structure.
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