ArticleJournal of proteome research2017
Expanding Proteome Coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) Combined with Broad Specificity Proteolysis.
Article in Journal of proteome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
57 citing papers in PubMed, 98 citations in OpenAlex.
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- Effect of a Laparoscopic Donor Nephrectomy in Healthy Living Kidney Donors on the Acute Phase Response Using Either Propofol or Sevoflurane Anesthesia.International journal of molecular sciences · 2025Article
- Case Report: Proteomic analysis of cerebrospinal fluid in a retinoblastoma patient.Frontiers in oncology · 2025Article
- A transphyletic study of metazoan β-catenin protein complexes.Zoological letters · 2024Article
- Compartmentalization proteomics revealed endolysosomal protein network changes in a goat model of atrial fibrillation.iScience · 2024Article
- General transcription factor from Escherichia coli with a distinct mechanism of action.Nature structural & molecular biology · 2024Article
- A noncanonical function of SKP1 regulates the switch between autophagy and unconventional secretion.Science advances · 2023Article
- Spatial distribution of three ARGONAUTEs regulates the anther phasiRNA pathway.Nature communications · 2023Article
- USP18 is an essential regulator of muscle cell differentiation and maturation.Cell death & disease · 2023Article
- Mass spectrometry of short peptides reveals common features of metazoan peptidergic neurons.Nature ecology & evolution · 2022Article
- Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The effects of endogenously- and exogenously-induced hyperketonemia on exercise performance and adaptation.Physiological reports · 2022Article
- Inheritance of repressed chromatin domains during S phase requires the histone chaperone NPM1.Science advances · 2022Article
- Interactome screening of C9orf72 dipeptide repeats reveals VCP sequestration and functional impairment by polyGA.Brain : a journal of neurology · 2022Article
- Sequence and structural variations determining the recruitment of WNK kinases to the KLHL3 E3 ligase.The Biochemical journal · 2022Article
- Proteomic analysis in primary T cells reveals IL-7 alters T cell receptor thresholding via CYTIP/cytohesin/LFA-1 localisation and activation.The Biochemical journal · 2022Article
- Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract.Nature communications · 2022Article
- Defactinib inhibits PYK2 phosphorylation of IRF5 and reduces intestinal inflammation.Nature communications · 2021Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
The "deep" proteome has been accessible by mass spectrometry for some time. However, the number of proteins identified in cells of the same type has plateaued at ∼8000-10 000 without ID transfer from reference proteomes/data. Moreover, limited sequence coverage hampers the discrimination of protein isoforms when using trypsin as standard protease. Multienzyme approaches appear to improve sequence coverage and subsequent isoform discrimination. Here we expanded proteome and protein sequence coverage in MCF-7 breast cancer cells to an as yet unmatched depth by employing a workflow that addresses current limitations in deep proteome analysis in multiple stages: We used (i) gel-aided sample preparation (GASP) and combined trypsin/elastase digests to increase peptide orthogonality, (ii) concatenated high-pH prefractionation, and (iii) CHarge Ordered Parallel Ion aNalysis (CHOPIN), available on an Orbitrap Fusion (Lumos) mass spectrometer, to achieve 57% median protein sequence coverage in 13 728 protein groups (8949 Unigene IDs) in a single cell line. CHOPIN allows the use of both detectors in the Orbitrap on predefined precursor types that optimizes parallel ion processing, leading to the identification of a total of 179 549 unique peptides covering the deep proteome in unprecedented detail.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.