ArticleJournal of proteome research2018
In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides.
Article in Journal of proteome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed.
- MeCP2 requires interactions with nucleosome linker DNA to read chromatin DNA methylation.Nature communications · 2026Article
- Nucleosome interaction of the CPC secures centromeric chromatin integrity and chromosome segregation fidelity.The EMBO journal · 2025Article
- Structural basis for DNA break sensing by human MRE11-RAD50-NBS1 and its regulation by telomeric factor TRF2.Nature communications · 2025Article
- Integrative structural analysis of NF45-NF90 heterodimers reveals architectural rearrangements and oligomerization on binding dsRNA.Nucleic acids research · 2025Article
- Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.Communications chemistry · 2024Article
- The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment.EMBO reports · 2024Article
- Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure.Nature communications · 2024Article
- Structural basis for Mis18 complex assembly and its implications for centromere maintenance.EMBO reports · 2024Article
- Structural mechanism of extranucleosomal DNA readout by the INO80 complex.Science advances · 2022Article
- Mechanistic basis for Sgo1-mediated centromere localization and function of the CPC.The Journal of cell biology · 2022Article
- Leveraging Parameter Dependencies in High-Field Asymmetric Waveform Ion-Mobility Spectrometry and Size Exclusion Chromatography for Proteome-wide Cross-Linking Mass Spectrometry.Analytical chemistry · 2022Article
- Accurate and Automated High-Coverage Identification of Chemically Cross-Linked Peptides with MaxLynx.Analytical chemistry · 2022Article
- Reliable identification of protein-protein interactions by crosslinking mass spectrometry.Nature communications · 2021Article
- Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry.Nature communications · 2021Article
- MS Annika: A New Cross-Linking Search Engine.Journal of proteome research · 2021Article
- Evaluation of mass spectrometry MS/MS spectra for the presence of isopeptide crosslinked peptides.PloS one · 2021Article
- Purified Smc5/6 Complex Exhibits DNA Substrate Recognition and Compaction.Molecular cell · 2020Article
- Open Search Strategy for Inferring the Masses of Cross-Link Adducts on Proteins.Analytical chemistry · 2020Article
- Open Database Searching Enables the Identification and Comparison of Bacterial Glycoproteomes without Defining Glycan Compositions Prior to Searching.Molecular & cellular proteomics : MCP · 2020Article
- Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins.Nature communications · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Cross-linking/mass spectrometry has undergone a maturation process akin to standard proteomics by adapting key methods such as false discovery rate control and quantification. A poorly evaluated search setting in proteomics is the consideration of multiple (lighter) alternative values for the monoisotopic precursor mass to compensate for possible misassignments of the monoisotopic peak. Here, we show that monoisotopic peak assignment is a major weakness of current data handling approaches in cross-linking. Cross-linked peptides often have high precursor masses, which reduces the presence of the monoisotopic peak in the isotope envelope. Paired with generally low peak intensity, this generates a challenge that may not be completely solvable by precursor mass assignment routines. We therefore took an alternative route by '"in-search assignment of the monoisotopic peak" in the cross-link database search tool Xi (Xi-MPA), which considers multiple precursor masses during database search. We compare and evaluate the performance of established preprocessing workflows that partly correct the monoisotopic peak and Xi-MPA on three publicly available data sets. Xi-MPA always delivered the highest number of identifications with ∼2 to 4-fold increase of PSMs without compromising identification accuracy as determined by FDR estimation and comparison to crystallographic models.
Indexed as
Identifiers
What OpenQuestion holds
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.