Discover Community Create You

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

A bioinformatics workflow for variant peptide detection in shotgun proteomics.

Molecular & cellular proteomics : MCP - 1 May 2011

Li Jing, Su Zengliu, Ma Ze-Qiang, Slebos Robbert J C, Halvey Patrick, Tabb David L, Liebler Daniel C, Pao William, Zhang Bing

Abstract excerpt

Shotgun proteomics data analysis usually relies on database search. However, commonly used protein sequence databases do not contain information on protein variants and thus prevent variant peptides and proteins from been identified. Including known coding variations into protein sequence databases could help alleviate this problem. Based on our recently published human Cancer Proteome Variation Database, we have...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Carcinoma
Share to Databases, Protein

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Share to Genes, ras

Share to Mutant Proteins

Share to Neoplasm Proteins

Share to Proteome

Share to Proteomics

Share to Workflow

Source

Open in PubMed Open full text

Identifiers

PMID: 21389108
DOI: 10.1074/mcp.M110.006536
PMCID: PMC3098595

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 6 Sept 2026. Manifest publication-graph-cohort-2026-09-06.1.

Source receipt: pubmed, retrieved 6 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

A bioinformatics workflow for variant peptide detection in shotgun proteomics.PMID 21389108Read ↗

Proteogenomic Analysis of Single Amino Acid Polymorphisms in Cancer Research.Semantic proximity Read ↗

CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasetsSemantic proximity Read ↗

Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines.Semantic proximity Read ↗

Quality control of single amino acid variations detected by tandem mass spectrometry.Semantic proximity Read ↗

Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data.Semantic proximity Read ↗

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.Semantic proximity Read ↗

Variant peptide detection utilizing mass spectrometry: laying the foundations for proteogenomic identification and validation.Semantic proximity Read ↗

Proteogenomics of Malignant Melanoma Cell Lines: The Effect of Stringency of Exome Data Filtering on Variant Peptide Identification in Shotgun Proteomics.Semantic proximity Read ↗

Exome-based proteogenomics of HEK-293 human cell line: Coding genomic variants identified at the level of shotgun proteome.Semantic proximity Read ↗

A proteogenomic approach for protein-level evidence of genomic variants in cancer cells.Semantic proximity Read ↗

XMAn: a Homo sapiens mutated-peptide database for the MS analysis of cancerous cell states.Semantic proximity Read ↗

TagRecon: high-throughput mutation identification through sequence tagging.Semantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.