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Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS: Phosphopeptide-enriched data set

ABSTRACT: This data set represent an experiment comparing enriched phosphopeptides of a human U2OS cell line. Phosphopeptide-enriched samples of ten nocodazole treated and ten control U2OS cell line samples were acquired each in DDA and DIA (SWATH-MS) modes.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: George Rosenberger

LAB HEAD: Ruedi Aebersold

PROVIDER: PXD006056 | Pride | 2017-06-12

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	MaxQuant.tgz	Other
	db_assays_ptms_decoys.TraML	Other
	feature_alignment.csv	Csv
	mqpar.xml	Xml
	uniprot-human_20161219.fasta	Fasta

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Publications

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS.

Rosenberger George G Liu Yansheng Y Röst Hannes L HL Ludwig Christina C Buil Alfonso A Buil Alfonso A Bensimon Ariel A Soste Martin M Spector Tim D TD Dermitzakis Emmanouil T ET Collins Ben C BC Malmström Lars L Aebersold Ruedi R

Nature biotechnology 20170612 8

Consistent detection and quantification of protein post-translational modifications (PTMs) across sample cohorts is a prerequisite for functional analysis of biological processes. Data-independent acquisition (DIA) is a bottom-up mass spectrometry approach that provides complete information on precursor and fragment ions. However, owing to the convoluted structure of DIA data sets, confident, systematic identification and quantification of peptidoforms has remained challenging. Here, we present ...[more]

PMID: 28604659

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