PXD008787

PXD008787 is an original dataset announced via ProteomeXchange.

Title	Efficient Parsing and Quantification of Native Mass Spectrometer Files with RawQuant
Description	Effective analysis of protein samples by mass spectrometry (MS) instrumentation requires careful selection and optimization of a range experimental parameters. As the output from the primary detection device, the ‘raw’ MS data file can be used to gauge the success of a given sample analysis. However, the closed-source nature of the standard raw MS file can complicate effective parsing of the data contained within. To overcome this challenge, the RawQuant tool was developed to enable parsing of raw MS files to yield meta and scan data in an openly readable text format. RawQuant can be commanded to export user-friendly files containing MS1, MS2, and MS3 meta data, as well as matrices of quantification values based on isobaric tagging approaches. In this study, RawQuant is demonstrated through application in a combination of scenarios: 1. Re-analysis of shotgun proteomics data aimed at identification of the human proteome, 2. Re-analysis of experiments utilizing isobaric tagging for whole-proteome quantification, 3. Analysis of a novel bacterial proteome and synthetic peptide mixture for assessing quantification accuracy when using isobaric tags. Together, these analyses successfully demonstrate RawQuant for the efficient parsing and quantification of data from raw MS files acquired in a range common proteomics experiments. In addition, the individual analyses using RawQuant highlights parametric considerations in the different experimental sets, and suggests targetable areas to improve depth of coverage in identification-focused studies, and quantification accuracy when using isobaric tags.
HostingRepository	PRIDE
AnnounceDate	2018-05-07
AnnouncementXML	Submission_2018-05-07_01:49:52.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD008787
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christopher Hughes
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Ammonia-loss; Glu->pyro-Glu; TMT6plex; Oxidation; iTRAQ8plex; Acetyl; Carbamidomethyl; Gln->pyro-Glu
Instrument	Orbitrap Fusion Lumos; Orbitrap Fusion ETD; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-29 03:29:27	ID requested
⏵ 1	2018-05-07 01:49:53	announced

Kovalchik KA, Moggridge S, Chen DDY, Morin GB, Hughes CS, Parsing and Quantification of Raw Orbitrap Mass Spectrometer Data Using RawQuant. J Proteome Res, 17(6):2237-2247(2018) [pubmed]

curator keyword: Technical

submitter keyword: TMT, isobaric labeling, Orbitrap, SPS-MS3, quantitative proteomics, iTRAQ

Gregg Morin
contact affiliation	Head of Proteomics
contact email	gmorin@bcgsc.ca
lab head
Christopher Hughes
contact affiliation	British Columbia Cancer Research Centre
contact email	chughes@bcgsc.ca
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008787
     1. Label: PRIDE project
     2. Name: Efficient Parsing and Quantification of Native Mass Spectrometer Files with RawQuant