PXD001187

PXD001187 is an original dataset announced via ProteomeXchange.

Title	Influence of digestion protocol in Protein Quantitation
Description	Quantitative determination of absolute and relative protein amounts is an essential requirement for most current bottom-up proteomics applications, but protein quantitation estimates are affected by several sources of variability such as sample preparation, mass spectrometric acquisition, and data analysis. Among them, sample digestion has attracted much attention from the proteomics community, as protein quantitation by bottom-up proteomics relies on the efficiency and reproducibility of protein enzymatic digestion, with the presence of missed cleavages, nonspecific cleavages, or even the use of different proteases having been postulated as important sources of variation in protein quantitation. Here we evaluated both in-solution and filter-aided digestion protocols and assessed their influence in the estimation of protein abundances using five E. coli mixtures with known amounts of spiked proteins. We observed that replicates of trypsin specificity digestion protocols are highly reproducible in terms of peptide quantitation, with digestion technique and the chosen proteolytic enzyme being the major sources of variability in peptide quantitation. Finally, we also evaluated the result of including peptides with missed cleavages in protein quantitation and observed no significant differences in precision, accuracy, specificity, and sensitivity compared with the use of fully tryptic peptides.
HostingRepository	PRIDE
AnnounceDate	2014-10-23
AnnouncementXML	Submission_2014-10-23_05:00:42.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cristina Chiva
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2014-07-30 07:22:21	ID requested
1	2014-07-30 08:21:43	announced
⏵ 2	2014-10-23 05:00:43	announced	Updated project metadata.

Chiva C, Ortega M, Sabid, ó E, Influence of the digestion technique, protease, and missed cleavage peptides in protein quantitation. J Proteome Res, 13(9):3979-86(2014) [pubmed]

curator keyword: Biomedical, Biological

submitter keyword: Protein quantitation, Digestion Protocols, FASP

Eduard Sabidó
contact affiliation	Proteomics Unit UPF/CRG
contact email	eduard.sabido@crg.eu
lab head
Cristina Chiva
contact affiliation	University Pompeu Fabra
contact email	cristina.chiva@upf.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001187
     1. Label: PRIDE project
     2. Name: Influence of digestion protocol in Protein Quantitation