PXD027701

PXD027701 is an original dataset announced via ProteomeXchange.

Title	De novo identification of the blood plasma and serum peptides from samples of healthy donors
Description	Previously, we published a dataset of human blood plasma and serum samples of 10 healthy males and 10 healthy females, fractionated on a set of sorbents (cation exchange Toyopearl CM-650M, CM Bio-Gel A, SP Sephadex C-25 and anion exchange QAE Sephadex A-25) and analyzed by LC-MS/MS individually and pooled in equal amounts (Supplementary Table S1, Sheet 1) [33]. Blood is a complex tissue and can theoretically contain products of all processes occurring in different parts of the body. To identify potential sources of “alien” (non-human) plasma peptides, we performed a de novo analysis of mass spectrometry data. De novo analysis is a less efficient method of identification than search against databases, since the accuracy and resolution of modern mass spectrometers such as QTOF or Orbitrap remains not high enough. However, we use de novo analysis to identify organisms that include the most abundant components of the complex peptide mixture. This procedure allows us to develop a hypothesis and then perform a standard search against a database of proteins of identified organisms. The de novo identification was carried out using PEAKS Studio 8.0 (Bioinformatics Solutions Inc., Canada) and mass spectrometry driven BLAST analysis against the RefSeq non-redundant database NCBInr (https://www.ncbi.nlm.nih.gov/protein/). Mass spectra identified as fragments of proteins from different organisms were assigned to a taxonomic level at which these different organisms converged (Supplementary Table S2). 33. Arapidi, G. et al. Peptidomics dataset: Blood plasma and serum samples of healthy donors fractionated on a set of chromatography sorbents. Data Brief 18, 1204–1211 (2018).
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:44:59.160.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Georgij Arapidi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-05 04:37:31	ID requested
1	2024-06-14 09:04:17	announced
⏵ 2	2024-10-22 06:44:59	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: peptidomics, mass spectrometry, blood plasma and serum,Healthy donors

Georgij Pavlovich Arapidi
contact affiliation	Systems Biology Laboratory, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency
contact email	arapidi@gmail.com
lab head
Georgij Arapidi
contact affiliation	Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency
contact email	arapidi@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD027701
     1. Label: PRIDE project
     2. Name: De novo identification of the blood plasma and serum peptides from samples of healthy donors