PXD008821

PXD008821 is an original dataset announced via ProteomeXchange.

Title	Confirmation of SOMAmer® Enrichment from Biological Matrices using Mass Spectrometry, plasma
Description	In an effort to confirm binding of SOMAmer®s to their respective targets in an endogenous matrix, we have conducted a series of experiments using SOMAmer®s to enrich target proteins followed by measurement using two mass spectrometry techniques: data dependent analysis (DDA) and multiple reaction monitoring (MRM). For data dependent analysis, the library of 4783 SOMAmer®s were multiplexed in sets of 8 and used for enrichment of target proteins from cell lysate and conditioned media, as well as human plasma and serum. A subset of the SOMAmer®s were screened in urine by this global profiling technique as well. Cell lines were selected from Cancer Cell Line Encyclopedia for screening by comparing gene expression of the target proteins measured by RNA sequencing across the CCLE.1 Using the criterion of FPKM value greater than 5 for the target protein, the minimum number of cell lines was grown to maximize protein coverage across the SOMAmer® library. For a given cell line, the presence of at least 8 target proteins with FPKM values greater than 5was required for inclusion. Approximately 400 target proteins were not covered by this strategy were screened in serum and plasma only. For enrichment from biological matrices, SOMAmer®s were combined into sets of 8 such that the potential interaction with similar proteins or binding partners was minimized. Non-specific binding of the SOMAmer®s was assessed in each matrix by using a SOMAmer® generated against the bacterial protein CysH. Target protein spectral counts in the SOMAmer® enriched samples were compared to the respective CysH control. A positive hit is defined as target protein detection with a minimum of 2 spectral counts and signal over CysH background greater than 10X (if applicable).
HostingRepository	PRIDE
AnnounceDate	2018-08-03
AnnouncementXML	Submission_2018-08-08_00:40:37.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nancy Finkel
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-31 03:30:20	ID requested
1	2018-08-03 04:36:03	announced
⏵ 2	2018-08-08 00:40:38	announced	Updated publication reference for PubMed record(s): 30072576.

Emilsson V, Ilkov M, Lamb JR, Finkel N, Gudmundsson EF, Pitts R, Hoover H, Gudmundsdottir V, Horman SR, Aspelund T, Shu L, Trifonov V, Sigurdsson S, Manolescu A, Zhu J, Olafsson Ö, Jakobsdottir J, Lesley SA, To J, Zhang J, Harris TB, Launer LJ, Zhang B, Eiriksdottir G, Yang X, Orth AP, Jennings LL, Gudnason V, Co-regulatory networks of human serum proteins link genetics to disease. Science, 361(6404):769-773(2018) [pubmed]

curator keyword: Technical

submitter keyword: Blood serum, blood plasma, cell lysate, conditioned media, aptamer, SOMAmer

Nancy Finkel
contact affiliation	Novartis Institute for Biomedical Research, Cambridge MA
contact email	nancy.finkel@novartis.com
lab head
Nancy Finkel
contact affiliation	Novartis
contact email	nancy.finkel@novartis.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008821
     1. Label: PRIDE project
     2. Name: Confirmation of SOMAmer® Enrichment from Biological Matrices using Mass Spectrometry, plasma