PXD076747-1

PXD076747 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of plasma samples from multiple myeloma patients with or without myeloma bone disease.
Description	Plasma proteomic analysis was performed in 71 consecutive newly diagnosed multiple myeloma (NDMM) patients. Myeloma bone disease (MBD) remains a common manifestation in patients with NDMM and was present in 25 of the patients. Plasma samples were prepared with the filter aided sample preparation (FASP) method. Briefly, samples were reduced with 10 mM DTE for 20 min, RT and alkylated with 0.05 M iodoacetamide for 20 min, RT, in the dark. Sequential washes with urea buffer (8 M Urea in 0.1 M Tris HCl pH 8.5; UA buffer) were performed in the filter units (0.5 ml, 30 kDa MW cutoff) by centrifugation (14000 rcf, 15 min, RT) followed by buffer exchange with ammonium bicarbonate (50 mM NH4HCO3 in ultrapure water, pH 8.5) under the same centrifugation conditions. Tryptic digestion was performed overnight in the dark at RT by utilizing a trypsin : protein ratio of 1:100 w/w. After trypsinization, peptides were eluted via centrifugation with 50 mM NH4HCO3, pH 8.5 and lyophilized. Dried peptides were resuspended in 0.1% formic acid, 2% acetonitrile and diluted to a final concentration of 0.2 ug/uL. A 5 uL volume, equivalent to 1 ug of protein, was injected for the LC-MS/MS analysis that was performed with a Dionex Ultimate 3000 UHPLC system coupled with the high resolution nano ESI Q Exactive Plus Orbitrap mass spectrometer (Thermo Scientific). DDA mode and HCD collision method were used for the MS/MS analysis. Raw files were analyzed with Proteome Discoverer (Thermo Scientific) software package, employing the Sequest search engine and the Uniprot human database (including only canonical reviewed entries). The search was performed with carbamidomethylation of cysteine as a static modification and methionine oxidation as a dynamic modification. Two missed cleavages were allowed, with a precursor mass tolerance of 10 ppm and a fragment mass tolerance of 0.05 Da. Validation was based on the adjusted FDR P-value, termed as the q-value, with a confidence level of 95% (a = 0.05). Label-free quantification was carried out by using the precursor peak area values for each protein, as defined by Proteome Discoverer.
HostingRepository	MassIVE
AnnounceDate	2026-09-07
AnnouncementXML	Submission_2026-09-07_05:49:18.258.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manousos Makridakis
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2026-04-08 04:19:48	ID requested
⏵ 1	2026-09-07 05:49:18	announced

no publication

submitter keyword: proteomics, multiple myeloma, myeloma bone disease, plasma, LC-MS/MS, DatasetType:Proteomics

Evangelos Terpos
contact affiliation	Department of Clinical Therapeutics, Alexandra Hospital, School of Medicine, National and Kapodistrian University of Athens, 80 Vas. Sophias Ave, 11528 Athens
contact email	eterpos@med.uoa.gr
lab head
Manousos Makridakis
contact affiliation	Biomedical Research Foundations, Academy of Athens
contact email	mmakrid@bioacademy.gr
dataset submitter

MassIVE dataset URI

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive-ftp.ucsd.edu/v12/MSV000101409/