PXD033355

PXD033355 is an original dataset announced via ProteomeXchange.

Title	DirectMS1Quant: ultrafast quantitative proteomics with MS/MS-free mass spectrometry. Part 2/2
Description	Recently, we presented the DirectMS1 method of ultrafast proteome-wide analysis based on minute-long LC gradients and MS1-only mass spectra acquisition. Currently, the method provides the depth of human cell proteome coverage of 2500 proteins at 1% false discovery rate (FDR) when using 5-min LC gradients and 7.3 min runtime in total. While the standard MS/MS approaches provide 4000 to 5000 protein identifications within a couple of hours of instrumentation time, we advocate here that the higher number of identified proteins does not always translate into better quantitation quality of the proteome analysis. To further elaborate on this issue we performed one-by-one comparison of quantitation results obtained using DirectMS1 with three most popular MS/MS-based proteomic methods: label-free quantification (LFQ) and tandem mass tag (TMT) -based data dependent acquisition (DDA), and data independent acquisition (DIA). For the comparison we performed a series of proteome-wide analysis of well-characterized (ground truth) and real world biological samples, including a mix of UPS1 proteins spiked at different concentrations into E. coli digest used as a background and a set of glioblastoma cell lines. MS1-only data was analyzed using a novel quantitation workflow called DirectMS1Quant developed in this work. The results obtained in this study demonstrated comparable quantitation efficiency of 5 min DirectMS1 with both TMT and DIA methods utilizing 10 to 20-fold longer instrumentation time.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:01:46.406.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mark Ivanov
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-21 07:07:51	ID requested
1	2023-08-25 03:02:14	announced
2	2023-11-14 07:14:31	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 06:01:46	announced	2024-10-22: Updated project metadata.

10.1021/ACS.ANALCHEM.2C02255;

submitter keyword: DDA LFQ, TMT,Glioblastoma, MS1-only

Mikhail V. Gorshkov
contact affiliation	V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
contact email	mike.gorshkov@gmail.com
lab head
Mark Ivanov
contact affiliation	INEP CP RAS
contact email	markmipt@gmail.com
dataset submitter

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://ftp.pride.ebi.ac.uk/pride/data/archive/2023/08/PXD033355

PRIDE project URI

• PRIDE
  1. PXD033355
     1. Label: PRIDE project
     2. Name: DirectMS1Quant: ultrafast quantitative proteomics with MS/MS-free mass spectrometry. Part 2/2