PXD014415-3

PXD014415 is an original dataset announced via ProteomeXchange.

Title	Evaluating False Transfer Rates from the Match-Between-Runs algorithm with a two-proteome model
Description	Stochasticity between independent LC-MS/MS runs is a challenging problem in the field of proteomics resulting in significant missing values (i.e., abundance measurements) among observed peptides. To address this issue, several approaches have been developed including computational methods such as MaxQuant’s Match-Between-Runs (MBR) algorithm. Often dozens of runs are all considered at once by MBR, transferring identifications from any one run to any of the others. To evaluate the error associated with these transfer events, we created a two-sample/two-proteome approach. In this way, samples containing no yeast lysates were assessed for false identification transfers from samples containing yeast. Overall, transfers from any of 20 runs with yeast were assessed to any of 20 runs without yeast were measured. While MBR increased the total number of spectral identifications by ~40%, we also found that 44% of all identified yeast proteins had identifications transferred to at least one sample without yeast. However, of these only 2.7% remained in the final dataset after applying the MaxQuant LFQ algorithm. We conclude that false transfers by MBR are plentiful, but likely have only a small impact on the final dataset due to downstream removal.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:05:49.816.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-27 08:37:36	ID requested
1	2019-09-25 07:43:00	announced
2	2019-10-25 05:58:28	announced	2019-10-25: Updated publication reference for PubMed record(s): 31547658.
⏵ 3	2024-10-22 04:05:55	announced	2024-10-22: Updated project metadata.

Lim MY, Paulo JA, Gygi SP, Evaluating False Transfer Rates from the Match-between-Runs Algorithm with a Two-Proteome Model. J Proteome Res, 18(11):4020-4026(2019) [pubmed]

10.1021/acs.jproteome.9b00492;

submitter keyword: false transfer rate,match-between-runs, label-free quantitation, two-proteome mixture

Steven P. Gygi
contact affiliation	Dept of Cell Biology Harvard Medical School 240 Longwood Ave Boston, MA 02115
contact email	steven_gygi@hms.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD014415
     1. Label: PRIDE project
     2. Name: Evaluating False Transfer Rates from the Match-Between-Runs algorithm with a two-proteome model