PXD029663-2

PXD029663 is an original dataset announced via ProteomeXchange.

Title	Reprocessed dataset with Skyline Batch: Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues
Description	The data set represents a fair comparison of shotgun proteomics with HRM (swath type DIA). Additionally, a human liver microtissue was profiled with HRM. REPROCESSING METHODS: Skyline Batch is a newly developed Windows forms application that enables easy and consistent reprocessing of data with Skyline. Skyline has made previous advances in this direction; however, none enable seamless automated reprocessing of local and remote files. Skyline keeps a log of all the steps that were taken in the document; however, reproducing these steps takes time and allows room for human error. Skyline also has a command-line interface, enabling it to be run from a batch script, but using the program in this way requires expertise in editing these scripts. By formalizing the workflow of a highly used set of batch scripts into an intuitive and powerful user interface, Skyline Batch can reprocess data stored in remote repositories just by opening and running a Skyline Batch configuration file. When run, a Skyline Batch configuration downloads all necessary remote files and then runs a four-step Skyline workflow. By condensing the steps needed to reprocess the data into one file, Skyline Batch gives researchers the opportunity to publish their processing along with their data and other analysis files. These easily run configuration files will greatly increase the transparency and reproducibility of published work. Skyline Batch is freely available at https://skyline.ms/batch.url.
HostingRepository	PanoramaPublic
AnnounceDate	2021-11-12
AnnouncementXML	Submission_2022-01-07_13:28:50.073.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Reanalysis of http://www.peptideatlas.org/PASS/PASS00589
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Brendan MacLean
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Acetyl; Carbamidomethyl; Oxidation
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-10 17:17:58	ID requested
1	2021-11-12 15:17:16	announced
⏵ 2	2022-01-07 13:28:50	announced	: Added publication

Marsh AN, Sharma V, Mani SK, Vitek O, MacCoss MJ, MacLean BX, Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline. J Proteome Res, 21(1):289-294(2022) [pubmed]

submitter keyword: Skyline, workflow, reproducible, data analysis, reprocessing, software, mass spectrometry

Michael MacCoss
contact affiliation	Department of Genome Sciences, University of Washington, Seattle, WA, USA
contact email	maccoss@uw.edu
lab head
Brendan MacLean
contact affiliation	Department of Genome Sciences, University of Washington, Seattle, WA, USA
contact email	brendanx@uw.edu
dataset submitter

Panorama Public dataset URI