Evidence map›Paper›PMID 26265041›Full record

ArticleJournal of the American Society for Mass Spectrometry2015

Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications.

Bruce D Pascal, Graham M West, Catherina Scharager-Tapia, Ricardo Flefil, Tina Moroni, Pablo Martinez-Acedo, Patrick R Griffin, Anthony C Carvalloza

Abstract read
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In one paragraph

Article in Journal of the American Society for Mass Spectrometry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Bruce D PascalInformatics Core, The Scripps Research Institute, Jupiter, FL, 33458, USA. bpascal@scripps.edu.
Graham M WestProteomics Core, The Scripps Research Institute, Jupiter, FL, 33458, USA.
Catherina Scharager-TapiaProteomics Core, The Scripps Research Institute, Jupiter, FL, 33458, USA.
Ricardo FlefilProteomics Core, The Scripps Research Institute, Jupiter, FL, 33458, USA.
Tina MoroniProteomics Core, The Scripps Research Institute, Jupiter, FL, 33458, USA.
Pablo Martinez-AcedoProteomics Core, The Scripps Research Institute, Jupiter, FL, 33458, USA.
Patrick R GriffinDepartment of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, 33458, USA.
Anthony C CarvallozaInformatics Core, The Scripps Research Institute, Jupiter, FL, 33458, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The goal in proteomics to identify all peptides in a complex mixture has been largely addressed using various LC MS/MS approaches, such as data dependent acquisition, SRM/MRM, and data independent acquisition instrumentation. Despite these developments, many peptides remain unsequenced, often due to low abundance, poor fragmentation patterns, or data analysis difficulties. Many of the unidentified peptides exhibit strong evidence in high resolution MS(1) data and are frequently post-translationally modified, playing a significant role in biological processes. Proteomics Workbench (PWB) software was developed to automate the detection and visualization of all possible peptides in MS(1) data, reveal candidate peptides not initially identified, and build inclusion lists for subsequent MS(2) analysis to uncover new identifications. We used this software on existing data on the autophagy regulating kinase Ulk1 as a proof of concept for this method, as we had already manually identified a number of phosphorylation sites Dorsey, F. C. et al (J. Proteome. Res. 8(11), 5253-5263 (2009)). PWB found all previously identified sites of phosphorylation. The software has been made freely available at http://www.proteomicsworkbench.com . Graphical Abstract ᅟ.

Indexed as

Protein Processing, Post-TranslationalSoftwareAmino Acid SequenceAutophagy-Related Protein-1 HomologHEK293 CellsHumansIntracellular Signaling Peptides and ProteinsMolecular Sequence DataProtein Serine-Threonine KinasesTandem Mass SpectrometryAutophagy-Related Protein-1 HomologIntracellular Signaling Peptides and ProteinsProtein Serine-Threonine KinasesULK1 protein, humanComputational proteomicsMass spectrometryMS1 data analysisPeptide identificationPost-translational modificationsPTMs

Identifiers

PMID26265041

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.