Evidence map›Paper›PMID 33292179›Full record

ArticleClinical proteomics2020

Comparative analysis of differentially abundant proteins quantified by LC-MS/MS between flash frozen and laser microdissected OCT-embedded breast tumor samples.

Lori A Sturtz, Guisong Wang, Punit Shah, Richard Searfoss, Praveen-Kumar Raj-Kumar, Jeffrey A Hooke, J Leigh Fantacone-Campbell, Brenda Deyarmin, Mary Lou Cutler, Rangaprasad Sarangarajan and 5 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Clinical proteomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.5field-weighted citation impact, top 41% of its field
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

3 citing papers in PubMed, 6 citations in OpenAlex.

  1. Article
  2. Review
  3. 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

15 authors at 5 institutions in 2 countries.

Lori A SturtzChan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA.ORCID http://orcid.org/0000-0002-1197-0948
Guisong WangMurtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA.
Punit ShahBERG, Framingham, MA, USA.
Richard SearfossBERG, Framingham, MA, USA.
Praveen-Kumar Raj-KumarChan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA.
Jeffrey A HookeMurtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA.
J Leigh Fantacone-CampbellMurtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA.
Brenda DeyarminChan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA.
Mary Lou CutlerDepartment of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
Rangaprasad SarangarajanBERG, Framingham, MA, USA.
Niven R NarainBERG, Framingham, MA, USA.
Hai HuChan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA. h.hu@wriwindber.org.
Michael A KiebishBERG, Framingham, MA, USA. michael.kiebish@berghealth.com.
Albert J KovatichMurtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA. akovatich@hjfresearch.org.
Craig D ShriverMurtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA. craig.d.shriver.civ@mail.mil.
Framingham State University · USWindber Research Institute · USHenry M. Jackson Foundation · USUniformed Services University of the Health Sciences · USInstitut Bergonié · FR

Funding

U.S. Department of Defense HU0001-19-20058
6 · The paper itself

Abstract

backgroundProteomic studies are typically conducted using flash-frozen (FF) samples utilizing tandem mass spectrometry (MS). However, FF specimens are comprised of multiple cell types, making it difficult to ascertain the proteomic profiles of specific cells. Conversely, OCT-embedded (Optimal Cutting Temperature compound) specimens can undergo laser microdissection (LMD) to capture and study specific cell types separately from the cell mixture. In the current study, we compared proteomic data obtained from FF and OCT samples to determine if samples that are stored and processed differently produce comparable results.

methodsProteins were extracted from FF and OCT-embedded invasive breast tumors from 5 female patients. FF specimens were lysed via homogenization (FF/HOM) while OCT-embedded specimens underwent LMD to collect only tumor cells (OCT/LMD-T) or both tumor and stromal cells (OCT/LMD-TS) followed by incubation at 37 °C. Proteins were extracted using the illustra triplePrep kit and then trypsin-digested, TMT-labeled, and processed by two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS). Proteins were identified and quantified with Proteome Discoverer v1.4 and comparative analyses performed to identify proteins that were significantly differentially expressed amongst the different processing methods.

resultsAmong the 4,950 proteins consistently quantified across all samples, 216 and 171 proteins were significantly differentially expressed (adjusted p-value < 0.05; |log

conclusionsThe proteomic profiles of the OCT/LMD-TS samples were more similar to those from OCT/LMD-T samples than FF/HOM samples, suggesting a strong influence from the sample processing methods. These results indicate that in LC-MS/MS proteomic studies, FF/HOM samples exhibit different protein expression profiles from OCT/LMD samples and thus, results from these two different methods cannot be directly compared.

Indexed as

Breast tumorFlash-frozenLaser microdissectionOptimal cutting temperature compoundProteomicsStroma

Identifiers

PMID33292179
PMCPMC7648272
OpenAlexW3096226328

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.