Proteoform Analysis and Construction of Proteoform Families in Proteoform Suite.

Leah V Schaffer, Michael R Shortreed, Lloyd M Smith

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

3 authors.

Leah V SchafferDepartment of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.

Michael R ShortreedDepartment of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.

Lloyd M SmithDepartment of Chemistry, University of Wisconsin-Madison, Madison, WI, USA. smith@chem.wisc.edu.

Funding

BIOTECHNOLOGY TRAINING PROGRAMT32GM008349 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI FOX, BRIAN G · 1989 to 2019

$22.5M

Revealing Proteoforms: The Primary Effectors of Biological FunctionR35GM126914 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI Lloyd M Smith · 2018 to 2026

$6.2M

NIGMS NIH HHS R35 GM126914NIGMS NIH HHS T32 GM008349

6 · The paper itself

Abstract

Proteoform Suite is an interactive software program for the identification and quantification of intact proteoforms from mass spectrometry data. Proteoform Suite identifies proteoforms observed by intact-mass (MS1) analysis. In intact-mass analysis, unfragmented experimental proteoforms are compared to a database of known proteoform sequences and to one another, searching for mass differences corresponding to well-known post-translational modifications or amino acids. Intact-mass analysis enables proteoforms observed in the MS1 data without MS/MS (MS2) fragmentation to be identified. Proteoform Suite further facilitates the construction and visualization of proteoform families, which are the sets of proteoforms derived from individual genes. Bottom-up peptide identifications and top-down (MS2) proteoform identifications can be integrated into the Proteoform Suite analysis to increase the sensitivity and accuracy of the analysis. Proteoform Suite is open source and freely available at https://github.com/smith-chem-wisc/proteoform-suite .

Indexed as

ProteomicsTandem Mass SpectrometryHumansProtein Processing, Post-TranslationalProteomeSoftwareProteomeMass spectrometryPost-translational modificationProteoformProteoform familyTop-down proteomics

Identifiers

PMID35657588

DOI10.1007/978-1-0716-2325-1_7

PMCPMC9694099

What OpenQuestion holds

Textmetadata

LicenceTDM

Read underepoch 390

Registered trials

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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.