Abstract：
:In-source fragmentation occurs as a byproduct of electrospray ionization. We find that ions produced as a result of in-source fragmentation often match fragment ions produced during MS/MS fragmentation, and we take advantage of this phenomenon in a novel algorithm to analyze LC-MS metabolomics data sets. Our approach organizes coeluting MS1 features into a single peak group and then identifies in-source fragments among coeluting features using MS/MS spectral libraries. We tested our approach using previously published data of verified metabolites and compared the results to features detected by other mainstream metabolomics tools. Our results indicate that considering in-source fragment information as a part of the identification process increases the annotation quality, allowing us to leverage MS/MS data in spectrum libraries even if MS/MS scans were not collected.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Seitzer PM,Searle BCdoi
10.1021/acs.jproteome.8b00601subject
Has Abstractpub_date
2019-02-01 00:00:00pages
791-796issue
2eissn
1535-3893issn
1535-3907journal_volume
18pub_type
杂志文章abstract：:Diosgenin (DIO), the starting material for the synthesis of steroidal anti-inflammatory drugs in the pharmaceutical industry, has been previously demonstrated to display pharmaceutical effects against cerebral ischemic reperfusion (I/R). However, the alterations of brain proteome profiles underlying this treatment rem...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00667
更新日期：2020-03-06 00:00:00
abstract：:Chronic kidney disease (CKD) has emerged as a major public health problem worldwide. It frequently progresses to end-stage renal disease, which is related to very high cost and mortality. Novel biomarkers can provide insight into the novel mechanism, facilitate early detection, and monitor progression of CKD and its r...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00583
更新日期：2016-10-07 00:00:00
abstract：:Flooding has severe negative effects on soybean growth. To explore the flooding-responsive mechanisms in early-stage soybean, a phosphoproteomic approach was used. Two-day-old soybean plants were treated without or with flooding for 3, 6, 12, and 24 h, and root tip proteins were then extracted and analyzed at each tim...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500621c
更新日期：2014-12-05 00:00:00
abstract：:Many tumors display significant cellular heterogeneity as well as molecular heterogeneity. Sensitive biomarkers that differentiate between diagnostically challenging tumors must contend with this heterogeneity. Mass spectrometry-based molecular histology of a patient series of heterogeneous, microscopically identical ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr301190g
更新日期：2013-04-05 00:00:00
abstract：:"Dry eye" is a multifactorial inflammatory disease affecting the ocular surface. Tear hyperosmolarity in dry eye contributes to inflammation and cell damage. Recent research efforts on dry eye have been directed toward biomarker discovery for diagnosis, response to treatment, and disease mechanisms. This study employe...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00443
更新日期：2015-09-04 00:00:00
abstract：:Type-I procollagen aminoterminal propeptide (PINP) is a useful biomarker for bone formation activity that is used to monitor treatment of bone disorders including osteoporosis. Studies with human patients under long-term therapy for osteoporosis by daily injection of parathyroid hormone (PTH) demonstrated that the cir...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070288s
更新日期：2007-11-01 00:00:00
abstract：:Depletion of DNA replication initiation factors such as CDC7 kinase triggers the origin activation checkpoint in healthy cells and leads to a protective cell cycle arrest at the G1 phase of the mitotic cell division cycle. This protective mechanism is thought to be defective in cancer cells. To investigate how this ch...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr3010919
更新日期：2013-03-01 00:00:00
abstract：:The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked wit...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00370
更新日期：2017-12-01 00:00:00
abstract：:Reversible phosphorylations play a critical role in most biological pathways. Hence, in signaling studies great effort has been put into identification of a maximum number of phosphosites per experiment. Mass spectrometry (MS)-based phosphoproteomics approaches have been proven to be an ideal analytical method for map...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200092z
更新日期：2011-08-05 00:00:00
abstract：:This study demonstrates a direct role of venom protein expression alteration in the evolution of snake venom toxicity. Avian skeletal muscle contractile response to exogenously administered acetylcholine is completely inhibited upon exposure to South Australian and largely preserved following exposure to Queensland ea...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00764
更新日期：2015-11-06 00:00:00
abstract：:Flooding is a serious problem for soybeans because it reduces growth and grain yield. Proteomic and metabolomic techniques were used to examine whether mitochondrial function is altered in soybeans by flooding stress. Mitochondrial fractions were purified from the roots and hypocotyls of 4-day-old soybean seedlings th...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2001918
更新日期：2011-09-02 00:00:00
abstract：:Development of early embryonic stages before activation of the embryonic genome depends on sufficiently stored products of the maternal genome, adequate recruitment and degradation of mRNAs, as well as activation, deactivation, and relocation of proteins. By application of an isobaric tagging for relative and absolute...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500550t
更新日期：2014-10-03 00:00:00
abstract：:Equine grass sickness (EGS) is a frequently fatal disease of horses, responsible for the death of 1 to 2% of the U.K. horse population annually. The etiology of this disease is currently uncharacterized, although there is evidence it is associated with Clostridium botulinum neurotoxin in the gut. Prevention is current...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00784
更新日期：2018-03-02 00:00:00
abstract：:This study presents a comparative proteomic analysis of the membrane subproteome of whole Arabidopsis seedlings using 2% Brij-58 or 60% methanol to enrich and solubilize membrane proteins for strong cation exchange fractionation and reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 4...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060525b
更新日期：2007-05-01 00:00:00
abstract：:We investigated possible associations between sequence evolution of mammalian sperm proteins and their phosphorylation status in humans. As a reference, spermatozoa from three normozoospermic men were analyzed combining two-dimensional gel electrophoresis, immunoblotting, and mass spectrometry. We identified 99 sperm ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400228c
更新日期：2013-12-06 00:00:00
abstract：:Early findings propose that impaired neurotransmission in the brain plays a key role in the pathophysiology of schizophrenia. Recent advances in understanding its multiple etiologies and pathogenetic mechanisms provide more speculative hypotheses focused on even broader somatic systems. Using a targeted tandem mass sp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300459d
更新日期：2012-08-03 00:00:00
abstract：:Tumor invasion defines the transition between tissue-restricted carcinomas, related to good outcome as optimal surgery becomes possible, and metastatic tumors associated with poor prognosis and a dramatic decrease in survival. In endometrial cancer, myometrial infiltration represents a determinant parameter highly val...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900390t
更新日期：2009-10-01 00:00:00
abstract：:Tyrosine phosphorylation plays a major role in regulating cell signaling pathways governing diverse biological functions such as proliferation and differentiation. Systemically mapping phosphotyrosine (pTyr) sites is the key to understanding molecular mechanisms underlining pTyr-dependent signaling. Although mass spec...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00045
更新日期：2019-04-05 00:00:00
abstract：:Spectral library searching is a popular approach for MS/MS-based peptide identification. Because the size of spectral libraries continues to grow, the performance of searching algorithms is an important issue. This technical note introduces a strategy based on a minimum shared peak count between two spectra to reduce ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr401269z
更新日期：2014-09-05 00:00:00
abstract：:Endothelial cells (ECs) form the inner layer of blood vessels and physically separate the blood from the surrounding tissue. To support tissues with nutrients and oxygen, the endothelial monolayer is semipermeable. When EC permeability is altered, blood vessels are not functional, and this is associated with disease. ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00166
更新日期：2016-07-01 00:00:00
abstract：:Advances in liquid chromatography tandem mass spectrometry (LC-MS/MS) have permitted phosphoproteomic analysis on a grand scale, but ongoing challenges specifically associated with confident phosphate localization continue to motivate the development of new fragmentation techniques. In the present study, ultraviolet p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00289
更新日期：2016-08-05 00:00:00
abstract：:The time course of the thylakoid membranes proteomic profile changes upon cadmium (Cd) addition to hydroponic Spinacia oleracea L. plants has been investigated. Two different proteomic approaches have been used: blue native gel electrophoresis followed by SDS-PAGE (2D BN-SDS-PAGE) and sucrose density gradient ultracen...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800507x
更新日期：2009-01-01 00:00:00
abstract：:Birth weight is an important indicator of maternal and fetal health and a predictor of health in later life. However, the determinants of variance in birth weight are still poorly understood. We aimed to identify the biological pathways, which may be perturbed by environmental exposures, that are important in determin...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00846
更新日期：2018-03-02 00:00:00
abstract：:The Model Organism Protein Expression Database (MOPED, http://moped.proteinspire.org) is an expanding proteomics resource to enable biological and biomedical discoveries. MOPED aggregates simple, standardized and consistently processed summaries of protein expression and metadata from proteomics (mass spectrometry) ex...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400884c
更新日期：2014-01-03 00:00:00
abstract：:Microbes are known to regulate both gene expression and protein activity through the use of post-translational modifications (PTMs). Common PTMs involved in cellular signaling and gene control include methylations, acetylations, and phosphorylations, whereas oxidations have been implicated as an indicator of stress. S...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070531n
更新日期：2008-02-01 00:00:00
abstract：:"Omics" studies reported to date have dealt with either thoroughly characterized single species or poorly explored meta-microbial communities. However, these techniques are capable of producing highly informative data for the analysis of interactions between two organisms. We examined the bacterial interaction between...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100989c
更新日期：2011-02-04 00:00:00
abstract：:Mitosis is a highly regulated process in which errors can lead to genomic instability, a hallmark of cancer. During this phase of the cell cycle, transcription is silent and RNA translation is inhibited. Thus, mitosis is largely driven by post-translational modification of proteins, including phosphorylation, methylat...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100281h
更新日期：2010-09-03 00:00:00
abstract：:Acute stress may trigger systemic biochemical and physiological changes in living organisms, leading to a rapid loss of homeostasis, which can be gradually reinstated by self-regulatory mechanisms and/or drug intervention strategy. However, such a sophisticated metabolic regulatory process has so far been poorly under...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070051w
更新日期：2007-09-01 00:00:00
abstract：:We analyzed the whole-cell protein content of gastrocnemius muscles from rats in different thyroid states. Twenty differentially expressed proteins were unambiguously identified. They were involved in substrates and energy metabolism, stress response, cell structure, and gene expression. This study represents the firs...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0701299
更新日期：2007-08-01 00:00:00
abstract：:Salt stress is a major abiotic factor limiting maize yield. To characterize the mechanism underlying maize salt tolerance, we compared the seedling root proteomes of salt-tolerant Jing724 and salt-sensitive D9H. The germination rate and growth parameter values (weight and length) were higher for Jing724 than for D9H u...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00455
更新日期：2018-01-05 00:00:00
