Targeted Proteomics Course at ETH, Zurich

Institute of Molecular Systems Biology is organizing a targeted proteomics course at ETH, Zurich between 8-12 February, 2016.

The deadline for application is on 15 November, 2015.

For more details, visit this link

How to stop Excel converting your SEPT1 gene to September1

Several scientists around the world use Microsoft Excel to visualize or process their data. Excel can be fun to use when you know the commands well. However, when it comes to sorting gene symbols or creating protein databases using Excel, it may cause several problems. Some of the gene symbols are always converted into dates. 

For example:

SEPT1 becomes Sep-01

MARC1 becomes Mar-01

MARCH1 becomes Mar-01

This is true for the SEPT, MARC1 and MARCH1 gene families. 

Most often, you don't know that this has happened and you are forced to erroneously conclude that you haven't identified these genes in your data.

You can manually correct these by adding a single quote (') symbol before the gene name. This is very tedious and troublesome for downstream data processing. To make it worse, I found out that Excel does not have an option to turn off this annoying transmogrification.

By trial and error, I found out  a perfect way to overcome this problem in Excel.

STEP1: Save your database file in CSV (Comma separated) or TSV (Tab separated) formats

STEP 2: Start the "Import Text File" wizard by going to the "Data" Tab and clicking "From Text"

STEP 3: Select your CSV or TSV file and click "Import".

STEP 4: Choose the "delimited" option and click "Next"

STEP 5: Select "Comma" (if you used CSV file) or "Tab" (if you used TSV file) and click "Next"

STEP 6: Select the "Gene Symbol" column in the "Data Preview" and select the option "Text" in the "Column data format"

STEP 7: Click "Finish" and then click "OK".

Now scroll back and check that SEPT1 has not been touched by Excel.

If you want a video on it, use this link

RefSeq72 is out. Time to update your databases

RefSeq72 has been now released. Follow this link for more information.

Phosphoproteomic analysis of breast cancer cells to identify targets for tamoxifen resistance

A new study on the phosphoproteomics analysis of tamoxifen-resistant breast cancer cells has been published from Dr. Akhilesh Pandey's lab in the recent issue of Molecular and Cellular Proteomics. 

In this study, MCF7 breast cancer cell lines were chronically treated with tamoxifen for 6 months to acquire resistance. SILAC-based quantitative phosphoproteomic profiling  of treated and untreated cells with a Orbitrap Velos mass spectrometer identified over 5,000 unique phosphopeptides, with over 2,000 peptides differentially phosphorylated between the two conditions. 

Focal adhesion pathway was found to be enriched by pathway analysis. Silencing FAK2 suppressed cell proliferation and tumor formation. Further, high FAK2 expression was found to correlate with shorter metastasis-free survival in tamoxifen-treated breast cancer patients. 

The authors suggest that FAK2 could serve as a potential therapeutic target for management of hormone refractory breast cancers.

An optimized workflow for quantitative lysine acetylome

There are dozens of post-tranlational modifications out there, but there aren't enough techniques to study them all. Lysine acetylation has been studied before, but few labs work on this modification as opposed to phosphorylation due to lack of optimized protocols. A new paper from Steve Carr's lab on characterization of lysine acetylome  using an optimized protocol is an effort in this direction. The authors combined 7 monoclonal antibodies with specificity for lysine acetylated peptides and used this for enrichment. They used this method with Jurkat cells and combined it with a SILAC approach for quantitation. The authors identified over 10,000 lysine acetylated peptides from over 3,000 proteins!!

They applied this method to breast cancer xenografts and used TMT and iTRAQ for quantitation. Over 6,700 acetylated peptides from over 2,300 proteins were identified.

A combined RNAi and SILAC approach to characterize tyrosine kinase-regulated proteome in breast cancer

Tyrosine kinases are important players in cancer progression and are considered as good therapeutic targets. Knocking down the multiple kinases in cancer and studying the consequences has been done before. But in a new study published in Molecular and Cellular Proteomics, they took this to a whole new level by silencing 65 tyrosine kinases in breast cancer cell lines and studying the proteome using a SILAC-based approach and an Orbitrap Velos mass spectrometer.

The authors identified 10 signaling clusters in breast cancers and potential markers of drug sensitivity and resistance in breast cancer. The clusters also showed correlation with different breast cancer subtypes. In addition, the data revealed redundancy in signaling, explaining why tyrosine kinases can be sometimes ineffective because the cancers can proliferate through alternate signaling routes that are not blocked therapeutically.

Proteomics Research in India- Nature India Special Issue

A new special issue on "Proteomics Research in India" has been published in Nature India. The issue focuses on the accomplishment of Indian scientists in the field of proteomics. The highlight of the issue is, of course, the contribution of Indian scientists to the mass spectrometry-based as well as the antibody-based human proteome maps. (Did I mention that the issue is free?)

Salivary proteomics of oral squamous cell carcinoma and oral potentially malignant disorders

A new study on the oral squamous cell carcinoma in Proteomics, and I think about the old problem of understanding the difference between head-and-neck squamous cell carcinoma (HNSCC) and oral squamous cell carcinoma (OSCC). I understand the difference now, but it still troubles me that when you say HNSCC, you can compare cancer of the tongue with cancer of the buccal mucosa, or worse, with pharyngeal or laryngeal cancers. Talk about apples and oranges..

Thankfully, in this study, they used oral squamous cell carcinoma. They compared salivary proteomes of healthy individuals (controls) with that of potentially malignant oral disorders (erythroplakia, submucous fibrosis and others) and oral squamous cell carcinoma using a label free method (spectral counting, of course!!). The instrument of choice was a LTQ-Orbitrap (They don't say which one!!) mass spectrometer. They identified over a thousand proteins (with > 2 peptides) and found 33 proteins to be differentially expressed. RETN was selected and validated in a larger cohort using ELISA. They finally suggest that this protein could serve as a potential biomarker for prognosis.

Metaproteomics of sludge

Sludge, according to a wikipedia entry, is the residual material produced after sewage treatment of wastewater. As disgusting as it sounds, it is important to know what it contains which may play a role in sewage treatment, recycling water as well as protecting our water bodies from pollution.

SLUDGE anyone? Image Source:http://memegenerator.net/instance/59561637

I didn't want to spoil appetites by putting the picture of sludge. So here is Dr. Evil's picture.

Anyway, in a new study in Proteomics, they studied the metaproteome of sludge from a treatment plant. The experiment used SDS-PAGE and isoelectric focusing. LC-MS/MS analysis was carried out on a Bruker iontrap and data searched using Mascot with the usual 1% FDR. They identified several proteins and interestingly, 61% of spectra were of bacterial origin and 37% were eukaryotic (human and mouse). A small percentage included viruses. Central carbon and nitrogen metabolic pathways were found to be enriched.

High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics, Nature Biotechnology

People doing phosphoproteomics  have been achieving amazing numbers these days, partly because of many innovations in the field. Speaking of innovations, here is a new paper from the Mann lab published in Nature Biotechnology. Here, they talk about a novel approach to do phosphoproteomics called EasyPhos, which basically uses TFE (2,2,2-Trifluoroethanol) buffer for digestion and eliminates  fractionation steps because the TiO2 enrichment happens in a 96-well  deep well plate. 

They then studied insulin signaling in mice using this technique. They studied this with 11 time points and 6 biological replicates/time point. They analyzed 91 liver tissue phosphoproteomes, quantified about 31,000 phosphopeptides and accurately identified over 25,000 distinct phosphorylation sites in the liver.

The sheer scale of this study is overwhelming..

Image source: http://www.thebigmum.com/uploads/5/0/1/9/50199721/9797848_orig.jpg

Whitepaper for Glycopeptide analysis from Thermo

Thermo Scientific has released a whitepaper on "Orbitrap Fusion MS for Glycan and Glycopeptide Analysis". Please use this link to access the whitepaper. Glycoproteomic analysis is important as it can aid in the discovery of serum-based biomarkers for various diseases.

The human oral metaproteome

Please, fly into our open maw, and have at it.
 Image source: http://coglab.hbcse.tifr.res.in/teacher-resources/multimedia-resources/symbiosis/photographs/crocodileplover.jpg

In a recent article in Proteomics, scientists have identified a catalog of proteins from the human oral biofilm. They identified about 8000 bacterial proteins in 17 individuals and found out that 4 bacterial genera constitute 60-90% of the bacterial diversity. They also identified several proteins that could serve as potential biomarkers for dental caries. The methodology consisted of Hydrophilic interaction liquid chromatography (HILIC) and LTQ-Orbitrap Velos (Thermo Fisher Scientific, Germany) and XL (Thermo Fisher Scientific, Germany) instruments.

Agilent LC-MS teaching resources for academia

Agilent has introduced a set of teaching resources for liquid chromatography, mass spectrometry and bioanalyzer. Resources include power point presentations and videos. These will be especially useful to teachers, who can suggest these as extra reading material to students.

The link is as follows: http://www.agilent.com/en-us/promotions/academia-resources?cid=12635&sf11840441=1

Happy learning!!!

We are on Twitter now!!

Proteomics World is on Twitter now.
Start following @ProteomicsWorld for posts on proteomics

List of Proteomics blogs

I have been following some blogs on proteomics. Most blogs die after sometime. This post is not about such blogs (including mine). These are about those blogs that are currently active and followed by many people. I recommend these blogs to every person interested in proteomics, irrespective of their advancement level.

1. New in Proteomics Research http://proteomicsnews.blogspot.in/

Ben Orsburn is one of the best writers I have ever seen. He is quite quick in catching up on recent updates. One of the best places to update your knowledge.

2. Accelerating proteomics http://acceleratingscience.com/proteomics/

I recently started following this blog. They seem to be regular and have a long archive which shows consistency.

3. BioCode's Notes http://computationalproteomic.blogspot.in/

I wanted variety in my reading , therefore started following  this blog on computational proteomics.

If you (assuming I have at least one reader) find more such blogs, please  bring it to my attention. I will update the list.

OMICtools - A directory of tools for OMICS

OMICtools is a neat directory of tools and resources for OMICS type analysis. I found this one on the web when writing a review manuscript. It did a ton of good for my manuscript and I found that most of the tools our bioinformaticians were developing were already out there.

I found a section on Proteomic software tools and databases.

Mass spec-based proteomics is a separate section.

I was more interested in the proteogenomics tools section.

List of Proteomics Journals 2015

After completing an experiment, I would first choose a potential proteomics journal and then start writing the manuscript. I often had the problem of going back to every proteomics journal and search for the impact factor and the author guidelines. I first prepared this table a couple of years ago to choose journals for my manuscripts. I have removed the publication charges column for now.

Journal name	Website link	Impact factor	Publisher	Author Guidelines link
Molecular and Cellular Proteomics	Link	6.564	American Society for Biochemistry and Molecular Biology	Link
Journal of Proteome Research	Link	4.245	ACS Publications	Link
Journal of Proteomics	Link	3.888	Elsevier	Link
Proteomics	Link	3.807	Wiley	Link
Proteomics - Clinical Applications	Link	2.956	Wiley	Link
Expert Reviews Proteomics	Link	2.896	Informa Healthcare	Link
BBA Proteins and Proteomics	Link	2.747	Elsevier	Link
Proteome Science	Link	1.73	Springer	Link
EuPA Open Proteomics	Link	-NA-	Elsevier	Link
Genomics, Proteomics & Bioinformatics	Link	-NA-	Elsevier	Link
Clinical Proteomics	Link	3.43*	Springer	Link
Journal of Proteomics and Bioinformatics	Link	2.55 *	OMICS Group International	Link

* Unofficial Impact factor

NextGen Genomics, Biology, Bioinformatics and Technologies (NGBT) Conference, Hyderabad, October 2015

The Charminar at Hyderabad  Source and credit:https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgzSx8gWCOh70Daq3h2TZVbXBwJhGqfNmGBQvcj4oJHBF8PWsYEN2yqYa9mp30fYYdX1EmQYpnPqDS7NeqVhlUKUQvLQFN2476QohVs_98xszMmq_O1VGkNmaVeEmbHHaSXi6TLaDCdduOT/s400/Charminar+night+view.jpg

The NextGen Genomics, Biology, Bioinformatics and Technologies (NGBT) Conference, will be held at Hyderabad, between 1-3 October, 2015. This has nothing much to do with Proteomics of course, other than the fact that one of the organizers is Institute of Bioinformatics , of human proteome draft fame. The main organizers are SciGenom, and the Center for Cellular and Molecular Biology, India. SciGenom also provides mass spectrometry services.

There is also a pre-conference workshop (which seems to be a trend these days and profitable nonetheless!!!) on NextGen sequencing and Bioinformatic.

The deadlines for the conference are as follows:

Early Registration     31st Aug, 2015
Last Date of Abstract Submission     31st Aug, 2015

The conference link is as follows: http://www.sgrfconferences.org/2015/NGBT/index.php

Targeted Proteomics: Workshop & International Symposium,December 2015, IIT Bombay

Photocredit to Rohan Sethi. Source: https://commons.wikimedia.org/wiki/File:IITB_Main_Building.jpg

A Workshop & International Symposium on Targeted Proteomics will be held between 10-14 December, 2015 at Indian Institute of Technology, Bombay, India. Dr. Sanjeeva Srivastava's lab at IIT, Bombay will be playing host.
Three (Yes, three!!!) workshops will be held simultaneously. One on targeted proteomics, another on Trans-Proteomic Pipeline (TPP), and one on HR-LC-MS/MS Workshop. Big wigs of Proteomics including Dr. Robert Moritz, Institute of Systems Biology (of  TPP fame); Mr. Brendan MacLean, University of Washington (of Skyline fame); Dr. Jacob Jaffe (Broad Institute, USA); Dr. Ben Collins (ETH Zurich, Switzerland); Dr. Bruno Domon (Luxembourg Clinical Proteomics Center); Dr. Olga Vitek (Northeastern University, USA); Mr. Ariel Bensimon (ETH Zurich, Switzerland) and several scientists from ISB and ETH Zurich are designated as speakers. Wish Mike MacCoss and Ruedi Aebersold were coming too.

For registration details, visit the following link: http://www.bio.iitb.ac.in/~sanjeeva/itpws/

7th Annual Meeting of Proteomics Society, India 2015

Vellore Institute of Technology, Source:http://media2.intoday.in/college/institute_images/1430552225299_Vellore-Institute.jpg

Registrations are open for the conference and pre-conference workshop of 7th Annual Meeting of Proteomics Society, India, 2015 going to be held at Vellore Institute of Technology, Vellore, India between 1-6, December 2015.

Deadline for abstract submission is 31 August, 2015.
Deadline  for early bird registration is 31 August, 2015.
Deadline  for late registration is 30 September, 2015. (In the website it says 31 September!!)

For more information , follow this link: http://www.psivellore2015.org/

There's a fort at Vellore! Source: http://vellorecity.co.in/admincontrol/logo/Vellore-Fort2.png

 

We are back with a new face

After a long self-imposed hiatus of two years, we are finally back and are now called Proteomics World (formerly known as Proteomics network of India). Not that I wrote too often, but wish that I should have. Anyway, I'm done with Ph.D. and joined a research institute and things seem to be working for me for now.
Last year was pretty big for the Proteomics world, with the publication of two drafts of the human proteome from Dr. Pandey (currently cited 278 times on Google Scholar) and Dr. Kuster's (currently cited 255 times on Google Scholar) labs. It was published in Nature and was big news for Indian proteomics too. Part of the work of the draft from Pandey lab was carried out at the Institute of Bioinformatics, Bangalore and it received wide coverage in the Indian media. Good news for the Indian proteomic fraternity.