Questions tagged [mass-spectrometry]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
1 vote
0 answers
166 views

Peptide fragment software in mass spectrometry

I am trying to study peptide fragmentation in mass spectrometry. My goal is to find software with which I can retrieve the molecular structure of the peptide and see the a,b,c fragments. I found these ...
KGee's user avatar
  • 139
0 votes
0 answers
42 views

Left digested peptides in speedvac for hours

I had done phosphopeptide enrichment of proteomic samples and digested the peptides with trypsin. However, I forgot and left the samples in speedvac to dry at 45 deg for way too long, about 10hrs. It ...
Aksh's user avatar
  • 1
0 votes
0 answers
23 views

Mass Spectrometry Artefacts: R-deamidation / Oxidation?

Context: I am a student-researcher. I expressed GST-tagged protein (Pyruvate Kinase) in the yeast Saccharomyces cerevisiae on synthetic drop-out media. I then purified the GST-tagged protein, ran it ...
thefutureisnow's user avatar
3 votes
0 answers
45 views

Mass spectrometry: What is meant by the 'most intense peptide ions' in data dependent acquisition (DDA) mode?

I am learning about data dependent acquisition (DDA) mode in mass spectrometry from this online resource. I have come across the following statement: In DDA mode, the mass spectrometer selects the ...
ceno980's user avatar
  • 1,701
1 vote
0 answers
88 views

What are protein iBAQ abundance values in SWATH mass spectrometry?

I am reading a journal paper where they used SWATH mass spectrometry to quantify the abundance of proteins in synaptosomes isolated from different species. I am trying to determine whether some ...
ceno980's user avatar
  • 1,701
2 votes
1 answer
170 views

Does mass spectrometry data have units?

I am reading some journal papers about the proteome of certain brain structures. In these papers, they used mass spectrometry to identify the proteins that were present in the brain structure as well ...
ceno980's user avatar
  • 1,701
2 votes
1 answer
80 views

Identifying substance in body fluid (serum, urine)

I have a large number of serum and 24 hour urine samples from a collection of individuals on many consecutive days. Some of the samples contain a 'large' amount of a substance that has a brown color. ...
Mikkel Rev's user avatar
1 vote
1 answer
192 views

Why bovine serum albumin is used in mass-spectroscopy and how to interpret such data?

In the paper Network organization of the huntingtin proteomic interactome in mammalian brain, there is a description of a mass spectroscopy experiment where Bovine Serum Albumin (BSA) is added to a ...
Noob's user avatar
  • 257
2 votes
1 answer
260 views

Peptide oxidation bias during sample preparation for LC-MS/MS

Problem description In bottom-up proteomics, a commonly observed amino acid modification is the oxidation of methionine (Met-O). I wonder if the observed Met-O reflect natural protein oxidation or if ...
DaRealHonk's user avatar
0 votes
1 answer
357 views

How do carbon 13:12 ratios confirm the biological origin of oldest microfossils?

I was reading this article about how Schopf and Valley’s findings in 2017 confirmed that the 3.5 billion–year-old microfossils found in the Apex chert of Western Australia are indeed remnants of ...
WillG's user avatar
  • 103
1 vote
1 answer
128 views

Open Mass Spec Database

Wondering if there is an open (freely available) database of Mass Spec Data, particularly for the Substances/Compounds listed in NCBI. Specifically, I am not sure if NCBI includes the mass ...
Lance's user avatar
  • 759
1 vote
1 answer
73 views

False positives in TAP - MS experiments

Is anyone aware of a website where they show common false positives often found when doing a TAP-MS experiment to find protein-protein interaction experiments? Particularly the Acs1 protein (Acetyl-...
Loko's user avatar
  • 11
2 votes
2 answers
398 views

What happened to ProteomeCommons.org?

ProteomeCommons.org seems to once have been a resource for raw proteomics data. Thought, the website now offers gardening tools. It seems to be hacked. Does anyone know whether the data is still ...
Soerendip's user avatar
  • 147
2 votes
0 answers
40 views

Do "real" human samples tend to return fewer protein identifications in Proteomics experiments?

I'm working with bottom-up (shotgun) mass spectrometry-based proteomics and have encountered an issue. If I do a run with a HeLa digest standard, the resulting data returns many protein IDs. When I do ...
Nathan's user avatar
  • 29
0 votes
2 answers
62 views

Validated Protein-Protein interaction database for cancer

I need to use validated PPI data in my research. Is there any database of such validated (like Mass Spectrometry) database for cancer?
user38871's user avatar
2 votes
0 answers
1k views

Why do my peptide samples turn yellow and red?

The protocols for (brain) tissue digestion I am trying out are: lysis (buffer containing 0.1% SDC or SDS in 100mM TEAB + phosphatase inhibitor which is sort of yellow), reduction with TCEP, alkylation ...
E.T.'s user avatar
  • 41
2 votes
1 answer
1k views

Can I dry digested protein sample over weekend in a vacuum concentrator?

I have digested with trypsin the tissue protein extract for mass spectrometry, and forgot to transfer the sample from the SpeedVac to the -80C freezer. As I did this on Friday, I can transfer the ...
E.T.'s user avatar
  • 41
0 votes
1 answer
136 views

MS/MS for complex samples

I saw this figure in this atricle: It's a really nice representation of what happens when using MS/MS. However I was wondering how this works when there are more proteins present in the gel spot. ...
KingBoomie's user avatar
  • 2,380
3 votes
1 answer
2k views

Are both B and Y ions required to determine the sequence of a protein by mass spectrometry?

I was wondering if both all b and y ions are required to determine to order of the amio acids in a peptide. In my opinion knowing only ALL B ions or ALL y-ions is enough to determine the sequence of ...
user avatar
1 vote
2 answers
4k views

Mass Spectrometry (proteomics): How isotopes can be used to to determine charge of the peaks?

I'm trying to understand how isotopes can tell me something about the charge of the different peaks. This pdf file mentioned the following about isotopes in correlation with the charge of the peaks: ...
KingBoomie's user avatar
  • 2,380
0 votes
2 answers
566 views

What is the best way to analyze non-quantitative mass spec hits from an immunoprecipitation pull down?

I am studying a nuclear protein and want to come up with a list of potential proteins that it interacts with. From the nuclear fraction of 293T cells, I did an IP (immunoprecipitation) to pull down my ...
Charlie Parker's user avatar
0 votes
1 answer
61 views

Transfer of electrophoresis bands to MS

I have a lab question that is confusing me. Just to be clear this is a homework question but I've done some extensive research and can't find what seems to be a "good" answer. The question is this: ...
user2879934's user avatar
2 votes
2 answers
261 views

Techniques for detecting phosphorylation sites in proteins?

I would like to know how phosphorylated sites in proteins are detected in practice. I read some papers where the authors were talking about mass spectrometry techniques. But my question is that why ...
dexterdev's user avatar
  • 1,133
5 votes
3 answers
136 views

How to generate simulated mass-spectrometry data for phosphorylated proteins?

I am trying to generate simulated MS data (Top-down and Bottom-up) for phosphorylated protein such as platelet-derived growth factor receptor (PDGFR-B). There are 10 tyrosine sites which are ...
Deepesh's user avatar
  • 61
2 votes
2 answers
422 views

How does mass spectrometry detect histone methylation?

In this research paper they talk about the methylation of histone. They use mass spectrometry to identify which peptide position is methylated. Does the number yielded by the spectrometer calculate ...
Scsqpd's user avatar
  • 195
1 vote
0 answers
48 views

Why is carbonylation added as a fixed modification in mass spectrometry peptide analysis?

When using mass spectrometry analysis software we use carbonylation as a fixed modification. What is the significance of this modification and why doesn't it change?
I-heart-XBP1's user avatar
1 vote
2 answers
2k views

What is the importance of urea in mass spectrometry?

What is the importance of urea in mass spectrometry? We use 8M urea to FASP our proteins prior to mass spectrometry. What is the significance of using 8M urea? and how does it affect the proteins?
I-heart-XBP1's user avatar
10 votes
1 answer
3k views

Mass spectrometry versus western blotting for validation

I have mass spectrometry data (LC-MS/MS) from rat cortices under either drug or control treatments. The results were performed in triplicate (three pairs of rats, drug or control per pair). In ...
syntonicC's user avatar
  • 345
4 votes
2 answers
4k views

Why digest proteins into peptides for Liquid Chromatography - Mass Spectrometry?

Digesting (trypsin or whatever other proteolytic enzyme) proteins generates multiple peptides so the degree of complexity of the sample, at the peptide level, increases a lot. In addition there is ...
Vital V's user avatar
  • 141
0 votes
1 answer
48 views

To measure frequencies of eosinophils and neutrophils in airways

I am reading this paragraph about RS killed-vaccine in Encyclopedia of Virology, Third Edition (2008), vol. 3, pp. 70-77 What is this data called by which you can say that the frequencies of ...
Léo Léopold Hertz 준영's user avatar